Contacts of the helix formed by residues 97 - 117 (chain B) in PDB entry 1G3I
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 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A LYS* 5.8 1.7 + - - -
95B GLU* 3.2 20.3 + - - +
96B VAL* 1.3 84.6 - - - +
98B SER* 1.3 63.8 + - - +
100B ILE* 3.0 16.7 + - - +
101B ARG* 3.1 32.5 + - - +
284B PRO* 6.0 0.9 - - - +
285B LEU* 4.0 13.1 - - - +
291B VAL* 3.5 30.4 - - + +
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Residues in contact with SER 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LYS* 4.3 10.1 + - - -
86B PHE* 4.2 10.6 - - - -
95B GLU* 2.9 25.9 + - - +
96B VAL 2.8 0.8 - - - -
97B ASP* 1.3 79.5 - - - +
99B ILE* 1.3 57.9 + - - +
101B ARG* 2.6 22.0 + - - +
102B ASP* 2.6 49.2 + - - -
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Residues in contact with ILE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ILE* 4.2 5.8 - - + +
81B VAL* 3.9 33.4 - - + -
86B PHE* 3.8 27.1 - - + -
96B VAL* 3.1 14.6 + - + +
98B SER* 1.3 80.8 + - - +
100B ILE* 1.3 64.9 + - + +
102B ASP* 3.9 6.7 - - - +
103B LEU* 2.9 27.4 + - - +
254B VAL* 3.9 33.7 - - + -
256B ILE* 5.2 4.3 - - + -
282B LEU* 3.8 25.8 - - + -
285B LEU* 4.1 9.0 - - + -
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ASP 3.0 4.9 + - - +
99B ILE* 1.3 80.9 - - + +
101B ARG* 1.3 66.9 + - - +
103B LEU* 3.3 12.8 + - + +
104B THR* 3.0 28.0 + - - +
248B VAL* 4.9 8.1 - - + -
254B VAL* 4.9 1.6 - - + -
285B LEU* 3.6 28.7 - - + -
291B VAL* 3.3 20.0 - - + -
293B THR* 4.5 0.4 - - - -
298B VAL* 3.1 35.2 - - + -
300B THR* 3.4 33.7 - - + +
303B ILE* 4.9 3.4 - - + -
305B PHE* 4.6 8.7 - - + -
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B GLU* 4.1 23.4 + - - +
97B ASP* 3.1 34.4 + - - +
98B SER* 2.6 26.3 + - - +
100B ILE* 1.3 74.7 - - - +
102B ASP* 1.3 67.5 + - - +
104B THR* 3.0 2.8 + - - -
105B ASP* 2.9 23.5 + - - +
291B VAL* 4.5 1.4 - - + +
292B SER* 3.2 25.5 + - - +
293B THR* 3.8 24.4 - - + +
294B LYS* 4.9 4.7 - - + +
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Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ILE* 4.5 20.5 - - + +
81B VAL* 5.7 2.4 - - - +
85B LYS* 4.4 12.3 + - - -
98B SER* 2.6 34.5 + - - +
99B ILE* 3.9 4.4 + - - +
101B ARG* 1.3 75.4 - - - +
103B LEU* 1.3 63.7 + - - +
105B ASP* 3.0 13.8 + - - +
106B SER* 2.9 22.3 + - - -
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PRO* 3.3 35.4 - - + +
78B PHE 3.9 3.1 - - - +
79B ILE* 3.4 26.8 - - + +
99B ILE 2.9 18.7 + - - +
100B ILE* 3.4 11.4 - - + +
101B ARG 3.1 0.2 + - - -
102B ASP* 1.3 75.6 - - - +
104B THR* 1.3 64.5 + - - +
106B SER* 2.8 16.6 + - - -
107B ALA* 2.9 11.1 + - - +
248B VAL* 3.5 28.5 - - + -
252B GLY* 4.4 4.9 - - - -
253B ILE 4.2 1.6 - - - +
254B VAL* 3.8 21.3 - - + -
303B ILE* 3.8 15.3 - - + -
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Residues in contact with THR 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ILE 3.0 15.4 + - - -
101B ARG 3.4 6.1 - - - -
103B LEU* 1.3 74.1 - - - +
105B ASP* 1.3 63.4 + - - +
107B ALA* 3.0 3.3 + - - +
108B MET* 2.9 20.8 + - - +
244B ALA* 4.8 6.9 - - + +
245B ILE* 4.9 3.1 - - + -
248B VAL* 3.2 20.3 - - + +
293B THR* 3.4 31.9 - - - +
295B HIS* 3.9 21.8 - - + -
298B VAL* 3.4 20.4 - - + +
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Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ARG* 2.9 13.0 + - - +
102B ASP* 3.1 19.1 - - - +
104B THR* 1.3 76.8 - - - +
106B SER* 1.3 56.9 - - - +
108B MET* 3.1 25.1 - - - +
109B LYS* 3.4 5.0 + - - +
294B LYS* 3.1 36.6 + - - +
295B HIS* 3.3 12.9 + - - -
297C MET* 4.5 20.9 - - + +
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Residues in contact with SER 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PRO* 4.8 3.2 - - - +
78B PHE 3.9 25.5 + - - -
79B ILE* 5.8 0.7 - - - -
102B ASP 2.9 10.4 + - - -
103B LEU* 2.8 10.6 + - - -
105B ASP* 1.3 73.6 - - - +
107B ALA* 1.3 64.9 + - - +
108B MET 3.0 2.1 + - - -
109B LYS* 3.2 13.1 + - - +
