Contacts of the helix formed by residues 31 - 49 (chain G) in PDB entry 4JCQ
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 31 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G GLU* 3.3 37.5 + - - +
30G ILE* 1.3 73.8 - - - +
32G GLN* 1.3 58.7 + - - +
33G GLU* 3.3 22.4 + - - +
34G LEU* 2.9 34.4 + - - +
35G ALA* 2.9 24.6 + - - +
63G HIS* 4.0 13.7 - - + +
66G ALA* 3.4 14.4 - - - +
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Residues in contact with GLN 32 (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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27A TYR* 3.7 9.7 - - + +
28A GLY* 3.5 26.1 - - - +
58A ASN* 3.1 41.7 + - - +
60A GLN* 3.2 29.9 + - - +
88A TRP* 3.4 10.3 - - - +
31G ASN* 1.3 75.2 - - - +
33G GLU* 1.3 66.2 + - - +
35G ALA* 3.4 8.2 + - - +
36G GLU* 2.9 29.3 + - - +
63G HIS* 5.5 1.4 - - + +
65G GLU* 4.4 14.9 - - + +
66G ALA* 3.8 6.4 - - + +
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Residues in contact with GLU 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G ASN* 3.3 26.2 + - - +
32G GLN* 1.3 84.8 + - - +
34G LEU* 1.3 61.1 + - - +
36G GLU* 3.4 9.4 + - - +
37G ASP* 3.1 22.7 + - - +
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Residues in contact with LEU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F GLU* 6.2 0.2 - - - +
25G LEU 4.8 9.2 - - - +
26G ILE* 3.7 25.4 - - + -
27G TYR 5.0 11.7 - - - +
28G GLY 5.8 0.2 - - - +
29G GLU 4.0 13.7 - - - +
30G ILE* 4.1 11.2 - - + -
31G ASN* 2.9 21.0 + - - +
33G GLU* 1.3 72.9 - - - +
35G ALA* 1.3 59.7 + - - +
37G ASP* 3.2 14.2 + - + +
38G VAL* 2.8 48.4 + - + +
70G ILE* 3.7 23.6 - - + -
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Residues in contact with ALA 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 3.7 13.2 - - + -
58A ASN* 5.4 1.3 - - - +
31G ASN 2.9 17.0 + - - +
32G GLN* 3.6 10.3 - - - +
33G GLU 3.3 0.2 - - - -
34G LEU* 1.3 77.3 - - - +
36G GLU* 1.3 53.9 + - - +
38G VAL* 4.1 0.5 - - - +
39G SER* 2.7 38.3 + - - -
66G ALA* 3.9 25.4 - - + +
69G THR* 4.5 4.9 - - + -
70G ILE* 3.8 16.8 - - + +
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Residues in contact with GLU 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.6 31.8 - - + +
27A TYR* 3.5 34.9 + - + +
37A ASP* 5.6 1.7 - - - +
32G GLN 2.9 16.0 + - - +
33G GLU* 3.6 8.4 - - - +
34G LEU 3.2 0.2 - - - -
35G ALA* 1.3 74.1 - - - +
37G ASP* 1.3 58.9 + - - +
39G SER 3.4 0.3 + - - -
40G LYS* 2.9 56.5 + - - +
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Residues in contact with ASP 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F GLU* 5.5 2.4 - - - +
40F LYS* 6.0 0.2 + - - -
33G GLU 3.1 14.5 + - - +
34G LEU* 3.6 19.0 - - + +
36G GLU* 1.3 78.5 - - - +
38G VAL* 1.3 56.1 + - - +
40G LYS* 3.5 9.3 + - - +
41G GLN* 3.1 47.3 + - - +
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Residues in contact with VAL 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G VAL* 4.4 12.8 - - + -
25G LEU 4.8 2.0 - - - +
26G ILE* 3.8 30.1 - - + -
34G LEU* 2.8 42.5 + - + +
35G ALA 4.1 2.2 - - - +
37G ASP* 1.3 69.9 - - - +
39G SER* 1.3 60.6 + - - +
41G GLN* 3.3 10.4 + - - +
42G LEU* 2.9 49.2 + - + +
55G ILE* 5.5 1.3 - - + -
70G ILE* 4.0 25.8 - - + -
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Residues in contact with SER 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.9 11.7 - - - -
27A TYR* 2.9 27.0 + - - -
35G ALA 2.7 23.8 + - - -
36G GLU 3.6 4.3 - - - -
38G VAL* 1.3 76.7 - - - +
40G LYS* 1.3 57.0 + - - +
42G LEU* 3.4 5.7 + - - +
43G LEU* 3.0 37.7 + - - +
69G THR* 3.9 2.9 - - - +
70G ILE* 5.5 1.4 - - - +
73G MET* 3.7 26.1 - - - +
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Residues in contact with LYS 40 (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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18A LEU* 4.0 30.9 - - + +
25A LEU* 3.6 18.8 - - + +
41A GLN* 6.1 1.4 - - - +
36G GLU* 2.9 51.2 + - + +
37G ASP* 3.7 9.6 - - - +
38G VAL 3.3 0.2 - - - -
39G SER* 1.3 75.8 - - - +
41G GLN* 1.3 57.6 + - + +
43G LEU* 3.9 5.9 - - + +
44G LEU* 3.0 31.1 + - - +
