Contacts of the helix formed by residues 31 - 40 (chain G) in PDB entry 2DFS
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 GLU 31 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19G PHE* 3.4 36.3 - - + -
27G ILE* 4.1 4.3 - - + +
28G THR* 2.9 29.2 + - + +
30G LYS* 1.3 102.0 - - - +
32G LEU* 1.3 57.7 + - - +
33G GLY 3.3 2.0 - - - +
34G THR* 2.6 44.9 + - - +
35G VAL* 3.1 20.8 + - - +
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Residues in contact with LEU 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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28G THR 3.9 2.2 + - - -
29G THR 3.3 15.6 + - - +
30G LYS 3.3 0.4 - - - -
31G GLU* 1.3 73.8 - - - +
33G GLY* 1.3 66.4 + - - +
35G VAL* 3.0 20.3 - - - +
36G MET* 3.3 25.4 + - + +
48G LEU* 4.0 19.3 - - + +
51G MET* 4.3 11.4 - - + -
52G ILE* 3.5 38.4 - - + -
63G ILE* 3.6 27.1 - - + +
67G GLU* 5.1 3.8 - - - +
68G PHE* 3.7 19.1 - - + -
71G MET* 5.4 0.7 - - + -
951M MET* 4.7 7.9 - - + -
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Residues in contact with GLY 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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899A ARG* 4.3 14.1 - - - -
30G LYS 4.3 2.4 + - - -
31G GLU 3.3 0.4 - - - -
32G LEU* 1.3 74.0 - - - +
34G THR* 1.3 61.6 + - - +
36G MET* 3.1 11.9 + - - +
37G ARG* 2.9 33.5 + - - +
45G GLU* 5.4 0.4 - - - -
48G LEU* 3.1 28.5 - - - +
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Residues in contact with THR 34 (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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902A ALA* 3.2 47.8 - - + +
905A GLU* 4.9 7.4 - - + -
906A LEU* 4.5 0.5 - - - +
19G PHE* 3.1 15.9 - - - -
30G LYS 5.4 1.6 - - - +
31G GLU* 2.6 46.0 + - - +
33G GLY* 1.3 76.7 - - - +
35G VAL* 1.3 58.0 + - - +
37G ARG* 3.5 11.0 - - - +
38G SER* 3.5 4.7 - - - -
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Residues in contact with VAL 35 (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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906A LEU* 3.4 31.0 - - + -
12G PHE* 3.4 27.6 - - + -
16G PHE* 4.6 7.9 - - + -
19G PHE* 3.8 6.8 - - + -
27G ILE* 3.9 10.1 - - + -
31G GLU 3.1 15.3 + - - +
32G LEU* 3.0 24.2 - - - +
34G THR* 1.3 75.0 + - - +
36G MET* 1.3 54.7 + - - -
38G SER* 2.9 17.4 + - - -
39G LEU* 3.0 13.2 + - - +
68G PHE* 3.2 22.4 - - + -
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Residues in contact with MET 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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899A ARG* 3.0 26.9 - - - +
32G LEU* 3.3 26.0 + - + +
33G GLY* 3.1 4.9 + - - +
35G VAL* 1.3 70.8 - - - +
37G ARG* 1.3 65.2 + - - +
38G SER 3.2 0.7 + - - -
39G LEU* 3.4 3.6 + - - +
40G GLY 3.3 5.4 + - - -
41G GLN* 3.2 31.5 + - + +
43G PRO* 5.4 0.2 - - + -
47G GLU* 4.5 1.8 - - - +
51G MET* 3.5 42.2 - - + +
68G PHE* 3.4 34.8 - - + -
71G MET* 4.9 11.0 - - + -
72G MET* 5.3 7.0 - - + +
79G THR* 5.2 9.9 - - + -
951M MET* 4.9 0.2 - - - -
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Residues in contact with ARG 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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898A ARG* 3.3 28.6 + - - +
899A ARG* 2.9 58.9 - - - +
902A ALA* 3.1 34.0 - - + +
903A LYS* 3.1 15.4 - - - +
33G GLY* 2.9 19.3 + - - +
34G THR* 3.5 10.1 - - - +
36G MET* 1.3 72.4 - - - +
38G SER* 1.3 56.5 + - - +
40G GLY 3.2 21.0 + - - -
41G GLN 3.3 11.6 + - - -
43G PRO 4.1 1.0 + - - -
44G THR 3.6 13.1 + - - -
45G GLU* 2.6 44.5 + - - +
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Residues in contact with SER 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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902A ALA 3.1 19.7 - - - -
903A LYS* 2.7 43.0 + - - +
906A LEU* 3.0 49.7 + - - +
907A LYS* 4.5 2.3 - - - +
11G GLU* 5.2 1.2 - - - +
15G ALA* 5.3 0.9 - - - +
34G THR 3.5 2.0 - - - -
35G VAL 2.9 4.7 + - - -
37G ARG* 1.3 76.4 - - - +
39G LEU* 1.3 59.1 + - - +
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Residues in contact with LEU 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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903A LYS* 2.8 16.8 + - - -
906A LEU* 3.8 0.6 - - - +
8G GLN* 5.4 6.1 - - - +
11G GLU* 5.9 6.7 - - + +
12G PHE* 3.6 49.4 - - + +
35G VAL 3.0 6.6 + - - +
36G MET* 3.8 4.9 - - - +
38G SER* 1.3 78.3 - - - +
40G GLY* 1.3 55.7 + - - +
41G GLN* 3.3 23.6 - - - +
68G PHE* 5.0 4.9 - - + -
72G MET* 3.5 31.6 - - - -
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Residues in contact with GLY 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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899A ARG 4.7 2.3 - - - +
900A MET* 6.0 0.2 - - - -
903A LYS* 3.9 10.2 - - - +
36G MET 3.3 0.2 + - - -
37G ARG 3.2 16.8 + - - +
39G LEU* 1.3 80.7 - - - +
41G GLN* 1.3 62.9 + - - +
42G ASN* 3.4 2.4 - - - +
83G GLU* 3.2 10.8 - - - -
148G LYS* 2.7 33.4 + - - -
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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