Contacts of the helix formed by residues 91 - 107 (chain A) in PDB entry 3GNI
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 ASP 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A THR* 4.6 18.7 - - + +
43A VAL* 5.2 0.9 - - - +
44A SER* 3.6 31.9 + - - -
89A LEU 4.2 0.8 + - - -
90A ILE* 1.3 81.9 - - - +
92A PHE* 1.3 67.1 + - - +
93A GLU* 3.6 11.3 + - - +
94A GLY* 3.2 21.5 + - - -
95A LYS* 3.0 22.3 + - - +
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Residues in contact with PHE 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASP* 1.3 75.6 - - - +
93A GLU* 1.3 81.8 + - + +
95A LYS* 3.5 24.8 + - + +
96A LYS* 3.6 21.3 + - + +
142A ASN* 4.9 2.8 + - - -
123B LYS 3.3 26.2 - - - -
124B LEU* 3.5 22.7 - - - -
125B PHE 4.3 1.6 - - - -
126B ASN* 3.5 37.9 - - + +
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Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASP* 3.3 10.5 + - - +
92A PHE* 1.3 92.3 - - + +
94A GLY* 1.3 61.2 + - - +
96A LYS* 2.9 29.9 + - - +
97A ASP* 3.0 34.2 + - - +
126B ASN* 3.8 6.9 - - - +
185B TYR* 2.9 32.4 + - - -
189B MET* 3.9 8.6 - - - +
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Residues in contact with GLY 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A SER* 5.4 2.9 - - - -
47A LEU* 3.5 11.4 - - - +
90A ILE* 3.6 20.0 - - - -
91A ASP* 3.2 15.7 + - - -
93A GLU* 1.3 77.8 - - - +
95A LYS* 1.3 54.2 + - - +
97A ASP* 3.2 9.3 + - - +
98A VAL* 2.8 37.8 + - - +
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Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 3.4 42.9 - - + +
88A GLN* 4.1 8.9 + - - +
90A ILE* 2.7 27.4 + - + +
91A ASP* 3.0 18.6 + - - +
92A PHE* 3.6 16.0 - - + +
94A GLY* 1.3 76.0 - - - +
96A LYS* 1.3 59.6 + - - +
98A VAL* 3.5 3.6 + - - +
99A ALA* 3.3 16.6 + - - +
138A GLU* 3.6 37.6 + - - +
139A ILE* 3.8 15.7 - - + -
142A ASN* 3.6 26.9 - - - +
146A MET* 5.1 0.2 - - - +
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Residues in contact with LYS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A PHE* 3.6 23.1 + - + +
93A GLU* 2.9 34.1 + - - +
94A GLY 3.2 0.4 - - - -
95A LYS* 1.3 75.8 - - - +
97A ASP* 1.3 62.4 + - - +
99A ALA* 3.5 3.9 + - - +
100A GLN* 3.1 44.6 + - - +
142A ASN* 3.5 22.2 - - - +
124B LEU* 2.7 49.0 + - + +
185B TYR* 3.2 12.3 + - - -
189B MET* 3.3 25.6 - - - -
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A SER 4.7 0.3 - - - +
47A LEU* 4.0 19.8 - - + +
48A VAL* 3.5 30.1 + - - +
51A LYS* 2.9 32.4 + - - +
93A GLU* 3.0 23.0 + - - +
94A GLY* 3.2 13.0 + - - +
96A LYS* 1.3 74.3 - - - +
98A VAL* 1.3 65.4 + - - +
100A GLN* 3.3 10.6 + - - +
101A ILE* 2.9 32.0 + - + +
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.7 25.1 - - + -
83A LEU* 4.0 29.6 - - + +
84A VAL* 5.0 2.5 - - + +
87A LEU* 4.1 14.4 - - + -
90A ILE* 4.0 19.3 - - + -
94A GLY 2.8 21.1 + - - +
95A LYS 3.7 7.9 - - - +
96A LYS 3.4 0.2 - - - -
97A ASP* 1.3 71.8 - - - +
99A ALA* 1.3 58.7 + - - +
101A ILE* 3.3 7.1 + - - +
102A PHE* 2.9 35.1 + - + +
146A MET* 4.1 16.4 - - + -
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LYS 3.3 5.1 + - - +
96A LYS 3.6 9.0 - - - +
97A ASP 3.3 0.2 - - - -
98A VAL* 1.3 78.6 - - - +
100A GLN* 1.3 57.9 + - + +
102A PHE* 3.6 0.5 - - - +
103A ASN* 2.9 37.0 + - - +
142A ASN* 3.9 26.0 - - - +
145A ILE* 4.5 15.3 - - + -
146A MET* 3.7 25.3 - - + -
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Residues in contact with GLN 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LYS* 3.5 19.3 + - + +
55A TYR* 2.7 41.6 + - + +
96A LYS* 3.1 34.0 + - - +
97A ASP* 3.3 25.1 - - - +