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Residues in contact with GLN 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F LYS* 5.9 4.4 - - - +
23G THR 4.3 3.8 - - - +
24G VAL* 3.7 40.8 - - + +
25G LEU 4.6 5.5 + - - -
37G ASP* 3.1 49.4 + - - +
38G VAL* 3.6 8.9 - - - +
40G LYS* 1.3 76.8 - - + +
42G LEU* 1.3 56.6 + - - +
44G LEU* 3.4 6.7 + - - +
45G LEU* 2.9 38.5 + - + +
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Residues in contact with LEU 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G VAL* 4.2 15.3 - - + -
38G VAL* 2.9 37.2 + - + +
39G SER* 3.9 4.0 - - - +
41G GLN* 1.3 76.2 - - - +
43G LEU* 1.3 57.7 + - - +
45G LEU* 3.5 4.3 + - - +
46G GLU* 3.0 29.3 + - - +
53G ILE* 4.3 11.4 - - + -
55G ILE* 4.2 19.7 - - + -
70G ILE 4.9 0.4 - - - +
73G MET* 4.2 23.6 - - + -
74G ILE* 4.1 25.8 - - + +
77G ILE* 3.9 32.0 - - + +
81G VAL* 5.0 2.0 - - + -
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Residues in contact with LEU 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 5.4 5.2 - - + -
21A THR* 4.4 13.3 - - + +
23A THR* 3.9 29.6 - - + +
25A LEU* 4.3 13.2 - - + -
56A PHE* 4.3 9.6 - - + -
186A ARG* 3.4 29.2 - - - +
39G SER 3.0 25.0 + - - +
40G LYS* 4.0 5.6 - - + +
42G LEU* 1.3 73.0 - - - +
44G LEU* 1.3 63.7 + - - +
46G GLU* 3.5 11.2 + - - +
47G SER* 3.1 24.3 + - - -
73G MET* 3.9 26.0 - - + -
76G PHE* 5.1 1.1 - - + -
77G ILE* 4.6 2.2 - - + -
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Residues in contact with LEU 44 (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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14A LEU* 3.7 33.7 - - + +
17A LYS* 4.4 8.3 - - + -
18A LEU* 4.2 23.7 - - + +
21A THR* 5.4 0.9 - - - -
19G ILE* 3.8 26.7 - - + -
40G LYS 3.0 19.3 + - - +
41G GLN* 3.6 8.3 - - - +
43G LEU* 1.3 77.4 - - - +
45G LEU* 1.3 63.4 + - + +
47G SER* 2.7 27.2 + - - +
48G ILE* 3.3 34.1 + - + +
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Residues in contact with LEU 45 (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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19G ILE* 3.5 42.0 - - + +
22G ARG* 2.8 52.8 + - - +
23G THR 4.6 2.0 - - - +
24G VAL* 3.8 26.7 - - + -
41G GLN* 2.9 22.6 + - + +
42G LEU* 3.9 1.1 - - - +
44G LEU* 1.3 76.4 - - + +
46G GLU* 1.3 65.1 + - - +
48G ILE* 3.4 4.7 + - + +
49G SER 3.2 8.0 + - - +
53G ILE* 3.8 33.9 - - + -
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Residues in contact with GLU 46 (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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186A ARG* 3.1 48.9 + - - +
42G LEU 3.0 18.4 + - - +
43G LEU* 3.7 9.1 - - - +
45G LEU* 1.3 78.5 - - - +
47G SER* 1.3 61.8 + - - +
49G SER* 3.2 20.1 + - - +
50G ASN* 4.8 4.1 + - - +
77G ILE* 3.4 19.0 - - + +
78G LYS* 3.0 29.3 + - + +
79G PRO* 3.7 23.0 - - + +
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Residues in contact with SER 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LYS* 3.9 22.7 + - - +
21A THR* 3.7 23.4 - - - +
43G LEU 3.1 13.2 + - - -
44G LEU* 2.7 31.4 + - - +
46G GLU* 1.3 77.1 - - - +
48G ILE* 1.3 60.7 + - - +
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Residues in contact with ILE 48 (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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14A LEU* 5.9 1.6 - - + -
17A LYS* 4.1 32.9 + - + +
19G ILE* 3.7 29.4 - - + -
20G ASP* 6.2 0.7 - - - +
22G ARG* 4.1 8.7 - - - +
44G LEU* 3.3 32.1 + - + +
45G LEU* 3.7 11.9 - - + +
46G GLU 3.2 0.8 - - - -
47G SER* 1.3 82.5 - - - +
49G SER* 1.3 66.0 + - - +
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Residues in contact with SER 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G ARG* 3.3 29.6 + - - -
45G LEU 3.2 10.2 + - - +
46G GLU 3.2 16.7 + - - +
48G ILE* 1.3 85.7 - - - +
50G ASN* 1.3 60.7 + - - +
51G ASP* 3.3 22.4 + - - +
79G PRO* 3.7 4.7 - - - +
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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
------------------------------------------------------------
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