Contacts of the helix formed by residues 37 - 47 (chain B) in PDB entry 3I6A
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 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ILE* 3.7 2.0 - - - +
36B LYS* 1.3 82.5 - - - +
38B ALA* 1.3 64.5 + - - +
39B GLU* 3.4 13.1 + - - +
40B ASP* 3.0 36.4 + - - +
41B LEU 3.3 8.3 + - - -
218B ASN 5.8 0.7 - - - -
219B ILE* 3.8 16.1 - - - +
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B SER* 1.3 73.6 - - - +
39B GLU* 1.3 57.0 + - - +
41B LEU* 3.1 5.3 + - - +
42B ASP* 2.9 37.0 + - - +
218B ASN 4.8 1.0 + - - -
219B ILE* 3.3 33.9 - - - +
222B PRO* 4.0 22.9 - - + -
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B SER* 3.2 12.3 + - - +
38B ALA* 1.3 77.6 - - - +
40B ASP* 1.3 64.3 + - - +
42B ASP* 3.2 9.7 + - + +
43B LYS* 3.0 23.4 + - + +
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Residues in contact with ASP 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LYS* 6.4 2.9 - - - -
34B PHE 4.1 4.3 - - - +
35B ILE* 3.7 19.3 - - + -
36B LYS* 2.9 29.7 + - - +
37B SER* 3.0 26.7 + - - +
39B GLU* 1.3 79.1 - - - +
41B LEU* 1.3 63.8 + - - +
43B LYS* 3.4 8.0 + - - +
44B LEU* 3.3 24.2 + - + +
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PHE* 5.6 0.7 - - + -
35B ILE* 4.0 9.4 - - + +
37B SER 3.3 7.6 + - - +
38B ALA* 3.1 8.8 + - - +
40B ASP* 1.3 79.0 - - - +
42B ASP* 1.3 64.0 + - - +
44B LEU* 3.2 10.8 + - + +
45B ARG* 3.2 48.7 + - - +
50B LEU* 4.0 21.8 - - + -
53B GLN 4.8 2.7 - - - +
55B VAL* 4.1 24.5 - - + +
219B ILE* 4.1 16.6 - - + +
220B PHE* 3.3 37.2 - - + -
5102B GSH 5.5 0.7 - - - +
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Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ALA* 2.9 23.7 + - - +
39B GLU* 3.2 8.5 + - + +
41B LEU* 1.3 76.2 - - - +
43B LYS* 1.3 50.9 + - - +
45B ARG* 3.3 27.2 + - - +
46B ASN* 2.8 51.7 + - - +
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Residues in contact with LYS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LYS* 5.9 4.7 - - - +
39B GLU* 3.0 16.3 + - + +
40B ASP* 3.7 9.0 - - - +
42B ASP* 1.3 73.5 - - - +
44B LEU* 1.3 61.2 + - + +
46B ASN* 4.3 8.5 - - + +
47B ASP* 2.7 69.6 + - - +
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B HIS* 3.8 28.9 - - + +
33B LYS* 6.0 3.4 - - - +
35B ILE* 3.7 33.2 - - + -
40B ASP* 3.3 14.5 + - + +
41B LEU* 3.2 10.5 + - + +
43B LYS* 1.3 77.7 - - + +
45B ARG* 1.3 62.5 + - - +
47B ASP* 3.4 8.9 + - - +
49B TYR* 3.1 36.1 + - + +
50B LEU* 3.8 14.8 - - + -
55B VAL* 4.2 13.2 - - + -
57B MET* 3.8 19.5 - - + -
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ARG* 4.3 3.8 - - - +
41B LEU* 3.2 40.3 + - - +
42B ASP* 3.5 27.3 + - - +
44B LEU* 1.3 80.0 - - - +
46B ASN* 1.3 60.3 + - - +
48B GLY* 2.9 21.1 + - - -
49B TYR 4.2 0.2 + - - -
50B LEU* 4.0 17.4 + - + -
53B GLN* 2.9 56.4 + - - +
220B PHE* 4.5 2.2 - - - -
5102B GSH 3.5 26.5 + - - -
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Residues in contact with ASN 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ASP* 2.8 39.0 + - - +
43B LYS* 3.8 9.4 - - + +
45B ARG* 1.3 70.8 - - - +
47B ASP* 1.3 62.7 + - - +
48B GLY* 3.0 6.9 + - - -
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Residues in contact with ASP 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LYS* 2.7 56.8 + - - +
44B LEU* 3.7 7.2 - - - +
46B ASN* 1.3 76.3 - - - +
48B GLY* 1.3 56.5 + - - +
49B TYR* 3.3 46.6 - - + -
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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