Contacts of the strand formed by residues 165 - 170 (chain E) in PDB entry 1VQN
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 GLY 165 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87E PHE 2.7 31.6 + - - +
93E MET* 3.1 14.6 - - - +
152E THR* 3.4 19.5 - - - -
164E ASP* 1.3 74.4 - - - +
166E VAL* 1.3 64.0 + - - -
167E TYR* 3.4 15.0 - - - -
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Residues in contact with VAL 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E MET* 3.7 27.1 - - + -
85E GLU 3.7 13.7 - - - +
86E VAL* 4.0 15.5 - - + +
93E MET* 4.2 3.4 - - - -
95E VAL* 4.2 9.2 - - + -
104E ILE* 4.0 27.4 - - + -
131E LEU* 3.8 16.8 - - + -
148E ILE* 4.3 17.9 - - + +
149E GLU* 3.3 26.9 - - - +
152E THR* 3.5 7.1 + - + -
165E GLY* 1.3 75.5 - - - -
167E TYR* 1.3 64.3 + - - +
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Residues in contact with TYR 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E MET* 3.1 25.2 - - - -
85E GLU* 3.1 17.3 + - + +
87E PHE* 4.8 10.3 - + + -
149E GLU* 3.5 20.9 - - + +
152E THR* 5.8 1.1 - - - -
159E VAL* 5.0 8.6 - - + +
163E GLN* 2.5 39.8 + - + +
164E ASP 3.7 4.5 + - - -
165E GLY* 3.4 21.3 - - - -
166E VAL* 1.3 79.0 - - - +
168E ILE* 1.3 70.6 + - - +
169E THR* 3.1 2.4 + - - +
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Residues in contact with ILE 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E TYR* 4.4 9.9 - - + -
83E GLY 3.5 2.7 - - - +
84E MET* 3.6 20.6 - - + -
145E ALA* 3.3 39.3 - - + +
146E ALA* 4.3 3.4 - - - +
149E GLU* 2.8 26.4 + - + +
167E TYR* 1.3 73.6 - - - +
169E THR* 1.3 62.2 + - - +
170E ARG 4.0 11.0 - - - +
171E LYS* 3.9 35.2 - - + -
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Residues in contact with THR 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E GLY* 2.5 23.8 + - - -
85E GLU* 3.2 51.8 + - + +
167E TYR* 3.5 2.4 + - - +
168E ILE* 1.3 75.2 - - - +
170E ARG* 1.3 71.4 + - + +
171E LYS* 4.4 1.3 + - - +
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Residues in contact with ARG 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81E GLU* 4.6 18.9 + - - +
82E TYR* 3.4 13.3 - - - +
83E GLY* 3.1 45.6 + - - +
130E GLU* 5.8 2.6 + - - -
132E THR* 4.7 9.7 + - - -
168E ILE* 4.0 4.0 - - - +
169E THR* 1.3 96.3 - - + +
171E LYS* 1.3 64.7 + - - +
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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