Contacts of the helix formed by residues 35 - 57 (chain G) in PDB entry 4GUN
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 LYS 35 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F ASN* 3.7 38.8 - - + +
30G ASP 4.9 0.2 - - - +
31G LEU* 3.0 32.1 + - + +
34G ASN* 1.3 89.5 - - + +
36G HIS* 1.4 60.9 + - - +
37G HIS 3.7 0.7 - - - -
38G VAL* 3.5 3.6 + - - +
39G ALA* 3.0 29.6 + - - +
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Residues in contact with HIS 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173F GLU* 3.8 8.2 + - - -
176F TYR* 6.0 0.4 - - - -
177F TYR* 2.8 36.0 + + - -
182F ASN* 3.7 21.2 - - + +
31G LEU 3.0 29.5 + - - -
32G HIS* 3.4 20.0 - - + +
35G LYS* 1.4 71.3 - - - +
37G HIS* 1.4 63.6 + - - +
39G ALA* 3.2 18.1 + - - +
40G TYR* 3.2 26.6 + - + -
80G HIS* 5.0 0.2 - - - +
172G TRP* 6.0 0.2 - - - -
174G HIS* 3.4 43.5 + + + +
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Residues in contact with HIS 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G LEU* 3.6 9.0 - - + +
11G PRO* 3.3 19.2 - - + +
32G HIS 2.9 15.5 + - - +
33G ILE 3.4 12.5 + - - +
36G HIS* 1.4 67.9 - - - +
38G VAL* 1.3 65.6 + - - +
40G TYR* 3.1 10.5 + - + -
41G VAL* 3.1 24.6 + - + +
76G GLY 4.6 0.9 - - - -
77G HIS* 2.8 42.9 + - + -
80G HIS* 3.6 9.9 - - + +
81G SER* 3.3 25.1 - - - -
84G TRP* 2.9 32.7 + - + -
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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
----------------------------------------------------------
10G LEU* 4.0 21.8 - - + -
33G ILE 3.4 11.5 + - - +
34G ASN* 3.3 31.2 - - + +
35G LYS* 3.5 5.4 + - - +
36G HIS 3.3 0.6 - - - -
37G HIS* 1.3 77.8 - - - +
39G ALA* 1.3 55.5 + - - +
41G VAL* 3.2 9.4 + - + +
42G ASN* 3.0 44.5 + - - +
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Residues in contact with ALA 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G LYS 3.0 13.9 + - - +
36G HIS* 3.2 13.7 + - - +
38G VAL* 1.3 75.8 - - - +
40G TYR* 1.3 62.3 + - + +
42G ASN* 3.6 5.1 + - - +
43G GLY* 2.9 27.0 + - - -
73G HIS* 3.7 8.7 + - + -
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Residues in contact with TYR 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ILE* 4.2 1.9 - - - +
36G HIS* 3.2 29.4 + - + -
37G HIS* 3.1 10.1 + - - +
39G ALA* 1.3 76.0 - - + +
41G VAL* 1.3 60.6 - - - +
44G TYR* 2.9 32.7 + - - +
72G PHE* 3.7 25.2 - + - -
73G HIS* 3.5 37.4 - + - +
76G GLY* 3.8 15.9 - - - -
77G HIS* 3.8 9.2 - - - +
80G HIS* 3.3 30.3 - + - -
155G GLN* 2.8 27.6 + - + -
172G TRP* 3.7 18.5 - - - -
174G HIS* 4.3 5.4 - - - -
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Residues in contact with VAL 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G ILE* 3.4 32.2 - - + +
9G SER* 4.0 7.9 - - - -
10G LEU* 3.9 24.9 - - + +
37G HIS* 3.1 33.4 + - + +
38G VAL* 3.2 10.1 + - + +
40G TYR* 1.3 77.5 - - - +
42G ASN* 1.3 69.5 + - - +
44G TYR* 3.9 1.7 - - - +
45G ASN* 3.1 32.5 + - - +
77G HIS* 3.9 12.1 - - - +
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Residues in contact with ASN 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G VAL* 3.0 32.5 + - - +
39G ALA* 4.2 4.6 - - - +
41G VAL* 1.3 81.4 - - - +
43G GLY* 1.3 60.3 + - - +
45G ASN* 3.5 8.1 + - - +
46G ALA* 2.9 32.1 + - - +
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Residues in contact with GLY 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G ALA 2.9 18.8 + - - -
41G VAL 3.3 0.2 - - - -
42G ASN* 1.3 73.8 - - - +
44G TYR* 1.3 57.8 + - - +
46G ALA* 3.4 4.8 + - - +
47G ALA* 2.9 30.8 + - - +
73G HIS* 3.5 27.5 - - - -
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Residues in contact with TYR 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G GLU 4.0 14.9 + - - -
8G ILE* 3.7 42.2 - - + -
40G TYR 2.9 19.4 + - - +
43G GLY* 1.3 74.3 - - - +
45G ASN* 1.3 62.1 + - - +
47G ALA* 3.2 6.1 + - - +
48G ILE* 2.9 57.2 + - + +
70G ILE* 4.2 8.5 - - + -
73G HIS* 3.2 12.8 - - + +
74G GLY* 3.5 23.3 - - - -
55H VAL* 4.2 7.8 + - - +
60H LEU* 3.5 29.9 - - + +
63H VAL* 3.8 30.4 - - + +
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Residues in contact with ASN 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G ILE* 3.3 22.8 - - + +
7G LYS* 3.3 30.5 - - - +
8G ILE* 3.0 46.5 + - - +
41G VAL* 3.1 24.8 + - - +
42G ASN* 3.8 8.8 + - - +
44G TYR* 1.3 81.3 - - - +
46G ALA* 1.3 59.7 + - - +
49G ASP* 3.2 20.4 + - - +
