Contacts of the helix formed by residues 47 - 57 (chain B) in PDB entry 2ZV6
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 ASP 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B LYS* 1.3 76.3 - - - +
48B ASN* 1.3 60.2 + - + +
49B THR 3.0 2.5 - - - +
50B ALA* 2.7 28.2 + - - +
51B GLN* 2.9 10.2 + - - +
313B ASP* 3.1 22.2 - - + +
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Residues in contact with ASN 48 (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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47B ASP* 1.3 77.9 + - + +
49B THR* 1.3 62.8 + - - +
51B GLN* 2.8 38.6 + - - +
52B GLN* 2.9 35.9 + - - +
306B ASP* 2.7 24.7 + - - +
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Residues in contact with THR 49 (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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45B ALA* 4.5 3.4 - - + -
46B LYS 3.5 9.2 - - - -
47B ASP* 2.9 0.8 + - - +
48B ASN* 1.3 80.6 - - - +
50B ALA* 1.3 59.8 + - - +
52B GLN* 3.3 12.3 - - - +
53B ILE* 3.5 7.4 - - - +
306B ASP* 3.6 13.6 + - - +
307B ILE* 3.2 44.6 - - + +
311B ASP 3.7 4.5 + - - -
312B ALA* 3.6 4.7 - - - -
313B ASP* 2.6 45.8 + - - +
314B LEU* 4.4 7.0 - - + -
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Residues in contact with ALA 50 (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 LEU* 3.7 19.1 - - + -
45B ALA* 3.5 31.0 - - - +
46B LYS* 3.7 3.1 + - - +
47B ASP 2.7 15.0 + - - +
49B THR* 1.3 74.7 - - - +
51B GLN* 1.3 62.9 + - - +
53B ILE* 3.6 8.7 - - - +
54B LYS* 2.9 36.1 + - + +
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Residues in contact with GLN 51 (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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47B ASP 2.9 6.6 + - - +
48B ASN* 2.8 35.3 + - - +
50B ALA* 1.3 75.8 - - - +
52B GLN* 1.3 68.4 + - - +
54B LYS* 3.4 9.3 + - + +
55B LYS* 3.1 19.6 + - - +
60B ASP* 5.8 5.2 - - + +
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Residues in contact with GLN 52 (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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48B ASN* 2.9 37.0 + - - +
49B THR* 3.3 11.2 - - - +
51B GLN* 1.3 74.6 - - - +
53B ILE* 1.3 66.4 + - - +
55B LYS* 2.7 25.9 + - - +
56B VAL* 2.9 15.2 + - - -
303B GLY 3.6 18.3 + - - +
304B MET* 3.9 10.1 - - + -
305B VAL* 3.2 19.0 + - - +
306B ASP* 3.2 32.9 + - - -
307B ILE* 3.8 7.6 - - + -
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Residues in contact with ILE 53 (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 LEU* 4.4 6.7 - - + +
41B VAL* 4.1 24.9 - - + -
42B LEU* 3.8 34.8 - - + -
45B ALA* 4.4 5.6 - - + -
49B THR 3.5 16.4 - - - +
50B ALA* 3.6 12.3 - - - +
52B GLN* 1.3 78.4 - - - +
54B LYS* 1.3 57.7 + - - +
56B VAL* 4.4 0.2 - - - -
57B LEU* 3.0 52.5 + - + +
304B MET* 3.6 29.3 - - + +
307B ILE* 3.9 16.4 - - + -
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Residues in contact with LYS 54 (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 LEU* 3.5 31.2 - - + -
50B ALA* 2.9 34.3 + - + +
51B GLN* 3.6 9.6 - - + +
52B GLN 2.8 4.6 + - - -
53B ILE* 1.3 73.8 - - - +
55B LYS* 1.3 56.5 + - - +
58B HIS 3.0 4.3 + - - -
59B PHE* 2.5 49.9 + - + +
60B ASP* 3.2 39.3 + - + +
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Residues in contact with LYS 55 (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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51B GLN 3.1 9.5 + - - +
52B GLN* 2.7 23.4 + - - +
54B LYS* 1.3 73.3 - - - +
56B VAL* 1.3 69.1 + - + +
58B HIS* 2.9 26.6 + - - +
60B ASP* 4.8 8.7 - - + +
61B GLN* 3.9 10.5 - - - +
302B MET 3.3 24.4 + - - -
303B GLY* 3.3 19.5 + - - -
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Residues in contact with VAL 56 (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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11B PHE* 3.3 19.6 - - + -
14B ASP* 4.7 1.6 - - - +
52B GLN 2.9 10.2 + - - +
53B ILE 3.8 3.4 - - - +
55B LYS* 1.3 95.1 - - - +
57B LEU* 1.3 74.0 + - + +
58B HIS* 3.3 13.9 + - - -
299B LEU* 3.9 23.1 - - + -
302B MET* 4.2 13.7 - - + +
303B GLY* 3.7 22.7 - - - -
304B MET* 3.5 25.8 - - + +
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Residues in contact with LEU 57 (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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7B ALA* 3.8 9.5 - - - +
11B PHE* 3.8 20.5 - - + +
35B THR* 4.0 13.8 - - + +
38B LEU* 3.3 48.9 - - + -
53B ILE* 3.0 25.1 + - + +
56B VAL* 1.3 94.9 - - + +
58B HIS* 1.3 71.6 + - - +
59B PHE* 3.0 50.1 + - + -
304B MET* 4.7 0.2 - - - -
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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