Contacts of the helix formed by residues 10 - 25 (chain C) 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 ASN 10 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C ARG* 1.3 72.8 - - - +
11C ARG* 1.3 66.6 + - - +
13C GLU* 4.1 3.7 - - - +
14C GLU* 2.8 49.8 + - - +
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Residues in contact with ARG 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ARG* 3.1 2.8 - - + +
10C ASN* 1.3 84.7 + - - +
12C ARG* 1.3 65.5 + - - +
14C GLU* 2.9 34.4 + - - +
15C ILE* 2.9 33.7 + - - +
41C VAL* 5.1 4.4 + - - -
43C VAL* 2.8 41.0 - - - +
47C ALA* 6.5 0.2 - - - -
50C ARG* 5.5 2.7 - - - +
51C HIS* 3.3 35.0 - - + +
23Z G 5.1 13.0 + - - +
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Residues in contact with ARG 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ARG* 3.1 52.1 + - + +
11C ARG* 1.3 78.5 - - - +
13C GLU* 1.3 70.2 + - - +
15C ILE* 3.1 6.8 + - - +
16C LEU* 3.1 37.9 + - - +
51C HIS* 4.0 12.8 + - + +
52C PHE* 3.3 38.0 - - + -
57C ARG* 5.2 3.2 + - - +
61C SER* 3.1 28.1 + - - -
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Residues in contact with GLU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ARG 2.7 26.7 + - - +
10C ASN* 4.1 4.0 - - - +
12C ARG* 1.3 80.5 + - - +
14C GLU* 1.3 55.5 - - - +
16C LEU* 3.1 27.2 + - - +
17C GLN* 2.8 30.8 + - - +
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Residues in contact with GLU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ASN* 2.8 32.9 + - - +
11C ARG* 2.9 42.8 + - - +
13C GLU* 1.3 77.0 - - - +
15C ILE* 1.3 57.9 + - + +
17C GLN* 3.4 7.6 + - - +
18C SER* 2.9 35.4 + - - +
41C VAL* 3.8 27.8 - - + +
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Residues in contact with ILE 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ARG* 2.9 22.6 + - + +
12C ARG 3.1 6.5 + - - +
14C GLU* 1.3 75.2 - - - +
16C LEU* 1.3 59.9 + - + +
18C SER* 3.3 3.8 + - - -
19C LEU* 2.9 26.6 + - + +
37C LEU* 4.1 10.1 - - + +
41C VAL* 4.1 20.6 - - + -
43C VAL* 5.8 0.9 - - + -
47C ALA 5.3 0.2 - - - -
48C LEU* 3.8 29.2 - - + -
51C HIS* 3.8 28.3 - - + -
52C PHE* 3.9 27.4 - - + -
58C MET* 4.1 21.1 - - + -
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Residues in contact with LEU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ARG* 3.1 25.1 + - - +
13C GLU* 3.6 32.8 - - - +
15C ILE* 1.3 73.0 - - - +
17C GLN* 1.3 60.8 + - - +
19C LEU* 3.1 7.3 + - + +
20C ALA* 2.9 30.9 + - - +
52C PHE* 3.8 16.4 - - + -
58C MET* 3.7 26.7 - - + +
61C SER* 3.7 21.3 - - - -
62C LEU* 3.7 28.8 - - + +
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Residues in contact with GLN 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLU 2.8 17.3 + - - +
14C GLU* 3.6 7.9 - - - +
16C LEU* 1.3 77.1 - - - +
18C SER* 1.3 56.8 + - - +
20C ALA* 3.5 10.6 + - - +
21C LEU* 2.9 52.3 + - + +
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Residues in contact with SER 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU* 2.9 22.8 + - - +
15C ILE 3.5 5.2 - - - -
