Contacts of the helix formed by residues 6 - 24 (chain G) in PDB entry 1XK4
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 SER 6 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E THR 3.4 21.8 - - - -
41E GLU* 3.0 27.4 + - - -
4G LYS 3.5 3.4 + - - -
5G MET* 1.3 76.2 - - - +
7G GLN* 1.3 66.1 + - - +
8G LEU 3.4 0.7 + - - -
9G GLU* 2.8 31.9 + - - -
10G ARG* 2.9 24.6 + - - +
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Residues in contact with GLN 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E SER* 2.7 36.7 + - - +
14E ASP* 2.9 25.4 + - - +
15E VAL* 3.4 10.7 - - + +
18E LYS* 2.6 44.2 + - - +
41E GLU* 3.5 2.8 + - - +
6G SER* 1.3 74.1 - - - +
8G LEU* 1.3 64.5 + - - +
10G ARG* 3.2 10.4 + - - +
11G ASN* 3.0 29.0 + - - +
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Residues in contact with LEU 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ILE* 4.0 28.7 - - + -
15E VAL* 4.0 12.3 - - + +
37E LEU* 4.6 6.5 - - + -
41E GLU* 3.1 32.4 + - + +
71E PHE* 4.3 21.1 - - + -
75E VAL* 4.5 12.6 - - + -
78E MET* 3.8 27.4 - - + -
7G GLN* 1.3 80.0 - - - +
9G GLU* 1.3 63.1 + - - +
11G ASN* 3.2 6.7 + - - +
12G ILE* 3.1 38.8 + - + +
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Residues in contact with GLU 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E GLU 3.5 9.2 - - - +
42E SER 3.3 5.0 - - - +
43E PRO* 3.1 41.6 - - + +
78E MET* 4.9 3.4 - - + -
4G LYS 4.1 2.8 - - - +
5G MET* 3.4 24.5 - - + +
6G SER* 2.8 43.6 + - - +
8G LEU* 1.3 76.7 - - - +
10G ARG* 1.3 57.9 + - - +
12G ILE* 3.4 9.3 + - - +
13G GLU* 2.9 30.1 + - - +
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Residues in contact with ARG 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G MET* 4.2 39.1 - - + +
6G SER 2.9 22.7 + - - +
7G GLN* 3.5 8.3 - - - +
9G GLU* 1.3 76.4 - - - +
11G ASN* 1.3 60.1 + - - +
13G GLU* 3.3 4.3 + - - +
14G THR* 2.9 31.2 + - - +
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Residues in contact with ASN 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ALA* 3.5 31.0 - - + +
11E SER* 2.7 39.1 + - - -
12E ILE* 3.6 23.8 - - + +
15E VAL* 4.3 0.6 - - - +
7G GLN* 3.0 22.1 + - - +
8G LEU* 3.2 9.1 + - - +
10G ARG* 1.3 78.8 - - - +
12G ILE* 1.3 63.3 + - - +
14G THR* 3.2 5.5 + - - -
15G ILE* 3.1 26.9 + - - +
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Residues in contact with ILE 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E ILE* 5.1 1.6 - - + -
75E VAL* 4.4 11.4 - - + +
78E MET* 3.8 42.0 - - + -
79E GLY* 3.9 16.6 - - - +
82E ALA* 3.9 28.3 - - + -
8G LEU* 3.1 34.3 + - + +
9G GLU* 3.8 6.1 - - - +
11G ASN* 1.3 74.9 - - - +
13G GLU* 1.3 60.5 + - - +
15G ILE* 3.0 18.8 + - + +
16G ILE* 2.8 35.5 + - + +
76G PHE* 6.0 0.2 - - + -
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Residues in contact with GLU 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G MET* 2.7 45.6 - - - +
9G GLU 2.9 17.2 + - - +
10G ARG* 3.6 6.1 - - - +
12G ILE* 1.3 77.0 - - - +
14G THR* 1.3 58.1 + - - +
16G ILE* 3.8 9.6 - - + +
17G ASN* 2.8 33.4 + - + +
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Residues in contact with THR 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E GLU* 3.8 25.4 - - + +
5E LEU* 4.2 6.5 - - + +
8E ALA* 3.8 21.7 - - + +
10G ARG 2.9 16.5 + - - -
11G ASN 3.4 9.6 - - - -
12G ILE 3.1 0.2 - - - -
13G GLU* 1.3 75.6 - - - +
15G ILE* 1.3 64.3 + - - +
17G ASN* 4.1 3.9 - - - +
18G THR* 2.8 35.4 + - - +
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Residues in contact with ILE 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LEU* 4.0 21.8 - - + -
8E ALA* 5.0 2.2 - - + -
9E LEU* 3.9 22.7 - - + -
12E ILE* 4.0 17.5 - - + -
75E VAL* 5.8 2.2 - - + -
11G ASN 3.1 15.1 + - - +
12G ILE* 3.0 16.9 + - + +
14G THR* 1.3 77.2 - - - +
16G ILE* 1.3 64.5 + - - +
18G THR* 3.8 1.2 - - - -
19G PHE* 3.1 22.7 + - - +
