Contacts of the helix formed by residues 11 - 25 (chain B) 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 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B ASN* 1.3 80.0 - - - +
12B ARG* 1.3 65.9 + - - +
14B GLU* 2.8 43.6 + - + +
15B ILE* 2.8 24.5 + - + +
41B VAL* 5.5 2.9 - - + -
43B VAL* 3.5 30.6 - - + +
51B HIS* 3.1 34.0 + - + +
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Residues in contact with ARG 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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10B ASN* 3.1 4.5 - - - +
11B ARG* 1.3 81.3 - - - +
13B GLU* 1.3 61.7 + - + +
15B ILE* 3.7 0.5 + - - +
16B LEU* 3.2 32.4 + - + +
51B HIS* 2.6 47.6 + - + +
52B PHE* 3.3 42.5 - - + +
53B PRO* 5.8 0.8 - - - +
57B ARG* 4.9 9.9 - - - +
61B SER* 3.7 13.5 + - - -
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASN* 3.1 17.5 + - + +
11B ARG 3.0 0.6 - - - -
12B ARG* 1.3 81.1 - - + +
14B GLU* 1.3 63.4 + - + +
16B LEU* 3.5 20.0 + - - +
17B GLN* 3.1 49.8 + - + +
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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 ASN* 2.9 21.3 - - + +
11B ARG* 2.8 51.8 + - + +
13B GLU* 1.3 78.4 - - + +
15B ILE* 1.3 61.4 + - - +
17B GLN* 3.5 7.4 - - - +
18B SER* 3.1 27.1 + - - -
41B VAL* 4.6 16.1 - - + +
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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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11B ARG* 2.8 24.6 + - + +
12B ARG 3.8 3.6 - - - +
14B GLU* 1.3 73.6 - - - +
16B LEU* 1.3 61.2 + - - +
18B SER* 3.0 5.2 + - - -
19B LEU* 2.8 27.8 + - + +
37B LEU* 4.1 14.4 - - + +
41B VAL* 3.8 17.0 - - + -
43B VAL* 5.9 1.3 - - + -
48B LEU* 3.7 33.9 - - + +
51B HIS* 3.9 21.3 - - + +
52B PHE* 3.7 24.0 - - + -
58B MET* 3.9 27.8 - - + -
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Residues in contact with LEU 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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12B ARG* 3.2 24.8 + - + +
13B GLU* 3.9 23.1 - - - +
15B ILE* 1.3 74.6 - - - +
17B GLN* 1.3 63.7 + - - +
19B LEU* 3.3 6.2 + - + +
20B ALA* 2.9 24.6 + - - +
52B PHE* 3.8 21.1 - - + -
58B MET* 3.7 34.1 - - + +
61B SER* 3.8 20.0 - - - +
62B LEU* 3.7 22.2 - - + +
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Residues in contact with GLN 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 GLU* 3.1 42.4 + - + +
14B GLU* 3.5 7.6 - - - +
16B LEU* 1.3 75.7 - - - +
18B SER* 1.3 58.2 + - - +
20B ALA* 3.4 9.1 + - - +
21B LEU* 3.0 37.5 + - + +
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Residues in contact with SER 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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14B GLU 3.1 10.9 + - - -
15B ILE 3.0 9.0 + - - -
17B GLN* 1.3 76.3 - - - +
19B LEU* 1.3 67.7 + - - +
21B LEU* 2.8 12.5 + - - +
22B MET* 2.8 28.2 + - - +
37B LEU* 4.0 10.3 - - - -
40B SER* 3.8 21.4 + - - -
41B VAL* 3.8 20.0 - - - +
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Residues in contact with LEU 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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15B ILE* 2.8 16.1 + - + +
16B LEU* 3.6 10.5 - - + +
18B SER* 1.3 72.8 - - - +
20B ALA* 1.3 57.2 + - - +
22B MET* 3.2 2.3 + - - +
23B LEU* 2.8 45.9 + - + +
32B ILE* 3.7 35.0 - - + -
37B LEU* 3.6 16.2 - - + +
55B LYS* 5.9 1.1 - - + -
58B MET* 3.9 33.4 - - + -
59B PHE* 4.1 20.6 - - + -
62B LEU* 3.7 17.9 - - + -
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Residues in contact with ALA 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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16B LEU 2.9 14.3 + - - +
17B GLN* 3.4 12.1 - - - +
18B SER 3.1 0.2 - - - -
19B LEU* 1.3 76.2 - - - +
21B LEU* 1.3 58.8 + - + +
23B LEU* 3.2 12.6 + - - +
24B GLU* 2.9 30.0 + - - +
62B LEU* 4.7 3.8 - - + +
104B GLY* 4.0 3.1 - - - -
105B LEU* 4.6 21.8 - - + +
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Residues in contact with LEU 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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17B GLN* 3.0 23.6 + - + +
18B SER* 2.8 12.4 + - - +
20B ALA* 1.3 76.2 - - + +
22B MET* 1.3 61.1 + - + +
24B GLU* 3.2 23.0 + - - +
25B SER* 2.8 27.4 + - - -
40B SER* 6.0 0.7 - - - +
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Residues in contact with MET 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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18B SER 2.8 15.2 + - - +
19B LEU* 3.6 7.0 - - - +
21B LEU* 1.3 75.0 - - + +
23B LEU* 1.3 65.8 + - - +
25B SER* 2.6 27.9 + - - +
27B ASP* 3.9 10.9 - - + +
28B GLY* 3.2 12.5 + - - -
32B ILE* 4.2 26.7 - - + -
36B LYS* 3.4 36.8 - - + +
37B LEU* 3.9 24.2 - - - -
40B SER* 3.8 29.4 - - - +
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Residues in contact with LEU 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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19B LEU* 2.8 43.0 + - + +
20B ALA* 3.4 9.4 - - - +
22B MET* 1.3 72.5 - - - +
24B GLU* 1.3 60.9 + - - +
28B GLY* 3.4 11.6 - - - +
32B ILE* 3.9 24.7 - - + -
59B PHE* 4.0 15.9 - - + -
62B LEU* 4.1 11.2 - - + -
104B GLY* 3.4 29.0 - - - +
105B LEU* 5.7 0.2 - - + -
107B ARG* 2.8 30.1 + - + -
108B ILE* 4.2 3.6 - - + -
113B ALA* 3.9 24.0 - - + -
178B PHE* 4.5 0.2 - - - -
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Residues in contact with GLU 24 (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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20B ALA 2.9 13.0 + - - +
21B LEU* 3.5 24.3 - - - +
23B LEU* 1.3 74.3 - - - +
25B SER* 1.3 66.9 + - - +
103B PRO* 4.0 31.9 - - + +
104B GLY* 3.4 15.4 + - - +
178B PHE* 3.4 20.9 - - + -
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Residues in contact with SER 25 (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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21B LEU 2.8 13.4 + - - -
22B MET* 2.6 25.9 + - - +
24B GLU* 1.3 82.8 - - - +
26B SER* 1.3 60.5 + - - +
27B ASP* 2.9 17.7 + - - +
28B GLY 2.8 18.5 + - - -
107B ARG* 3.5 8.5 + - - -
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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