110B LEU* 3.0 20.7 + - - +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PRO* 3.6 25.9 - - + +
103B LEU 2.9 5.9 + - - -
104B THR 3.0 3.1 + - - +
106B SER* 1.3 76.5 - - - +
108B MET* 1.3 52.0 + - - +
110B LEU* 3.2 3.5 + - - +
111B VAL* 2.6 39.5 + - - +
244B ALA* 3.2 27.6 - - - +
247B ALA* 3.7 2.9 - - + -
248B VAL* 3.3 22.7 - - + -
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Residues in contact with MET 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B THR 2.9 7.6 + - - +
105B ASP* 3.1 13.5 - - - +
106B SER 3.0 0.2 - - - -
107B ALA* 1.3 76.1 - - - +
109B LYS* 1.3 57.9 + - - +
111B VAL 2.9 0.3 + - - -
112B ARG* 2.5 55.7 + - + +
240B LEU* 3.4 32.8 - - + -
241B LYS* 4.1 16.4 - - + -
244B ALA* 3.6 21.9 - - + +
295B HIS* 3.2 42.4 - - + +
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Residues in contact with LYS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ASP 3.4 4.7 + - - +
106B SER* 3.2 16.3 + - - +
108B MET* 1.3 76.6 - - - +
110B LEU* 1.3 62.8 + - + +
112B ARG* 4.3 7.4 - - - +
113B GLN* 2.8 56.4 + - + +
299C LYS* 4.7 20.0 - - - +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ASN* 3.6 46.2 - - - +
76B ALA 3.8 22.0 - - - +
77B PRO* 3.9 11.0 - - + -
106B SER 3.0 10.0 + - - +
107B ALA* 3.3 9.2 - - - +
108B MET 2.9 0.6 + - - -
109B LYS* 1.3 84.7 - - + +
111B VAL* 1.3 65.6 + - + +
113B GLN* 3.8 19.3 + - - +
114B GLN* 2.9 31.7 + - + +
247B ALA* 6.0 0.7 - - + -
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ALA 2.6 23.6 + - - +
108B MET 3.8 1.6 - - - +
110B LEU* 1.3 73.0 - - + +
112B ARG* 1.3 63.7 + - - +
114B GLN* 3.5 22.1 - - - +
115B GLU* 3.7 5.9 + - - +
240B LEU* 4.0 20.5 - - + +
243B LYS* 3.8 42.8 - - + +
244B ALA* 3.4 27.6 - - + +
247B ALA* 3.6 17.9 - - + -
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Residues in contact with ARG 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B MET* 2.5 37.0 + - + +
109B LYS* 3.7 6.7 - - - +
111B VAL* 1.3 69.0 - - - +
113B GLN* 1.3 55.1 + - - +
114B GLN 2.6 3.1 + - - -
115B GLU* 2.5 32.1 + - - +
116B ILE* 3.3 24.4 + - + +
235B ILE* 5.8 9.7 - - + +
240B LEU* 3.5 27.1 - - + +
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Residues in contact with GLN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ASN* 5.6 1.4 + - - -
109B LYS* 2.8 43.1 + - + +
110B LEU* 4.4 20.4 + - - +
112B ARG* 1.3 73.9 - - - +
114B GLN* 1.3 64.7 + - - +
115B GLU 3.1 2.1 + - - -
116B ILE* 3.6 28.1 + - + +
117B ALA* 3.9 8.6 + - + +
118B LYS* 4.7 1.4 + - - +
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Residues in contact with GLN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B ASN* 2.6 36.3 + - - +
110B LEU* 2.9 23.2 + - + +
111B VAL* 3.5 22.0 + - - +
112B ARG 2.6 5.3 + - - -
113B GLN* 1.3 82.6 - - - +
115B GLU* 1.3 57.7 + - + +
116B ILE 3.7 0.2 - - - -
118B LYS* 3.7 22.8 - - + +
119B ASN* 3.7 17.8 + - - -
243B LYS* 4.7 17.2 - - - +
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B VAL 4.1 7.0 - - - +
112B ARG 2.5 16.9 + - - +
114B GLN* 1.3 78.5 - - + +
116B ILE* 1.3 58.3 + - - +
117B ALA 3.3 2.2 - - - -
119B ASN* 4.0 25.6 - - + +
120B ARG 3.6 19.6 + - - +
234B LEU 5.1 5.0 - - - +
235B ILE* 4.7 18.1 - - + +
239B GLU* 3.8 18.0 - - - +
240B LEU* 3.8 24.2 - - + +
243B LYS* 4.0 27.1 + - - +
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ARG* 3.3 26.1 + - + +
113B GLN* 3.6 19.9 + - + +
115B GLU* 1.3 80.3 - - - +
117B ALA* 1.3 66.9 + - + +
120B ARG* 4.3 8.9 - - - +
231B ALA* 5.0 16.2 - - + -
235B ILE* 5.3 12.1 - - + -
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Residues in contact with ALA 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLN* 3.9 6.1 + - + +
115B GLU 3.3 0.6 - - - -
116B ILE* 1.3 91.4 - - + +
118B LYS* 1.3 65.9 + - - +
119B ASN 2.9 5.6 + - - -
120B ARG* 2.9 18.2 + - - +
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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
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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