Contacts of the helix formed by residues 95 - 114 (chain A) in PDB entry 2DFD
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 95 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 3.1 37.0 - - + +
85A PRO 3.7 13.2 - - - +
86A ARG* 3.9 22.7 - - + +
90A MET* 3.5 26.7 - - + -
91A THR 4.3 1.1 - - - +
92A ARG* 3.0 13.8 + - - +
93A ASP 3.0 1.2 - - - -
94A ASP* 1.3 77.2 - - - +
96A PHE* 1.3 61.5 + - - +
97A ASN 3.4 2.2 - - - -
98A THR* 3.3 5.1 + - - -
99A ASN* 2.9 32.6 + - - +
124A ASN* 3.9 17.7 - - + +
125A PRO* 4.3 1.1 - - - -
3003A NAD 3.7 17.0 - - - +
90D MET* 4.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ARG 4.0 0.8 + - - -
93A ASP* 2.9 18.5 + - - +
94A ASP 3.3 0.4 - - - -
95A LEU* 1.3 76.8 - - - +
97A ASN* 1.3 74.7 + - - +
100A ALA* 2.7 50.1 + - + +
125A PRO* 3.8 19.5 - - + -
128A SER* 3.5 35.7 - - - -
129A THR* 5.6 1.6 - - + -
132A ILE* 3.9 15.7 - - + -
311A LYS* 3.6 51.1 - - + -
312A GLY* 4.1 2.5 - - - -
315A PHE* 3.8 23.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASP 4.8 0.2 + - - -
94A ASP 4.7 0.6 + - - -
95A LEU 3.4 0.6 - - - -
96A PHE* 1.3 95.3 - - - +
98A THR* 1.3 60.0 + - - +
100A ALA* 4.5 3.2 + - - +
101A THR* 4.3 12.0 + - - +
311A LYS* 5.8 0.6 - - - -
315A PHE* 5.7 1.5 - - - -
89D GLY* 3.3 29.8 - - - +
91D THR* 3.9 17.6 + - - +
94D ASP* 2.8 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 3.5 25.4 - - + -
95A LEU* 3.3 7.1 + - - -
96A PHE 3.2 0.4 - - - -
97A ASN* 1.3 78.9 - - - +
99A ASN* 1.3 73.4 + - - +
101A THR* 2.7 25.1 + - - -
102A ILE* 3.6 13.1 - - + +
87D LYS* 3.5 10.3 - - + +
88D PRO* 2.8 26.6 + - + +
90D MET* 3.2 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLY* 3.4 10.0 - - - -
84A VAL* 2.8 46.4 + - - +
95A LEU* 2.9 22.0 + - - +
96A PHE 4.5 0.2 - - - +
98A THR* 1.3 85.7 - - - +
100A ALA* 1.3 65.8 + - - +
102A ILE* 3.3 6.6 + - + +
103A VAL* 3.0 29.1 + - + +
123A ALA* 5.0 4.7 - - + -
124A ASN 2.9 29.1 + - - +
125A PRO* 4.9 1.1 - - + -
129A THR* 4.9 4.3 - - + -
3003A NAD 3.3 7.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 2.7 37.0 + - + +
97A ASN* 4.7 4.3 - - - +
98A THR 3.4 0.2 - - - -
99A ASN* 1.3 72.1 - - - +
101A THR* 1.3 56.7 + - - +
103A VAL* 3.8 2.2 - - - +
104A ALA* 2.8 31.9 + - - +
129A THR* 5.2 1.9 - - - +
132A ILE* 3.7 22.4 - - + +
315A PHE* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASN 4.3 10.6 + - - +
98A THR* 2.7 25.0 + - - -
100A ALA* 1.3 76.8 - - - +
102A ILE* 1.3 68.4 + - - +
104A ALA* 3.7 3.2 - - - +
105A THR* 2.9 33.1 + - - -
315A PHE* 3.7 24.0 - - + -
319A LEU* 6.0 1.6 - - + -
88D PRO 5.1 2.1 + - - -
89D GLY* 5.5 5.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA* 3.7 24.7 - - + +
83A GLY* 4.0 7.6 - - - -
84A VAL* 4.6 3.4 - - + +
98A THR* 3.6 20.4 - - + +
99A ASN* 3.3 29.1 + - - +
100A ALA 3.3 0.4 - - - -
101A THR* 1.3 85.8 + - - +
103A VAL* 1.3 58.0 + - + +
105A THR* 3.3 3.0 + - - -
106A LEU* 2.9 50.8 + - + +
3003A NAD 3.6 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 5.2 6.3 - - + -
82A ALA 4.8 3.4 - - - +
99A ASN 3.0 20.5 + - - +
100A ALA* 3.9 2.9 - - - +
102A ILE* 1.3 73.8 - - - +
104A ALA* 1.3 55.6 + - - +
106A LEU* 4.8 4.3 - - - -
107A THR* 2.8 45.9 + - + +
121A VAL* 4.6 7.2 - - + -
123A ALA* 3.9 27.8 - - + -
129A THR* 3.8 29.4 - - + +
132A ILE* 4.0 9.2 - - + -