76G PHE* 4.0 21.5 - - + -
79G PHE* 4.1 7.1 - - + -
80G ILE* 4.9 8.1 - - + -
83G MET* 3.6 30.5 - - + -
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Residues in contact with ILE 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E GLY 4.0 1.6 - - - +
82E ALA* 3.6 22.0 - - + +
83E HIS* 3.5 38.8 - - + +
86E SER* 3.8 23.6 - - - +
12G ILE* 2.8 29.9 + - + +
13G GLU* 3.9 7.6 - - - +
15G ILE* 1.3 72.6 - - - +
17G ASN* 1.3 64.2 + - - +
19G PHE* 3.5 3.5 + - - +
20G HIS* 3.1 23.7 + - + +
76G PHE* 3.8 26.0 - - + -
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Residues in contact with ASN 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G GLU* 2.8 26.9 + - + +
14G THR* 4.1 4.3 - - - +
16G ILE* 1.3 76.7 - - - +
18G THR* 1.3 58.5 + - - +
20G HIS* 3.3 15.3 + - - +
21G GLN* 2.9 32.3 + - - +
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Residues in contact with THR 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LEU* 4.1 24.3 + - + +
14G THR* 2.8 28.7 + - - +
15G ILE* 3.8 3.4 - - - -
17G ASN* 1.3 76.0 + - - +
19G PHE* 1.3 64.8 + - - +
21G GLN* 3.4 9.9 + - - +
22G TYR* 3.2 22.8 - - + -
40G LEU* 4.1 15.5 - - + -
44G ASP* 3.9 29.6 + - - +
79G PHE* 5.7 1.1 - - + -
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Residues in contact with PHE 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E HIS* 4.6 3.8 - + - -
15G ILE 3.1 16.1 + - - +
16G ILE 3.6 5.4 - - - +
18G THR* 1.3 75.5 - - - +
20G HIS* 1.3 61.8 + - + +
22G TYR 3.4 1.6 + - - -
23G SER* 2.9 37.1 + - - -
30G ASP* 3.4 38.1 - - - -
31G THR* 4.0 4.0 - - - -
32G LEU* 3.6 28.8 - - + +
40G LEU* 4.3 9.2 - - - +
74G LEU 3.6 12.1 - - - -
76G PHE* 3.4 50.3 - + + -
79G PHE* 3.6 32.7 - + + -
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Residues in contact with HIS 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ILE* 3.1 18.5 + - + +
17G ASN* 3.5 16.2 - - - +
19G PHE* 1.3 80.8 - - + +
21G GLN* 1.3 68.4 + - - +
22G TYR 3.1 1.0 + - - -
23G SER* 3.5 8.6 + - - -
24G VAL* 3.2 53.4 + - + +
29G PRO* 4.7 4.1 + - + -
30G ASP* 5.7 2.4 + - - -
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Residues in contact with GLN 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G ASN* 2.9 19.4 + - - +
18G THR* 3.4 13.5 - - - +
20G HIS* 1.3 81.0 - - - +
22G TYR* 1.3 83.8 + - + +
24G VAL* 4.0 7.2 - - - +
25G LYS* 3.7 23.6 - - - +
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Residues in contact with TYR 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G THR* 3.2 24.2 - - + -
19G PHE 3.4 1.6 + - - +
20G HIS 3.1 0.2 - - - -
21G GLN* 1.3 98.7 - - + +
23G SER* 1.3 64.4 + - - +
24G VAL 3.3 3.4 + - - -
25G LYS* 3.3 18.3 + - + +
32G LEU* 3.8 17.9 - - + -
36G GLU* 3.1 29.9 - - + +
39G GLU* 3.5 47.1 - - + -
40G LEU* 3.7 21.5 - - + -
43G LYS* 3.9 22.6 - - - +
44G ASP* 2.7 31.9 + - - -
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Residues in contact with SER 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G PHE* 2.9 31.4 + - - -
20G HIS* 3.5 12.3 + - - -
22G TYR* 1.3 78.3 - - - +
24G VAL* 1.3 60.4 + - - +
25G LYS 3.3 1.1 + - - -
26G LEU 3.5 2.3 - - - +
28G HIS 3.2 5.4 - - - +
29G PRO* 2.7 22.8 + - - +
30G ASP* 4.0 0.7 + - - -
31G THR 3.2 30.3 - - - -
32G LEU* 3.6 5.3 - - - +
36G GLU* 3.7 3.1 - - - -
3512G CA 2.4 26.3 - - - -
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Residues in contact with VAL 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G HIS* 3.2 41.3 + - + +
21G GLN* 4.0 9.6 - - - +
23G SER* 1.3 76.9 + - - +
25G LYS* 1.3 67.7 + - + +
26G LEU* 3.3 2.7 + - - -
27G GLY 5.8 0.2 - - - +
29G PRO* 3.8 29.8 - - + +
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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
------------------------------------------------------------
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