Contacts of the helix formed by residues 30 - 42 (chain G) in PDB entry 6M4G
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 30 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G THR* 3.4 7.6 - - - -
29G PHE* 1.3 72.8 - - - +
31G VAL* 1.3 62.1 + - - +
32G SER* 4.3 3.1 - - - -
33G GLN* 3.0 32.4 + - - +
34G VAL* 3.4 21.7 + - - +
56G ALA* 4.9 0.7 - - - -
40H TYR* 3.2 37.1 + - - -
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Residues in contact with VAL 31 (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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21G ARG* 3.4 47.3 - - + +
22G THR* 3.4 19.2 + - - +
25G ALA* 6.0 0.9 - - + -
27G LEU* 5.1 7.6 - - + -
29G PHE 4.3 4.0 - - - +
30G SER* 1.3 73.8 - - - +
32G SER* 1.3 64.8 + - - +
34G VAL* 3.0 12.2 - - - +
35G GLU* 2.9 29.3 + - - +
52G PRO* 4.1 7.7 - - + +
53G VAL* 4.1 31.9 - - + -
56G ALA* 4.4 7.6 - - + -
31I A 6.1 0.2 - - - +
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Residues in contact with SER 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ARG* 3.6 12.8 + - - +
30G SER* 3.2 3.8 - - - +
31G VAL* 1.3 82.6 - - - +
33G GLN* 1.3 57.7 + - - +
35G GLU* 3.5 7.4 + - - +
36G ARG* 2.9 28.3 + - - +
30I G 4.9 13.9 + - - -
31I A 3.4 23.1 + - - -
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Residues in contact with GLN 33 (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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30G SER* 3.0 19.7 + - - +
32G SER* 1.3 77.1 - - - +
34G VAL* 1.3 60.2 + - - +
36G ARG* 3.2 36.2 + - - +
37G SER* 2.9 28.7 + - - -
36H SER* 2.6 41.2 + - - +
37H TYR* 3.7 17.7 - - + -
40H TYR* 3.5 24.8 + - - -
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Residues in contact with VAL 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G PHE* 5.3 7.6 - - + -
30G SER 3.4 13.0 - - - +
31G VAL* 3.0 21.3 - - - +
33G GLN* 1.3 76.1 - - - +
35G GLU* 1.3 57.2 + - - +
37G SER* 2.7 20.1 + - - +
38G LEU* 2.9 22.8 + - + +
52G PRO* 3.7 31.6 - - + +
55G LEU* 5.2 4.5 - - + -
56G ALA* 4.3 15.7 - - + +
59G ILE* 5.4 5.6 - - + -
37H TYR* 3.7 17.7 - - + +
70H PHE* 3.7 14.7 - - + -
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Residues in contact with GLU 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ARG* 3.7 23.0 + - - -
31G VAL 2.9 16.4 + - - +
32G SER* 3.8 6.3 - - - +
34G VAL* 1.3 80.0 - - - +
36G ARG* 1.3 56.3 + - - +
38G LEU* 3.1 8.0 + - - +
39G ARG* 2.9 60.5 + - + +
47G LEU* 3.6 19.8 - - + +
48G SER 5.0 4.3 - - - +
52G PRO* 4.0 22.8 - - + +
113J A 5.2 0.3 + - - -
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Residues in contact with ARG 36 (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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32G SER 2.9 19.4 + - - +
33G GLN* 3.2 39.0 + - - +
35G GLU* 1.3 76.6 - - - +
37G SER* 1.3 57.6 + - - +
39G ARG* 3.5 8.8 + - + +
40G GLU* 3.1 47.6 + - + +
30I G 4.5 13.9 + - - -
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Residues in contact with SER 37 (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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33G GLN* 2.9 11.2 + - - -
34G VAL 2.7 19.6 + - - -
36G ARG* 1.3 75.2 - - - +
38G LEU* 1.3 60.6 + - - +
40G GLU* 3.9 7.1 - - - +
41G GLY* 3.1 22.2 + - - -
43G TYR* 3.7 6.4 - - - -
37H TYR* 2.8 26.3 + - - -
70H PHE* 3.1 17.9 - - - -
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Residues in contact with LEU 38 (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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34G VAL 2.9 18.8 + - - +
35G GLU* 3.1 10.3 + - - +
37G SER* 1.3 77.0 - - - +
39G ARG* 1.3 60.5 + - - +
40G GLU 3.4 0.2 - - - -
42G HIS* 3.2 18.9 + - - -
43G TYR* 3.5 25.8 + - + +
44G ALA 5.0 1.0 + - - +
47G LEU* 3.7 38.0 - - + +
51G ALA* 5.8 2.2 - - + -
52G PRO* 4.8 13.0 - - + -
55G LEU* 4.5 14.8 - - + -
70H PHE* 3.7 11.7 - - + -
74H ALA* 3.6 31.2 - - + -
89H ILE* 5.5 5.6 - - + -
94H ILE* 6.0 4.5 - - + -
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Residues in contact with ARG 39 (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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35G GLU* 2.9 49.0 + - + +
36G ARG* 3.8 9.2 - - + +
37G SER 3.3 0.2 - - - -
38G LEU* 1.3 78.6 - - - +
40G GLU* 1.3 62.5 + - + +
41G GLY 3.2 0.4 - - - -
42G HIS* 3.2 29.9 + - - +
45G GLN 5.8 2.4 + - - -
46G ARG* 5.6 1.4 - - - +
47G LEU* 3.7 25.0 - - - +
113J A 3.4 36.4 + - - -
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Residues in contact with GLU 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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82D HIS* 3.5 11.3 + - - -
36G ARG* 3.1 40.3 + - + +
37G SER* 3.7 6.4 + - - +
39G ARG* 1.3 77.5 - - + +
41G GLY* 1.3 60.0 + - - +
42G HIS* 3.3 16.2 + - - -
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Residues in contact with GLY 41 (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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82D HIS* 3.2 30.1 - - - -
37G SER 3.1 10.5 + - - -
38G LEU 3.6 0.2 + - - -
39G ARG 3.2 0.4 - - - -
40G GLU* 1.3 77.2 - - - +
42G HIS* 1.3 72.9 + - - +
43G TYR* 3.3 28.7 + - - -
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Residues in contact with HIS 42 (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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42C HIS 5.7 1.4 - - - +
45C GLN* 2.6 40.5 + - + +
82D HIS* 5.5 1.6 - - - -
87D SER* 5.5 5.2 - - - -
38G LEU 3.2 7.0 + - - -
39G ARG* 3.2 22.1 + - - +
40G GLU* 3.4 17.2 + - - -
41G GLY* 1.3 80.7 - - - +
43G TYR* 1.3 63.6 + - - +
44G ALA* 3.2 15.4 + - - +
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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