Contacts of the helix formed by residues 9 - 23 (chain B) in PDB entry 3GSB
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 THR 9 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B PHE* 3.8 31.6 + - + -
8B LYS* 1.3 78.7 - - - +
10B ILE* 1.3 67.4 + - - +
12B SER* 3.3 8.6 + - - -
13B ASP* 3.0 40.3 + - - +
42B ILE* 4.7 16.2 - - + -
54B ASP* 4.9 5.8 - - - +
56B ASP* 3.1 11.9 - - - +
391B ARG* 4.7 11.7 + - - +
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Residues in contact with ILE 10 (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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8B LYS* 3.6 27.1 - - + +
9B THR* 1.3 75.4 - - - +
11B LYS* 1.3 76.5 + - + +
13B ASP* 3.0 19.4 + - - +
14B GLU* 3.1 25.6 + - + +
56B ASP* 3.4 6.4 + - - +
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Residues in contact with LYS 11 (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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8B LYS* 5.6 2.9 - - - +
10B ILE* 1.3 87.9 - - + +
12B SER* 1.3 63.4 + - - +
14B GLU* 3.4 31.1 + - + +
15B ILE* 2.9 34.9 + - + +
55B VAL* 3.6 32.5 - - + +
56B ASP* 3.3 16.5 + - - +
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Residues in contact with SER 12 (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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9B THR* 3.3 14.3 + - - -
11B LYS* 1.3 78.2 - - - +
13B ASP* 1.3 59.0 + - - +
15B ILE* 5.0 0.2 - - - -
16B PHE* 3.0 30.7 + - - +
41B PRO 4.1 5.6 - - - +
42B ILE* 3.7 12.5 - - - -
43B VAL* 2.7 51.5 + - - +
54B ASP* 4.2 5.6 + - - -
55B VAL* 4.2 5.0 + - - +
56B ASP* 3.4 9.7 + - - -
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Residues in contact with ASP 13 (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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9B THR* 3.0 35.7 + - - +
10B ILE* 3.0 12.4 + - - +
12B SER* 1.3 76.9 - - - +
14B GLU* 1.3 61.0 + - - +
16B PHE* 3.3 5.1 + - - +
17B ALA* 2.9 31.1 + - - +
40B GLN* 3.0 33.4 - - - +
41B PRO* 4.6 5.9 - - - +
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Residues in contact with GLU 14 (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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10B ILE* 3.1 16.2 + - + +
11B LYS* 3.4 44.7 + - - +
13B ASP* 1.3 76.7 - - - +
15B ILE* 1.3 68.5 + - + +
17B ALA* 3.4 7.0 - - - +
18B ALA* 3.0 28.1 + - - +
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Residues in contact with ILE 15 (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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97A CYS 5.4 0.4 - - - -
98A ALA* 4.4 25.6 - - + +
101A ASN* 3.5 20.4 + - - +
11B LYS* 2.9 26.0 + - + +
12B SER 4.0 2.5 - - - +
14B GLU* 1.3 82.8 - - + +
16B PHE* 1.3 64.4 + - - +
18B ALA* 3.3 5.2 + - - -
19B ALA* 3.1 19.3 + - + +
43B VAL* 4.3 21.1 - - + -
55B VAL* 3.6 34.1 - - + -
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Residues in contact with PHE 16 (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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96A PRO* 5.4 6.3 - - + -
12B SER 3.0 18.6 + - - +
13B ASP* 3.9 4.9 - - - +
15B ILE* 1.3 78.0 - - - +
17B ALA* 1.3 63.1 + - - +
19B ALA* 3.4 4.3 - - + +
20B GLN* 3.3 44.9 + - - +
25B GLY 3.8 21.5 - - - -
26B GLY 4.0 10.3 - - - -
27B VAL* 3.9 15.7 - - + -
33B ALA* 4.4 10.3 - - + -
39B GLY 4.0 3.8 - - - -
