Contacts of the helix formed by residues 9 - 25 (chain A) in PDB entry 4GCK
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 ARG 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ASN* 1.3 77.2 + - - +
11A ARG* 2.8 44.4 + - - +
12A ARG* 3.3 26.4 + - - +
13A GLU* 3.4 14.9 + - - +
50A ARG* 4.9 2.6 - - - +
51A HIS* 3.5 17.6 + - - -
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Residues in contact with ASN 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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9A ARG* 1.3 91.7 - - - +
11A ARG* 1.3 51.2 + - - +
13A GLU* 4.0 6.6 - - - +
14A GLU* 2.7 48.4 + - + +
17A GLN* 5.3 0.3 + - - -
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Residues in contact with ARG 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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9A ARG* 2.8 29.8 - - - +
10A ASN* 1.3 78.1 - - - +
12A ARG* 1.3 63.2 + - - +
14A GLU* 3.4 15.1 + - - +
15A ILE* 3.0 35.3 + - + +
41A VAL* 6.3 2.5 - - + -
43A VAL* 3.3 32.8 - - + +
47A ALA* 3.4 22.6 + - - +
50A ARG* 3.1 13.5 - - - +
51A HIS* 2.9 50.1 + - + +
2W G 2.9 36.0 + - - -
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Residues in contact with ARG 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 ARG 3.3 17.9 + - - +
11A ARG* 1.3 77.6 - - - +
13A GLU* 1.3 83.9 + - - +
15A ILE* 3.1 22.1 + - - +
16A LEU* 3.2 16.0 + - - +
51A HIS* 4.3 21.8 + - + +
52A PHE* 3.4 31.2 - - + -
61A SER* 2.7 34.8 + - - -
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Residues in contact with GLU 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 ARG 3.4 13.2 + - - +
10A ASN* 4.0 6.1 - - - +
12A ARG* 1.3 98.2 + - - +
14A GLU* 1.3 59.0 + - - +
16A LEU* 3.3 20.9 + - - +
17A GLN* 2.8 48.9 + - - +
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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 ASN* 2.7 32.5 + - + +
11A ARG* 3.4 20.0 - - + +
13A GLU* 1.3 71.5 - - - +
15A ILE* 1.3 68.0 + - + +
17A GLN* 3.0 19.6 + - - +
18A SER* 2.9 28.9 + - - +
41A VAL* 4.6 21.7 - - + +
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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 ARG* 3.0 21.1 + - + +
12A ARG 3.1 4.9 + - - +
14A GLU* 1.3 78.3 - - - +
16A LEU* 1.3 59.8 + - + +
18A SER* 3.1 4.3 + - - -
19A LEU* 2.9 27.1 + - + +
37A LEU* 4.1 16.1 - - + +
41A VAL* 4.2 20.4 - - + +
43A VAL* 5.9 0.9 - - + -
47A ALA 4.8 0.4 - - - +
48A LEU* 4.0 27.1 - - + -
51A HIS* 3.7 35.9 - - + -
52A PHE* 3.8 13.0 - - + -
58A MET* 3.8 26.9 - - + -
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Residues in contact with LEU 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 ARG* 3.2 20.6 + - - +
13A GLU* 3.4 32.8 - - - +
14A GLU 3.2 0.2 - - - -
15A ILE* 1.3 78.6 - - + +
17A GLN* 1.3 61.7 + - + +
19A LEU* 3.2 6.8 + - + +
20A ALA* 3.0 23.9 + - - +
52A PHE* 3.6 19.7 - - + -
58A MET* 3.7 32.1 - - + +
61A SER* 3.7 23.3 - - - +
62A LEU* 3.8 23.2 - - + +
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Residues in contact with GLN 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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10A ASN 5.3 0.6 + - - -
13A GLU* 2.8 30.6 + - - +
14A GLU* 3.0 26.1 + - - +
16A LEU* 1.3 76.3 - - - +
18A SER* 1.3 63.6 + - - +
20A ALA* 3.4 6.8 + - - +
21A LEU* 3.1 31.2 + - + +
