Contacts of the helix formed by residues 100 - 125 (chain A) in PDB entry 1CD9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 100 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.7 19.1 - - + -
35A LYS* 3.7 27.1 - - + -
36A LEU* 3.4 39.9 - - + +
39A THR* 4.3 7.0 - - - +
40A TYR* 4.0 21.1 - - + -
95A GLY 3.7 9.2 - - - +
96A ILE* 4.1 11.2 - - + -
97A SER* 3.0 11.1 + - - +
99A GLU* 1.3 90.4 - - + +
101A GLY* 1.3 65.6 + - - +
102A PRO* 3.1 4.3 - - - -
103A THR* 3.1 6.2 + - - +
104A LEU* 3.0 22.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLY* 3.4 19.6 + - - -
97A SER 2.7 17.6 + - - -
98A PRO* 4.3 1.8 - - - -
100A LEU* 1.3 70.7 - - - +
102A PRO* 1.3 62.8 - - - +
104A LEU* 3.8 1.3 - - - +
105A ASP* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PRO 3.5 15.7 - - - +
99A GLU 3.9 6.5 - - - +
100A LEU 3.4 3.6 - - - -
101A GLY* 1.3 88.3 - - - +
103A THR* 1.3 64.6 + - - +
105A ASP* 3.1 6.4 + - + +
106A THR* 3.1 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASP* 4.7 2.6 - - - +
31A ALA* 4.0 14.8 - - + +
32A LEU* 3.6 39.9 - - + +
35A LYS* 4.4 21.5 - - + +
99A GLU 4.9 2.4 + - - -
100A LEU* 3.1 9.9 + - - -
102A PRO* 1.3 80.0 - - - +
104A LEU* 1.3 63.6 + - - +
106A THR* 3.5 8.0 + - - -
107A LEU* 3.3 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.7 34.7 - - + +
90A LEU* 3.8 43.1 - - + +
93A LEU* 4.2 7.2 - - + -
95A GLY* 3.7 33.7 - - - +
96A ILE* 3.8 15.0 - - + -
100A LEU 3.0 15.5 + - - +
101A GLY 4.0 2.5 - - - +
103A THR* 1.3 74.0 - - - +
105A ASP* 1.3 61.2 + - - +
107A LEU* 3.1 6.9 + - + +
108A GLN* 2.8 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A GLY 2.9 20.7 + - - +
102A PRO* 3.1 6.0 + - + +
104A LEU* 1.3 72.8 - - - +
106A THR* 1.3 65.1 + - - +
108A GLN* 3.2 12.5 + - - +
109A LEU* 3.0 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASP* 3.8 17.3 - - - +
102A PRO 3.1 13.2 + - - -
103A THR* 3.6 10.6 - - - -
104A LEU 3.2 0.2 - - - -
105A ASP* 1.3 77.2 + - - +
107A LEU* 1.3 65.6 + - - +
109A LEU* 3.3 5.9 + - - +
110A ASP* 3.0 42.9 + - - +
72B ARG* 6.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 3.7 24.9 - - + -
28A ASP* 3.6 30.0 - - + +
29A GLY* 3.9 19.1 - - - +
32A LEU* 3.7 28.0 - - + -
90A LEU* 3.9 22.2 - - + -
103A THR 3.3 9.4 + - - +
104A LEU* 3.1 10.6 + - - +
106A THR* 1.3 80.7 - - - +
108A GLN* 1.3 57.4 + - - +
110A ASP* 3.5 1.2 + - - +
111A VAL* 3.0 35.7 + - + +
155A ALA* 5.5 2.5 - - + -
158A LEU* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLN* 3.1 40.8 + - - +
90A LEU* 4.0 25.6 - - + +
91A GLN* 3.5 24.2 + - + +
104A LEU* 2.8 18.8 + - + +
105A ASP* 3.2 15.9 + - - +
107A LEU* 1.3 72.0 - - - +
109A LEU* 1.3 69.5 + - + +
111A VAL* 3.8 0.6 - - - +
112A ALA* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP* 3.0 39.2 + - - +
106A THR* 4.0 4.9 - - - +
108A GLN* 1.3 84.4 - - - +
