Contacts of the helix formed by residues 9 - 23 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.7 30.4 + - + +
8A LYS* 1.3 78.8 - - - +
10A ILE* 1.3 58.9 + - - +
11A LYS 3.3 2.9 - - - -
12A SER* 3.4 3.4 + - - -
13A ASP* 2.9 44.2 + - - -
41A PRO 5.8 0.4 - - - -
42A ILE* 4.0 24.5 - - + -
54A ASP* 4.9 1.3 - - - +
56A ASP* 3.5 10.3 - - - -
58A ASN* 4.9 2.0 - - - +
391A ARG* 4.4 12.3 + - - +
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Residues in contact with ILE 10 (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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8A LYS* 4.8 17.0 - - + -
9A THR* 1.3 77.7 - - - +
11A LYS* 1.3 68.1 + - + +
13A ASP* 3.2 11.2 - - + +
14A GLU* 3.0 46.8 + - + +
56A ASP* 3.5 7.0 + - - +
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Residues in contact with LYS 11 (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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8A LYS* 5.7 6.1 - - - +
10A ILE* 1.3 80.8 - - + +
12A SER* 1.3 66.7 + - - +
13A ASP 3.0 2.3 + - - -
14A GLU* 3.2 29.4 + - - +
15A ILE* 3.1 28.6 + - + +
55A VAL* 3.2 36.6 - - + +
56A ASP* 3.1 24.7 + - - +
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Residues in contact with SER 12 (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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9A THR* 3.4 8.3 + - - -
11A LYS* 1.3 76.3 - - - +
13A ASP* 1.3 58.8 + - - +
16A PHE* 3.1 32.1 + - - +
41A PRO 3.7 15.0 - - - +
42A ILE* 3.8 10.0 - - - +
43A VAL* 3.0 42.3 + - - +
54A ASP* 3.9 7.8 + - - -
55A VAL* 3.3 10.3 - - - +
56A ASP* 3.2 8.8 + - - -
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Residues in contact with ASP 13 (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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9A THR* 2.9 34.4 + - - +
10A ILE* 3.2 15.4 - - + +
11A LYS 3.0 1.2 - - - -
12A SER* 1.3 77.3 - - - +
14A GLU* 1.3 65.4 + - + +
16A PHE* 3.5 3.6 + - - +
17A ALA* 3.1 23.6 + - - +
40A GLN* 3.8 28.7 - - - +
41A PRO 5.3 1.6 - - - +
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Residues in contact with GLU 14 (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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10A ILE* 3.0 32.0 + - + +
11A LYS* 3.8 26.5 + - - +
13A ASP* 1.3 75.5 - - + +
15A ILE* 1.3 66.5 + - + +
17A ALA* 3.3 7.5 + - - +
18A ALA* 3.1 23.6 + - - +
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Residues in contact with ILE 15 (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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11A LYS* 3.1 19.2 + - + +
14A GLU* 1.3 81.0 - - + +
16A PHE* 1.3 57.7 + - - +
18A ALA* 3.4 4.4 + - - -
19A ALA* 3.0 25.5 + - + +
43A VAL* 3.8 37.5 - - + -
55A VAL* 3.9 23.3 - - + -
96B PRO* 6.3 0.7 - - + -
97B CYS 5.1 1.3 - - - +
98B ALA* 4.3 22.2 - - + -
101B ASN* 3.5 22.1 + - + +
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Residues in contact with PHE 16 (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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12A SER 3.1 20.7 + - - +
13A ASP* 4.0 4.0 - - - +
14A GLU 3.3 0.2 - - - -
15A ILE* 1.3 75.1 - - - +
17A ALA* 1.3 65.7 + - - +
19A ALA* 3.3 6.0 + - + +
20A GLN* 3.0 50.9 + - - -
25A GLY 3.4 24.2 - - - -
26A GLY* 3.7 18.8 - - - -
27A VAL* 4.0 11.4 - - + -
33A ALA* 5.8 3.6 - - + -
35A LYS* 5.9 3.8 - - - -