99A ALA* 1.3 77.1 - - + +
101A ILE* 1.3 61.7 + - - +
103A ASN* 3.8 3.5 - - - +
104A ASN* 3.1 13.5 + - - +
124B LEU* 6.1 1.8 - - - +
189B MET* 5.5 6.1 + - - -
221B ILE* 6.1 4.8 - - + +
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Residues in contact with ILE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.5 45.5 - - + +
50A MET* 3.7 19.5 - - + -
51A LYS* 3.9 21.8 - - + +
54A LEU* 3.8 20.6 - - + +
55A TYR* 4.5 0.9 - - - -
74A LEU* 4.2 21.8 - - + -
80A LEU* 5.2 4.9 - - + -
83A LEU* 5.5 6.1 - - + -
97A ASP* 2.9 23.8 + - + +
98A VAL* 3.7 3.8 - - - +
100A GLN* 1.3 74.4 - - - +
102A PHE* 1.3 64.0 + - - +
104A ASN* 3.4 2.6 + - - +
105A ILE* 3.1 30.1 + - + +
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Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A LEU* 4.0 34.8 - - + -
83A LEU* 6.5 0.2 - - + -
84A VAL* 3.8 20.9 - - + -
98A VAL* 2.9 21.2 + - + +
99A ALA 3.6 3.8 - - - +
101A ILE* 1.3 79.0 - - - +
103A ASN* 1.3 60.1 + - - +
105A ILE* 3.7 5.4 - - - +
106A LEU* 3.0 55.8 + - + +
116A THR* 5.3 2.5 - - + +
120A ILE* 4.1 15.5 - - + -
126A ILE* 3.8 23.1 - - + -
130A LEU* 4.5 3.8 - - + -
146A MET* 3.7 32.5 - - + -
150A CYS* 3.7 13.2 - - - -
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Residues in contact with ASN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A TYR* 4.5 4.5 - - - +
99A ALA 2.9 22.1 + - - +
100A GLN* 3.8 7.2 - - - +
102A PHE* 1.3 78.5 - - - +
104A ASN* 1.3 62.3 + - - +
106A LEU* 3.5 8.3 + - - +
107A ARG* 3.2 30.5 + - + +
145A ILE* 3.6 21.8 - - - +
146A MET* 3.7 20.4 - - - +
149A GLU* 3.2 40.1 - - + +
224B GLY* 6.6 0.2 - - - -
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Residues in contact with ASN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.5 47.5 + - + +
55A TYR* 3.5 27.4 + - + +
67A VAL* 5.1 3.6 - - - +
100A GLN 3.1 17.5 + - - +
101A ILE 3.8 4.0 - - - +
103A ASN* 1.3 76.0 - - - +
105A ILE* 1.3 66.6 + - - +
107A ARG* 3.4 14.4 + - - +
108A ARG* 3.4 10.4 + - - +
224B GLY* 4.8 4.6 + - - -
225B GLN* 6.0 2.8 - - - +
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.0 24.7 - - + -
71A ALA* 3.9 25.8 - - + +
74A LEU* 3.9 28.0 - - + -
75A TYR* 3.8 18.4 - - + +
80A LEU* 4.2 11.4 - - + -
101A ILE* 3.1 18.7 + - + +
102A PHE* 3.7 6.1 - - - +
104A ASN* 1.3 76.0 + - - +
106A LEU* 1.3 57.6 + - - +
108A ARG* 2.8 29.2 + - - +
116A THR* 2.8 37.5 + - + +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A PHE* 3.0 42.1 + - + +
103A ASN* 3.6 6.3 - - - +
104A ASN 3.3 0.2 - - - -
105A ILE* 1.3 77.4 - - - +
107A ARG* 1.3 60.7 + - + +
108A ARG 3.1 1.6 + - - +
114A THR* 3.7 15.8 + - - -
116A THR* 3.7 28.6 - - + +
117A VAL* 4.5 9.2 - - + -
120A ILE* 3.7 16.4 - - + -
149A GLU* 3.9 12.3 - - + +
150A CYS* 3.7 27.8 - - - +
153A HIS* 3.9 18.9 - - + +
156A LEU* 4.2 13.7 - - + -
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Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASN* 3.2 18.0 + - - +
104A ASN* 3.9 8.1 - - - +
105A ILE 3.2 0.4 - - - -
106A LEU* 1.3 76.7 - - + +
108A ARG* 1.3 64.6 + - - +
109A GLN* 3.4 12.5 + - - +
114A THR* 5.1 0.7 - - - -
149A GLU* 3.2 27.6 + - + +
152A ARG* 3.3 36.8 - - - +
153A HIS* 5.1 4.9 - - + -
342A CIT 2.7 28.9 + - - -
223B HIS* 3.4 63.0 + - - +
224B GLY* 4.1 9.8 - - - +
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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
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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) + - + + + + + -
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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