110A ASP* 1.3 66.4 + - - +
112A ALA* 3.1 4.7 + - + +
113A ASP* 3.0 36.4 + - - +
72B ARG* 4.0 32.5 - - - +
73B LYS* 4.8 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN* 4.5 2.9 + - - -
24A LYS* 3.0 33.3 + - + +
25A ILE* 3.6 17.4 - - + +
28A ASP* 2.6 29.5 - - - +
106A THR* 3.0 29.2 + - - +
107A LEU 3.8 2.9 - - - +
109A LEU* 1.3 79.2 - - - +
111A VAL* 1.3 58.7 + - - +
113A ASP* 4.1 3.6 - - - +
114A PHE* 3.2 23.4 + - - +
72B ARG* 3.2 18.2 + - - +
77B LEU* 4.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 3.8 31.4 - - + -
83A LEU* 3.4 38.5 - - + +
86A TYR* 4.6 5.4 - - + -
87A GLN* 4.2 13.0 - - - +
90A LEU* 4.1 8.5 - - + -
107A LEU* 3.0 25.3 + - + +
108A GLN 3.9 3.8 - - - +
109A LEU 3.2 0.2 - - - -
110A ASP* 1.3 73.2 - - - +
112A ALA* 1.3 66.3 + - - +
114A PHE* 3.3 2.9 + - - +
115A ALA* 3.0 21.0 + - - +
158A LEU* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLN* 3.6 32.2 + - + +
108A GLN* 2.9 25.9 + - - +
109A LEU* 3.1 8.0 + - + +
111A VAL* 1.3 76.5 - - - +
113A ASP* 1.3 63.4 + - - +
115A ALA* 3.0 6.1 + - - +
116A THR* 2.8 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLN* 4.0 4.3 - - - +
109A LEU* 3.0 18.2 + - - +
110A ASP* 4.2 3.8 - - - +
112A ALA* 1.3 77.0 - - - +
114A PHE* 1.3 62.3 + - - +
116A THR* 3.6 3.9 + - - -
117A THR* 2.8 34.1 + - - -
72B ARG* 2.4 34.1 + - - +
75B LEU 3.6 12.2 - - - +
76B LEU* 3.7 21.6 - - + +
77B LEU* 3.6 16.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A CYS* 3.8 35.7 - - + -
21A GLN* 3.2 32.2 - - + +
22A VAL* 3.5 28.5 - - + -
25A ILE* 3.5 22.2 - - + -
79A LEU* 4.7 4.5 - - + -
83A LEU* 3.4 24.7 - - + -
110A ASP 3.2 17.7 + - - +
111A VAL 3.7 4.3 - - - +
113A ASP* 1.3 78.0 - - - +
115A ALA* 1.3 64.0 + - - +
117A THR* 3.4 1.2 - - + -
118A ILE* 3.1 45.8 + - + +
162A LEU* 4.7 2.2 - - + -
169A LEU* 4.6 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A HIS* 3.2 29.3 - - + +
83A LEU* 3.8 24.2 - - + +
84A PHE* 4.2 5.6 - - + +
87A GLN* 4.2 14.6 - - - +
111A VAL 3.0 13.8 + - - +
112A ALA 3.0 9.2 + - - +
114A PHE* 1.3 78.4 - - - +
116A THR* 1.3 61.6 + - - +
118A ILE* 3.2 4.3 + - - +
119A TRP 3.0 16.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A HIS* 5.6 0.2 - - - -
87A GLN* 5.5 1.0 + - - -
112A ALA* 2.8 20.0 + - - +
113A ASP* 3.2 12.3 + - - -
115A ALA* 1.3 76.5 - - - +
117A THR* 1.3 62.6 + - - +
119A TRP* 3.0 9.0 + - + +
120A GLN* 3.0 48.0 + - + +
44B ARG* 5.7 2.7 - - - +
76B LEU* 4.1 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 4.4 15.7 - - + -
17A LYS* 6.2 1.8 - - + -
18A CYS* 5.0 1.1 - - - -
21A GLN* 3.2 23.5 + - - +
113A ASP 2.8 21.7 + - - -
114A PHE* 3.4 9.0 - - + +
116A THR* 1.3 73.8 - - - +
118A ILE* 1.3 65.5 + - + +
120A GLN* 3.5 8.2 + - - +
121A GLN* 3.1 22.7 + - - +
76B LEU* 4.3 5.1 - - - +
77B LEU 3.4 19.9 + - - -
78B TYR* 3.7 18.5 + - + +
