Contacts of the helix formed by residues 101 - 119 (chain A) in PDB entry 3WAJ
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 SER 101 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A GLU* 3.3 20.2 - - - -
99A ALA 3.6 1.2 - - - -
100A THR* 1.3 86.4 + - - +
102A GLY* 1.3 71.0 + - - +
104A SER* 3.7 8.1 + - - -
105A LEU* 3.2 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 3.5 18.7 + - - -
56A GLU* 3.9 3.0 + - - -
101A SER* 1.3 77.5 - - - +
103A GLU* 1.3 62.9 + - - -
105A LEU* 3.5 1.1 - - - +
106A ARG* 3.1 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TRP 5.6 0.5 - - - +
40A THR* 4.2 15.9 + - - +
41A VAL* 3.3 37.0 + - + +
102A GLY* 1.3 70.7 - - - -
104A SER* 1.3 59.1 + - - +
106A ARG* 3.2 16.3 + - - +
107A ALA* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A SER 5.5 0.2 - - - -
99A ALA* 3.5 28.4 - - - +
101A SER 4.0 6.9 + - - -
102A GLY 3.3 0.6 - - - -
103A GLU* 1.3 79.0 - - - +
105A LEU* 1.3 64.3 + - - +
107A ALA* 3.4 6.1 + - - +
108A VAL* 3.2 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A TYR* 3.6 29.2 - - + -
55A ILE* 4.2 9.9 - - + -
56A GLU* 4.2 23.3 - - + +
59A ILE* 4.2 5.2 - - + -
94A GLY* 4.5 6.7 - - - -
99A ALA* 3.5 23.2 - - - +
100A THR 3.8 17.5 - - - +
101A SER* 3.2 19.8 + - - +
102A GLY 3.5 4.3 - - - +
104A SER* 1.3 77.7 - - - +
106A ARG* 1.3 58.5 + - - +
108A VAL* 3.2 5.1 + - + +
109A LEU* 2.9 55.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A THR* 3.1 22.0 + - - +
41A VAL* 2.8 51.3 + - + +
43A LEU* 3.6 22.0 - - + +
49A TRP* 3.9 20.6 - - - -
52A TYR* 3.3 36.0 + - + -
102A GLY* 3.1 9.0 + - - +
103A GLU* 3.6 34.4 - - - +
105A LEU* 1.3 78.7 - - - +
107A ALA* 1.3 53.9 + - - +
109A LEU* 3.2 8.3 + - - -
110A ALA* 2.7 36.4 + - - +
504A TYR* 3.3 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 4.1 18.6 - - + -
41A VAL* 3.6 11.6 - - + +
103A GLU 2.8 17.8 + - - +
104A SER* 3.5 8.1 - - - +
106A ARG* 1.3 74.7 - - - +
108A VAL* 1.3 66.9 + - + +
110A ALA* 3.1 14.7 + - - +
111A PHE* 3.1 22.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA* 3.6 39.3 - - + +
94A GLY* 4.5 1.8 - - - +
97A PHE* 4.1 26.7 - - + -
99A ALA* 4.0 17.0 - - + -
104A SER 3.2 11.6 + - - +
105A LEU* 3.2 10.6 + - + +
107A ALA* 1.3 78.4 - - + +
109A LEU* 1.3 66.0 + - + +
111A PHE* 3.0 22.5 + - - +
112A ILE* 3.6 10.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
43A LEU* 4.6 5.6 - - + -
52A TYR* 4.0 34.1 - - + -
55A ILE* 3.7 35.0 - - + -
90A GLY* 3.8 24.0 - - - +
105A LEU* 2.9 41.5 + - + +
106A ARG* 3.6 5.6 - - - +
108A VAL* 1.3 72.9 - - + +
110A ALA* 1.3 62.1 + - - +
112A ILE* 3.2 24.3 + - + +
113A PRO* 3.3 11.3 - - - +
160A ASN* 3.5 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 4.1 12.8 - - + -
37A PHE* 4.6 2.0 - - + -
41A VAL* 4.9 0.9 - - + -
43A LEU* 4.2 5.8 - - + +
106A ARG 2.7 18.1 + - - +
107A ALA* 3.1 16.8 + - - +
109A LEU* 1.3 73.8 - - - +
111A PHE* 1.3 58.9 + - - +
113A PRO* 3.3 6.6 - - - +
157A LEU* 3.2 22.5 - - + +