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Residues in contact with SER 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* 2.9 17.0 + - - +
15A ILE 3.5 6.3 - - - -
17A GLN* 1.3 78.1 - - - +
19A LEU* 1.3 62.9 + - - +
21A LEU* 3.4 12.3 + - - +
22A MET* 3.1 28.6 + - - +
37A LEU* 4.3 3.6 - - - -
40A SER* 4.1 15.3 + - - -
41A VAL* 3.7 31.9 - - - +
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Residues in contact with LEU 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* 2.9 13.4 + - + +
16A LEU* 3.2 11.0 + - + +
18A SER* 1.3 75.0 - - - +
20A ALA* 1.3 64.5 + - - +
22A MET* 3.3 2.5 + - - +
23A LEU* 3.0 36.3 + - + +
32A ILE* 3.8 34.3 - - + -
37A LEU* 3.9 15.5 - - + +
55A LYS* 5.9 0.9 - - + -
58A MET* 3.9 31.9 - - + -
59A PHE* 4.2 21.1 - - + -
62A LEU* 3.4 27.8 - - + -
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Residues in contact with ALA 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 LEU 3.0 15.6 + - - +
17A GLN* 3.8 7.0 - - - +
18A SER 3.4 0.2 - - - -
19A LEU* 1.3 76.0 - - - +
21A LEU* 1.3 53.2 + - + +
23A LEU* 3.1 14.4 + - - +
24A GLU* 2.8 32.4 + - - +
62A LEU* 4.6 4.0 - - + +
104A GLY* 3.5 8.6 - - - -
105A LEU* 4.4 23.1 - - + -
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Residues in contact with LEU 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 GLN* 3.1 21.9 + - + +
18A SER* 3.6 14.1 - - - +
19A LEU 3.3 0.2 - - - -
20A ALA* 1.3 76.1 - - + +
22A MET* 1.3 61.7 + - + +
24A GLU* 3.3 21.8 + - - +
25A SER* 2.9 27.9 + - - -
40A SER* 6.0 1.6 - - - +
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Residues in contact with MET 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 SER 3.1 18.9 + - - +
19A LEU 3.3 4.5 + - - +
21A LEU* 1.3 74.2 - - + +
23A LEU* 1.3 65.8 + - - +
25A SER* 2.7 24.3 + - - +
27A ASP* 3.7 21.5 - - + +
28A GLY* 3.0 16.8 + - - -
32A ILE* 3.8 33.9 - - + -
36A LYS* 4.1 23.8 - - + +
37A LEU* 3.8 24.2 - - - -
40A SER* 3.7 30.5 - - - +
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Residues in contact with LEU 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 LEU* 3.0 36.5 + - + +
20A ALA* 3.1 14.8 - - - +
22A MET* 1.3 79.5 - - - +
24A GLU* 1.3 54.8 + - - +
28A GLY* 3.5 10.0 - - - +
32A ILE* 3.9 27.4 - - + -
59A PHE* 4.2 5.8 - - + -
62A LEU* 4.2 1.8 - - + -
104A GLY* 3.4 23.5 - - - +
105A LEU* 5.5 0.2 - - + -
107A ARG* 3.0 36.1 + - + -
108A ILE* 4.1 23.6 - - + -
113A ALA* 3.9 24.9 - - + -
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Residues in contact with GLU 24 (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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20A ALA 2.8 15.6 + - - +
21A LEU* 3.6 23.6 - - + +
22A MET 3.2 0.2 - - - -
23A LEU* 1.3 78.3 - - - +
25A SER* 1.3 62.2 + - - +
103A PRO* 3.2 33.0 - - + +
104A GLY* 3.4 17.2 - - - +
178A PHE* 3.2 24.7 - - + -
181A ARG* 5.6 1.4 + - - -
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Residues in contact with SER 25 (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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21A LEU 2.9 15.1 + - - -
22A MET* 2.7 18.6 + - - -
24A GLU* 1.3 83.5 - - - +
26A SER* 1.3 63.6 + - - +
27A ASP* 3.0 24.0 + - - +
28A GLY 3.1 10.7 + - - -
107A ARG* 3.2 9.2 + - - -
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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