Contacts of the helix formed by residues 56 - 62 (chain B) in PDB entry 5NVN
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 ARG 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ARG* 5.6 4.0 - - - +
149A GLU* 3.3 23.6 + - - -
150A ASN* 2.5 34.8 + - - +
153A LEU* 4.2 22.6 - - + +
159A GLN* 5.1 2.0 - - - +
203A VAL 5.7 2.7 - - - -
55B ASP* 1.3 75.9 - - - +
57B LYS* 1.3 65.8 + - - +
59B LEU* 3.2 10.6 + - - +
60B MET* 2.9 42.9 + - + +
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Residues in contact with LYS 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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55B ASP* 3.3 7.2 + - - +
56B ARG* 1.3 80.7 - - - +
58B PHE* 1.3 63.1 + - - +
60B MET* 3.3 8.6 + - + +
61B GLU* 3.0 39.5 + - - +
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Residues in contact with PHE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A HIS* 3.4 32.5 - + + -
54B TYR* 3.3 44.0 - + + -
55B ASP* 2.8 25.7 + - - +
57B LYS* 1.3 76.3 - - - +
59B LEU* 1.3 66.0 + - + +
61B GLU* 3.0 10.1 + - + +
62B CYS* 3.0 40.2 + - - -
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Residues in contact with LEU 59 (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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56A LEU* 5.4 2.5 - - + -
91A VAL* 3.5 34.1 - - + -
94A PHE* 6.4 0.4 - - + -
95A TRP* 2.8 26.8 + - + +
153A LEU* 3.3 54.5 - - + +
156A LEU* 5.0 4.5 - - + -
157A GLY* 4.3 6.1 - - - +
54B TYR* 3.5 32.8 - - + +
55B ASP 3.3 12.9 + - - +
56B ARG* 3.2 7.4 + - - +
58B PHE* 1.3 78.2 - - + +
60B MET* 1.3 63.1 + - - +
62B CYS* 3.1 10.4 + - - +
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Residues in contact with MET 60 (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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95A TRP* 3.7 21.1 - - - -
149A GLU* 4.1 15.3 - - - +
153A LEU* 3.8 13.7 - - + -
56B ARG* 2.9 43.9 + - + +
57B LYS* 3.5 11.2 - - - +
58B PHE 3.2 0.2 - - - -
59B LEU* 1.3 76.4 - - - +
61B GLU* 1.3 60.0 + - - +
63B ARG* 3.2 53.2 + - - +
64B ASN* 4.4 4.9 + - - +
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Residues in contact with GLU 61 (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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57B LYS* 3.0 35.8 + - - +
58B PHE* 3.0 8.9 + - + +
60B MET* 1.3 73.8 - - - +
62B CYS* 1.3 63.6 + - - +
63B ARG 3.1 0.2 - - - -
64B ASN* 3.1 37.7 + - + +
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Residues in contact with CYS 62 (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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54A HIS* 3.9 19.3 - - - -
91A VAL* 3.7 22.0 - - + -
92A GLU* 4.1 11.1 - - - +
95A TRP* 4.2 2.7 - - + -
58B PHE* 3.0 51.6 + - - -
59B LEU 3.1 10.3 + - - +
61B GLU* 1.3 75.6 - - - +
63B ARG* 1.3 62.1 + - - +
64B ASN 3.1 1.0 + - - -
65B SER* 3.5 18.0 + - - -
68B THR* 4.2 4.2 - - - +
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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