Contacts of the strand formed by residues 86 - 90 (chain E) in PDB entry 3NVQ
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 86 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E PHE 4.6 0.2 - - - +
80E HIS* 3.0 25.1 - - - +
81E GLU* 5.0 0.7 + - - +
84E SER* 2.9 13.9 + - - -
85E SER* 1.3 85.8 + - - +
87E VAL* 1.3 62.3 + - - +
88E TRP* 4.2 14.0 - - - -
97E LEU* 3.9 18.1 - - - +
98E PHE 3.2 9.1 + - - -
99E ASP* 3.9 9.2 + - - -
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Residues in contact with VAL 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E LEU* 3.9 34.5 - - + -
79E PHE 3.7 3.8 - - - +
80E HIS* 3.6 18.2 - - + -
85E SER 5.0 1.6 - - - +
86E SER* 1.3 81.1 - - - +
88E TRP* 1.3 66.0 + - - +
89E VAL* 4.3 6.7 - - + -
96E TYR 3.6 1.9 - - - +
97E LEU* 3.6 0.9 - - - -
98E PHE* 2.7 49.8 + - + +
100E PHE* 4.0 11.0 - - + -
478E TYR* 3.8 25.8 - - + -
485E VAL* 4.4 11.2 - - + -
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Residues in contact with TRP 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E VAL 3.7 0.2 - - - +
78E LEU* 3.3 1.0 - - - +
79E PHE* 2.8 64.7 + + + +
80E HIS* 5.5 0.2 - - - -
81E GLU* 5.6 5.1 + - + +
86E SER* 4.2 13.0 - - - -
87E VAL* 1.3 76.8 - - - +
89E VAL* 1.3 69.7 + - - +
95E VAL* 3.7 22.7 - - + -
96E TYR 3.3 7.9 - - - -
97E LEU* 3.5 46.3 - - + +
111E VAL* 5.0 9.0 - - + -
133E LEU* 3.8 17.4 - - + +
140E LEU* 3.6 28.5 - - + +
155E LEU* 4.5 12.8 - - + -
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Residues in contact with VAL 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E PHE* 3.9 22.9 - - + -
76E THR* 4.1 13.0 - - + -
77E VAL 3.1 10.5 - - - +
78E LEU* 4.2 16.8 - - + -
87E VAL* 4.3 1.6 - - + -
88E TRP* 1.3 81.8 - - - +
90E GLY* 1.3 71.9 + - - +
95E VAL* 3.4 2.3 - - - +
96E TYR* 2.8 50.8 + - + -
98E PHE* 4.0 20.2 - - + -
133E LEU* 4.1 2.2 - - - -
480E SER* 5.6 2.5 - - - +
485E VAL* 4.1 13.7 - - + -
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Residues in contact with GLY 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E HIS 3.7 0.2 - - - +
76E THR* 3.2 28.8 - - - -
77E VAL* 3.0 13.4 + - - -
89E VAL* 1.3 73.2 - - - +
91E GLY* 1.3 57.6 + - - -
94E LYS 4.0 3.1 - - - -
95E VAL* 4.4 1.6 - - - -
130E ILE* 3.5 37.1 - - - +
133E LEU* 3.7 6.8 - - - +
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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