133A THR* 3.5 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ALA 2.8 20.9 + - - +
101A THR* 3.7 5.2 - - - +
103A VAL* 1.3 73.5 - - - +
105A THR* 1.3 63.7 + - - +
107A THR* 3.5 6.2 + - - -
108A ALA* 3.1 26.5 + - - +
132A ILE* 3.9 11.4 - - + +
136A VAL* 4.0 5.9 - - + +
315A PHE* 3.9 10.8 - - + -
319A LEU* 3.8 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO* 6.5 1.1 - - + -
68A LEU* 5.1 3.4 - - + +
101A THR* 2.9 20.0 + - - -
102A ILE* 3.8 4.0 - - - -
104A ALA* 1.3 75.5 - - - +
106A LEU* 1.3 70.5 + - + +
108A ALA* 3.4 7.6 + - + +
109A ALA* 3.3 19.1 + - - +
3003A NAD 6.0 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.0 20.8 - - + +
38A TYR* 4.0 10.3 - - + +
68A LEU* 3.7 24.7 - - + -
80A ILE* 4.0 17.9 - - + -
82A ALA* 3.5 31.6 - - + -
102A ILE* 2.9 28.6 + - + +
103A VAL 4.1 2.0 - - - +
105A THR* 1.3 82.0 - - + +
107A THR* 1.3 61.2 + - - +
109A ALA* 3.1 8.9 + - - +
110A CYS* 3.1 24.8 + - - -
3003A NAD 3.7 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 3.9 22.7 - - + -
103A VAL* 2.8 35.7 + - + +
104A ALA* 3.5 4.5 + - - -
106A LEU* 1.3 69.9 - - - +
108A ALA* 1.3 61.0 + - - +
110A CYS* 3.3 6.8 + - - -
111A ALA* 2.8 25.6 + - - +
119A ILE* 4.6 3.1 - - + -
121A VAL* 4.9 0.9 - - + -
133A THR* 3.5 41.9 - - + +
136A VAL* 3.6 19.1 - - - +
137A PHE* 3.4 14.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA 3.1 20.3 + - - +
105A THR* 3.7 7.2 - - - +
106A LEU 3.2 0.2 - - - -
107A THR* 1.3 75.8 + - - +
109A ALA* 1.3 63.4 + - - +
111A ALA* 3.2 2.8 + - - +
112A GLN* 3.0 38.0 + - - +
136A VAL* 3.5 11.9 - - + +
140A HIS* 3.8 20.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 3.6 31.9 - - + -
69A PRO* 6.1 0.7 - - + -
72A LEU* 3.7 11.2 - - + -
105A THR 3.3 6.6 + - - +
106A LEU 3.1 10.2 + - - +
108A ALA* 1.3 80.4 - - - +
110A CYS* 1.3 51.5 + - - +
112A GLN* 3.2 5.9 + - - +
113A HIS* 2.8 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.1 9.6 - - - -
72A LEU* 3.7 7.4 - - - +
78A VAL* 3.9 35.4 - - - -
80A ILE* 4.5 4.7 - - - -
106A LEU 3.1 17.9 + - - -
107A THR* 3.3 13.4 + - - +
109A ALA* 1.3 75.3 - - - +
111A ALA* 1.3 59.0 - - - +
114A CYS* 2.8 43.2 + - - -
119A ILE* 4.0 12.8 - - + -
137A PHE* 4.0 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR 2.8 20.5 + - - +
108A ALA* 3.5 6.5 - - - +
110A CYS* 1.3 71.8 - - - +
112A GLN* 1.3 61.5 + - - +
115A PRO* 3.3 21.0 - - - +
137A PHE* 3.7 21.5 - - + -
140A HIS* 3.7 33.4 - - + +
142A VAL* 3.8 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA* 3.0 31.1 + - - +
109A ALA* 3.2 9.5 + - - +
111A ALA* 1.3 78.5 - - - +
113A HIS* 1.3 82.4 + - + +
114A CYS 3.8 0.2 - - - -
115A PRO* 4.3 5.3 - - - +
140A HIS* 3.4 29.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A PRO* 3.6 45.6 - - + +
72A LEU* 4.1 16.8 - - + -
73A LYS* 4.0 35.5 - - + +
74A GLY 4.6 1.9 + - - -
109A ALA* 2.8 36.7 + - + +
112A GLN* 1.3 97.8 + - + +
114A CYS* 1.3 62.9 + - - +
115A PRO* 3.7 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 3.5 33.7 - - - +
74A GLY 5.1 1.3 - - - +
75A CYS* 4.1 9.4 - - - +
78A VAL* 3.7 29.4 - - - -
110A CYS* 2.8 29.5 + - - +
113A HIS* 1.3 74.8 - - - +
115A PRO* 1.3 67.0 - - - +
116A GLU 3.1 3.4 - - - -
117A ALA* 3.1 24.3 + - + +
119A ILE* 4.7 2.9 - - - +
----------------------------------------------------------
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