40B GLN* 3.9 21.1 - - - -
41B PRO* 3.6 43.5 - - + +
43B VAL* 4.7 7.8 - - + +
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Residues in contact with ALA 17 (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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13B ASP 2.9 18.5 + - - +
14B GLU* 3.4 10.3 - - - +
16B PHE* 1.3 76.6 - - - +
18B ALA* 1.3 67.4 + - - +
19B ALA 3.4 0.3 + - - -
20B GLN* 3.4 29.3 + - - +
21B LYS* 4.0 11.0 + - - +
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Residues in contact with ALA 18 (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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101A ASN* 3.7 12.1 - - - +
14B GLU 3.0 14.2 + - - +
15B ILE* 3.3 9.6 + - - +
17B ALA* 1.3 74.6 - - - +
19B ALA* 1.3 63.9 + - - +
21B LYS* 3.0 34.7 + - - +
22B LEU* 3.4 12.4 - - + +
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Residues in contact with ALA 19 (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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101A ASN* 3.6 15.8 - - - +
15B ILE* 3.1 14.3 + - + +
16B PHE* 3.4 13.0 - - + +
18B ALA* 1.3 76.7 - - - +
20B GLN* 1.3 58.2 + - - +
22B LEU* 2.8 29.6 + - - +
23B MET* 2.9 19.0 + - - +
26B GLY* 3.4 26.9 - - - +
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Residues in contact with GLN 20 (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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116A MET* 4.2 7.4 - - - +
288A ARG* 4.6 4.0 + - - -
292A GLN* 5.7 0.9 + - - -
16B PHE* 3.3 33.9 + - + +
17B ALA* 3.6 23.8 + - - +
18B ALA 3.3 0.6 + - - -
19B ALA* 1.3 76.5 - - - +
21B LYS* 1.3 59.5 + - + +
22B LEU 3.3 0.2 - - - -
23B MET 3.6 8.8 - - - +
25B GLY* 3.8 21.8 + - - +
26B GLY* 3.5 10.3 - - - +
40B GLN* 5.6 0.3 + - - -
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Residues in contact with LYS 21 (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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108A ASN* 5.3 0.2 + - - -
115A GLU 4.5 4.7 - - - +
116A MET* 3.1 20.0 - - - +
288A ARG* 4.6 7.3 + - - +
17B ALA 4.2 10.5 - - - +
18B ALA* 3.0 21.0 + - - +
20B GLN* 1.3 78.4 - - + +
22B LEU* 1.3 66.9 + - + +
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Residues in contact with LEU 22 (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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101A ASN* 3.9 25.4 - - + +
104A ALA* 4.1 14.4 - - + -
105A GLU* 4.6 25.6 - - + +
108A ASN* 4.2 17.0 + - - +
116A MET* 3.5 7.9 - - - -
117A VAL* 3.0 26.3 + - - +
18B ALA* 3.4 25.1 - - + +
19B ALA* 2.8 15.8 + - - +
21B LYS* 1.3 90.1 - - + +
23B MET* 1.3 66.7 + - + +
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Residues in contact with MET 23 (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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100A GLU* 4.4 19.3 - - - +
101A ASN* 5.2 5.2 - - - +
104A ALA* 4.0 19.5 - - + -
116A MET* 4.1 7.5 - - - +
117A VAL 3.1 20.2 - - - +
118A ARG* 4.6 0.4 - - - -
119A PHE* 3.8 22.0 - - + +
19B ALA* 2.9 12.6 + - - +
20B GLN 3.6 10.7 - - - +
21B LYS 3.7 0.2 - - - -
22B LEU* 1.3 88.2 - - + +
24B PRO* 1.3 62.1 - - + +
25B GLY 3.0 1.9 + - - -
26B GLY* 2.7 30.5 + - - +
27B VAL 3.6 18.8 - - - +
28B SER* 3.0 28.9 - - - +
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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