39A GLY 5.9 0.2 - - - -
40A GLN* 3.8 30.3 - - + -
41A PRO* 3.8 34.1 - - + +
43A VAL* 4.6 5.1 - - + +
96B PRO* 5.2 6.5 - - + -
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Residues in contact with ALA 17 (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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13A ASP 3.1 17.3 + - - +
14A GLU* 3.5 8.1 - - - +
16A PHE* 1.3 77.7 - - - +
18A ALA* 1.3 63.2 + - - +
20A GLN* 3.2 28.0 + - - +
21A LYS* 3.9 13.5 + - - +
40A GLN* 5.9 0.4 + - - +
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Residues in contact with ALA 18 (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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14A GLU 3.1 13.6 + - - +
15A ILE* 3.7 5.4 - - - +
16A PHE 3.3 0.2 - - - -
17A ALA* 1.3 74.9 - - - +
19A ALA* 1.3 64.7 + - - +
21A LYS* 3.0 22.9 + - - +
22A LEU* 3.5 15.1 - - + +
101B ASN* 3.6 17.0 - - - +
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Residues in contact with ALA 19 (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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15A ILE* 3.0 12.3 + - + +
16A PHE* 3.3 13.9 + - + +
18A ALA* 1.3 76.3 - - - +
20A GLN* 1.3 55.2 + - - +
22A LEU* 2.9 6.7 + - - +
23A MET* 2.8 35.5 + - + +
26A GLY* 3.4 26.7 - - - +
101B ASN* 3.3 26.6 - - - +
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Residues in contact with GLN 20 (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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16A PHE* 3.0 49.8 + - - +
17A ALA* 3.5 18.4 + - - +
18A ALA 3.1 1.6 + - - -
19A ALA* 1.3 76.9 - - - +
21A LYS* 1.3 61.6 + - + +
22A LEU 3.2 0.7 - - - -
23A MET 3.4 10.2 - - - +
25A GLY* 3.7 13.0 + - - +
26A GLY* 3.7 19.3 - - - +
35A LYS* 5.4 6.2 + - - -
116B MET* 4.3 8.3 - - - +
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Residues in contact with LYS 21 (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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17A ALA* 4.0 12.6 - - - +
18A ALA* 3.0 14.1 + - - +
20A GLN* 1.3 79.7 - - + +
22A LEU* 1.3 65.9 + - + +
108B ASN* 5.0 0.3 + - - -
115B GLU 4.3 5.9 - - - +
116B MET* 3.9 16.3 - - - +
288B ARG* 4.3 11.8 + - - +
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Residues in contact with LEU 22 (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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18A ALA* 3.5 13.2 - - + +
19A ALA 2.9 4.9 + - - +
21A LYS* 1.3 88.5 - - + +
23A MET* 1.3 71.6 + - + +
101B ASN* 3.7 51.6 - - + +
104B ALA* 4.2 6.7 - - + -
105B GLU* 4.4 27.6 - - + +
108B ASN* 4.3 17.8 + - - +
116B MET* 3.3 8.5 - - - +
117B VAL* 3.2 25.6 + - - +
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Residues in contact with MET 23 (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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19A ALA* 2.8 21.9 + - + +
20A GLN 3.4 8.8 - - - +
22A LEU* 1.3 86.2 - - + +
24A PRO* 1.3 67.5 - - + +
25A GLY 2.9 10.7 + - - -
26A GLY 2.9 15.0 + - - +
27A VAL* 4.2 19.1 - - - +
28A SER* 4.1 19.7 - - - -
100B GLU* 3.6 37.5 - - + +
101B ASN* 3.7 22.4 - - - +
104B ALA* 4.2 7.0 - - + -
116B MET* 3.9 5.2 - - - -
117B VAL 3.4 13.7 - - - +
118B ARG* 5.4 0.9 - - - -
119B PHE* 4.5 13.7 - - - -
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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