158A GLY* 2.7 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 3.8 39.7 - - + -
33A TRP* 3.7 27.4 - + - -
37A PHE* 4.0 16.4 - + - -
107A ALA* 3.1 29.8 - - + -
108A VAL* 3.0 11.2 + - - +
110A ALA* 1.3 77.4 - - - +
112A ILE* 1.3 60.1 + - + +
113A PRO 3.4 0.2 - - - -
114A ALA* 3.1 5.5 + - - +
115A ILE* 2.9 44.3 + - + +
157A LEU* 4.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.9 15.3 - - + -
89A LEU* 3.9 21.8 - - + +
90A GLY* 3.9 19.5 - - - +
93A ALA* 4.1 17.0 - - + -
108A VAL* 3.9 8.5 - - + +
109A LEU* 3.2 37.6 + - + +
111A PHE* 1.3 76.3 - - - +
113A PRO* 1.3 60.5 - - + +
115A ILE* 3.4 10.9 + - + +
116A GLY 3.0 22.0 + - - -
160A ASN* 3.5 16.6 - - - +
165A TRP* 3.7 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU 3.3 14.1 - - - +
110A ALA 3.3 9.4 - - - +
112A ILE* 1.3 91.6 - - + +
114A ALA* 1.3 57.9 + - - +
116A GLY* 3.3 0.5 + - - -
117A GLY 2.9 24.9 + - - -
154A ARG 4.3 10.3 - - - +
155A SER* 3.3 12.5 + - - +
156A ILE 3.3 22.9 - - - +
159A PHE 3.3 32.3 - - - +
160A ASN* 3.6 11.0 - - - +
161A ASP 4.8 1.1 - - - +
164A ILE* 4.2 16.1 - - + +
165A TRP* 4.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 4.0 18.2 - - + +
29A ILE* 3.5 31.9 - - + -
111A PHE* 3.1 10.7 + - - +
113A PRO* 1.3 83.5 - - - +
115A ILE* 1.3 62.5 + - - +
117A GLY* 3.2 1.7 + - - -
118A VAL* 2.9 28.6 + - - +
155A SER 3.3 11.7 + - - +
157A LEU* 4.0 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 5.1 9.6 - - + -
111A PHE* 2.9 36.3 + - + +
112A ILE* 3.8 10.5 - - + +
114A ALA* 1.3 75.3 - - - +
116A GLY* 1.3 57.8 + - - +
118A VAL* 3.2 6.8 + - + +
119A LEU* 2.8 53.1 + - + +
165A TRP* 5.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE 3.0 10.7 + - - -
113A PRO 3.7 2.9 - - - -
115A ILE* 1.3 78.1 - - - +
117A GLY* 1.3 59.3 + - - +
119A LEU* 3.5 2.8 + - - -
120A ALA* 3.3 18.0 + - - +
164A ILE* 3.8 10.6 - - - +
165A TRP* 3.5 35.0 - - - -
168A PHE* 3.7 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A SER* 3.9 4.0 + - - -
28A ARG* 3.2 18.4 + - - -
113A PRO 2.9 11.5 + - - -
114A ALA 3.2 2.2 + - - -
116A GLY* 1.3 74.7 - - - +
118A VAL* 1.3 63.7 + - - +
120A ALA* 3.4 13.7 - - - +
121A ILE* 4.8 3.1 + - - +
144A ILE* 5.3 2.3 - - - +
145A ALA* 5.6 0.5 - - - -
151A PHE* 5.0 1.0 - - - -
155A SER* 3.1 24.0 - - - -
164A ILE* 3.6 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 4.1 25.1 - - + +
24A SER* 3.3 39.5 - - - +
25A VAL* 3.8 17.3 - - + +
28A ARG* 4.5 2.5 - - + -
29A ILE* 5.7 2.9 - - + -
114A ALA 2.9 19.5 + - - +
115A ILE* 3.7 7.0 - - + +
117A GLY* 1.3 72.1 - - - +
119A LEU* 1.3 67.6 + - + +
120A ALA 3.0 9.8 + - - -
121A ILE* 3.2 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE* 2.8 42.8 + - + +
116A GLY* 3.9 5.2 - - - +
118A VAL* 1.3 76.6 - - + +
120A ALA* 1.3 60.5 + - - +
121A ILE* 3.0 7.9 + - - -
122A LEU* 3.0 35.1 + - + +
123A PRO* 3.2 8.7 - - - +
165A TRP* 5.1 7.0 - - + -
168A PHE* 3.2 22.5 - - + -
----------------------------------------------------------
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