79B GLN* 4.9 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PHE* 4.6 3.4 - - + -
18A CYS* 4.5 11.2 - - - -
76A LEU* 4.0 35.6 - - + +
79A LEU* 3.8 29.4 - - + -
80A HIS* 4.1 12.1 - - + +
83A LEU* 4.0 13.7 - - + -
114A PHE* 3.1 41.8 + - + +
115A ALA 3.6 7.2 - - - +
116A THR 3.2 0.2 - - - -
117A THR* 1.3 76.5 - - + +
119A TRP* 1.3 68.7 + - - +
121A GLN* 3.4 6.5 + - - +
122A MET* 3.0 22.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A HIS* 3.9 24.2 - + + +
115A ALA 3.0 11.7 + - - +
116A THR* 3.0 13.1 + - + +
118A ILE* 1.3 77.5 - - - +
120A GLN* 1.3 63.6 + - + +
122A MET* 2.8 51.8 + - + +
123A GLU* 2.9 44.7 + - + +
128A ALA* 4.1 9.4 - - + -
129A PRO* 3.7 42.2 - - + -
132A GLN* 4.2 35.1 + - + -
133A PRO* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A THR* 3.0 36.5 + - + +
117A THR* 4.0 4.5 - - - +
119A TRP* 1.3 80.1 - - + +
121A GLN* 1.3 62.1 + - - +
123A GLU* 3.4 17.8 + - - +
124A GLU* 3.1 23.4 + - - +
44B ARG* 5.9 3.2 - - - +
45B SER 4.9 1.3 - - - +
46B ARG* 3.7 16.1 + - - +
76B LEU* 3.6 11.7 - - - +
79B GLN* 3.1 39.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 4.9 0.9 - - + -
11A PRO* 3.7 24.9 - - - +
14A PHE* 3.4 56.9 - - + +
76A LEU* 5.3 1.1 - - + -
117A THR 3.1 11.1 + - - +
118A ILE 3.7 3.8 - - - +
119A TRP 3.0 1.0 + - - -
120A GLN* 1.3 74.3 - - - +
122A MET* 1.3 66.9 + - + +
124A GLU* 3.1 27.9 + - - +
125A LEU* 3.1 39.3 + - + +
79B GLN* 4.9 8.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA 4.6 3.4 - - - +
76A LEU* 3.8 24.0 - - + +
77A SER* 3.7 32.5 - - - -
80A HIS* 4.2 15.7 - - + -
118A ILE* 3.0 14.4 + - + +
119A TRP* 2.8 48.7 + - + +
121A GLN* 1.3 76.0 - - - +
123A GLU* 1.3 57.6 + - - +
125A LEU* 3.5 1.4 + - - -
126A GLY 3.1 4.9 + - - -
127A MET* 2.7 48.1 + - + +
128A ALA* 3.8 11.4 - - - +
129A PRO* 4.6 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A TRP* 2.9 49.1 + - + +
120A GLN* 3.7 13.2 - - - +
121A GLN 3.2 0.2 - - - -
122A MET* 1.3 75.2 - - - +
124A GLU* 1.3 56.1 + - - +
126A GLY* 2.8 25.5 + - - -
128A ALA* 3.5 25.0 - - + +
46B ARG* 3.7 18.3 + - - +
51B TYR* 5.4 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLN 3.1 13.2 + - - +
121A GLN* 3.5 31.8 + - - +
123A GLU* 1.3 76.5 - - - +
125A LEU* 1.3 65.5 + - + +
126A GLY 3.4 0.5 + - - -
46B ARG* 3.4 45.8 - - - +
47B ALA* 4.6 12.1 + - - +
79B GLN* 5.1 2.6 + - - +
161D TRP 5.2 2.4 - - - +
163D LEU* 5.8 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER 3.5 19.5 - - - +
10A LEU* 3.5 23.6 - - + -
11A PRO* 4.3 2.0 - - + -
76A LEU* 5.6 0.2 - - + -
121A GLN* 3.1 37.0 + - + +
122A MET 4.2 1.1 - - - +
124A GLU* 1.3 82.4 - - + +
126A GLY* 1.3 62.2 + - - +
127A MET* 3.5 21.7 - - + +
161D TRP 3.8 17.1 - - - +
162D THR* 4.8 7.3 + - - +
163D LEU* 4.6 15.8 + - + +
165D PHE* 3.6 33.2 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il