16C LEU 3.2 0.2 - - - -
17C GLN* 1.3 74.6 - - - +
19C LEU* 1.3 59.1 + - - +
21C LEU* 3.7 10.1 - - - +
22C MET* 2.9 34.5 + - - +
37C LEU* 4.1 3.8 - - - -
40C SER* 4.1 16.2 + - - -
41C VAL* 3.7 30.5 - - - +
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Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 2.9 13.0 + - + +
16C LEU* 3.3 11.0 - - + +
18C SER* 1.3 73.8 - - - +
20C ALA* 1.3 65.5 + - - +
22C MET* 3.1 3.1 + - - +
23C LEU* 2.9 42.7 + - + +
32C ILE* 4.1 21.8 - - + -
37C LEU* 3.7 21.2 - - + +
55C LYS* 6.0 1.1 - - + -
58C MET* 3.8 29.8 - - + -
59C PHE* 4.1 25.8 - - + +
62C LEU* 3.2 25.4 - - + -
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Residues in contact with ALA 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU 2.9 15.2 + - - +
17C GLN* 3.7 14.8 - - - +
19C LEU* 1.3 74.2 - - - +
21C LEU* 1.3 62.6 - - - +
23C LEU* 3.2 23.2 + - - +
24C GLU* 3.3 10.9 + - - +
62C LEU* 4.4 4.1 - - + +
104C GLY* 3.4 8.6 - - - -
105C LEU* 4.1 27.4 - - + +
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Residues in contact with LEU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLN* 2.9 46.8 + - + +
18C SER* 3.7 8.1 - - - +
20C ALA* 1.3 74.3 - - - +
22C MET* 1.3 65.7 + - - +
24C GLU* 3.2 33.4 + - - +
25C SER* 3.2 13.3 + - - -
40C SER* 6.1 0.2 - - - +
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Residues in contact with MET 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C SER 2.9 23.1 + - - +
19C LEU* 3.1 5.8 + - - +
21C LEU* 1.3 73.0 - - - +
23C LEU* 1.3 62.4 + - - +
25C SER* 2.6 25.1 + - - -
27C ASP* 3.9 24.9 - - + +
28C GLY* 3.2 12.7 + - - -
32C ILE* 3.8 35.9 - - + -
36C LYS* 3.9 23.3 - - + +
37C LEU* 3.6 32.8 - - - -
40C SER* 3.6 22.7 - - - +
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 2.9 35.2 + - + +
20C ALA* 3.4 14.1 - - - +
21C LEU 3.2 0.2 - - - -
22C MET* 1.3 77.2 - - - +
24C GLU* 1.3 56.1 + - - +
28C GLY* 3.5 11.3 - - - +
32C ILE* 4.0 21.5 - - + -
59C PHE* 4.3 6.7 - - + -
62C LEU* 4.4 2.5 - - + -
104C GLY* 3.4 20.9 - - - +
105C LEU* 5.3 0.2 - - - -
107C ARG* 2.6 36.4 + - - +
108C ILE* 3.7 30.7 - - + -
113C ALA* 3.8 24.0 - - + -
178C PHE* 4.3 0.5 - - - -
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Residues in contact with GLU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ALA 3.3 7.0 + - - +
21C LEU* 3.2 30.3 + - - +
22C MET 3.1 0.6 - - - -
23C LEU* 1.3 73.5 - - - +
25C SER* 1.3 65.4 + - - +
103C PRO* 3.1 40.7 - - + +
104C GLY* 3.6 11.4 - - - +
107C ARG* 3.8 0.3 + - - -
177C GLU* 4.4 1.6 - - - +
178C PHE* 3.2 29.6 - - + -
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Residues in contact with SER 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C LEU 3.2 7.5 + - - -
22C MET* 2.6 23.7 + - - -
24C GLU* 1.3 84.8 - - - +
26C SER* 1.3 61.5 + - - +
27C ASP* 3.0 21.6 + - - +
28C GLY 3.0 15.1 + - - -
107C ARG* 3.3 10.4 + - - -
177C GLU* 4.4 2.4 - - - +
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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