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Residues in contact with ALA 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G ASN 2.9 18.8 + - - +
43G GLY* 3.9 5.2 - - - +
45G ASN* 1.3 73.4 - - - +
47G ALA* 1.4 60.2 + - - +
49G ASP* 3.5 6.4 + - - +
50G ALA* 3.1 28.4 + - - +
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Residues in contact with ALA 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G GLY 2.9 18.6 + - - +
44G TYR 3.2 5.1 + - - +
46G ALA* 1.4 77.0 - - - +
48G ILE* 1.4 56.9 + - - +
50G ALA* 3.4 3.7 + - - +
51G LEU* 2.9 24.6 + - - +
66G ILE* 3.3 15.7 - - + +
69G ASN* 4.0 27.8 - - + +
70G ILE* 3.7 22.2 - - + -
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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
----------------------------------------------------------
2G ILE* 3.7 26.7 - - + -
6G GLU* 4.3 3.1 - - + +
44G TYR* 2.9 49.2 + - + +
47G ALA* 1.4 75.1 - - - +
49G ASP* 1.3 59.7 + - - +
51G LEU* 3.2 6.0 + - + +
52G GLU* 3.1 38.3 + - + +
70G ILE* 4.1 27.1 - - + -
51H LEU* 5.2 3.1 - - + -
55H VAL* 3.7 43.5 - - + -
63H VAL* 4.8 0.2 - - + -
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Residues in contact with ASP 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G ILE* 3.2 39.6 + - + +
45G ASN 3.2 16.6 + - - +
46G ALA* 3.8 7.4 - - - +
48G ILE* 1.3 76.8 - - - +
50G ALA* 1.3 61.3 + - - +
52G GLU* 3.8 5.2 + - - +
53G LYS* 3.5 49.1 + - - +
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Residues in contact with ALA 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ALA 3.1 17.5 + - - +
47G ALA* 3.8 6.1 - - - +
49G ASP* 1.3 75.0 - - - +
51G LEU* 1.4 58.2 + - - +
53G LYS* 3.4 12.8 + - - +
54G ALA* 3.1 23.7 + - - +
66G ILE* 3.5 25.4 - - + +
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Residues in contact with LEU 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G ALA 2.9 17.5 + - - +
48G ILE* 3.2 8.7 + - + +
50G ALA* 1.4 76.3 - - - +
52G GLU* 1.3 61.8 + - + +
54G ALA 3.4 0.7 + - - -
55G VAL* 2.8 46.9 + - + +
63G VAL* 3.7 28.0 - - + +
66G ILE* 3.8 9.6 - - + +
67G GLN* 3.3 25.4 - - - +
70G ILE* 3.6 21.1 - - + -
48H ILE* 5.4 1.8 - - + -
51H LEU* 3.7 30.3 - - + -
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Residues in contact with GLU 52 (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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2G ILE* 3.7 21.4 + - - +
6G GLU* 3.0 38.2 - - - +
48G ILE* 3.1 25.4 + - + +
49G ASP* 3.8 3.7 + - - +
50G ALA 3.5 0.2 - - - -
51G LEU* 1.3 81.1 - - + +
53G LYS* 1.4 60.0 - - - +
55G VAL* 4.3 6.7 - - + +
56G GLY* 3.2 19.4 + - - -
6H GLU* 5.3 1.4 - - - +
52H GLU* 5.8 7.1 - - + +
55H VAL* 4.4 5.1 - - + +
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Residues in contact with LYS 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G ASP* 3.5 44.4 + - - +
50G ALA* 3.4 11.5 + - - +
51G LEU 3.3 0.6 - - - -
52G GLU* 1.4 75.7 - - + +
54G ALA* 1.3 63.9 + - - +
56G GLY* 3.6 0.9 + - - -
57G LYS* 3.3 34.0 + - + +
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Residues in contact with ALA 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G ALA 3.1 14.0 + - - +
51G LEU 3.9 2.5 - - - +
53G LYS* 1.3 76.7 - - - +
55G VAL* 1.4 63.1 + - - +
57G LYS* 3.2 4.7 + - - -
58G ARG 3.1 3.1 + - - -
59G ASP* 3.0 35.7 + - + +
62G SER* 3.7 25.8 - - - -
63G VAL* 3.6 17.4 - - + +
66G ILE* 4.0 7.4 - - + -
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Residues in contact with VAL 55 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G LEU* 2.8 45.3 + - + +
52G GLU* 4.3 5.2 - - + +
54G ALA* 1.4 69.2 - - - +
56G GLY* 1.3 58.0 + - - +
58G ARG* 3.0 21.8 + - - +
63G VAL* 3.8 17.0 - - + -
6H GLU* 3.6 42.2 - - + +
44H TYR* 3.9 6.0 + - - +
48H ILE* 3.8 30.3 - - + -
52H GLU* 3.8 10.8 - - - +
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Residues in contact with GLY 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G GLU 3.2 18.1 + - - -
53G LYS 4.0 1.8 - - - -
55G VAL* 1.3 76.5 - - - +
57G LYS* 1.4 59.2 + - - +
5H ASN* 2.8 39.7 + - - +
6H GLU* 4.1 7.9 - - - -
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Residues in contact with LYS 57 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G LYS* 3.3 21.2 + - + +
54G ALA* 3.2 6.0 + - - +
55G VAL 3.2 0.6 - - - -
56G GLY* 1.4 76.1 - - - +
58G ARG* 1.4 67.8 + - - +
59G ASP* 3.3 16.0 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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