Contacts of the strand formed by residues 119 - 122 (chain E) in PDB entry 3V5I
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 GLU 119 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72D THR* 4.1 11.0 - - + +
75D PHE* 5.9 0.4 - - - -
142D HIS* 2.9 30.2 + - - -
146D THR* 3.5 19.4 + - - +
149D LYS* 3.3 29.8 + - - +
92E CYS* 3.9 2.1 - - - -
94E GLY 2.9 11.2 + - - +
95E MET* 3.2 27.6 - - + +
96E ALA 2.9 24.3 + - - -
117E ASN 4.6 0.4 - - - +
118E ALA* 1.3 72.3 - - - +
120E VAL* 1.3 68.1 + - - +
174E PHE* 5.3 2.7 - - + -
175E LEU 3.7 11.2 - - - +
176E THR* 5.3 3.8 - - + -
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Residues in contact with VAL 120 (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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92E CYS* 4.5 5.4 - - + -
95E MET* 4.5 1.8 - - - -
96E ALA 3.3 13.0 - - - +
101E SER* 3.6 17.5 - - - -
104E LEU* 3.9 25.1 - - + -
114E ALA* 5.5 4.5 - - + -
118E ALA 5.5 1.6 - - - +
119E GLU* 1.3 80.5 - - - +
121E MET* 1.3 64.7 + - - +
122E ILE* 4.5 1.1 - - + -
174E PHE* 3.7 2.1 - - - +
175E LEU* 2.7 47.5 + - + +
176E THR 5.4 0.7 - - - +
177E ALA* 5.7 1.6 - - - -
180E ALA* 4.1 17.5 - - + -
185E LEU* 3.9 23.8 - - + -
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Residues in contact with MET 121 (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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67E PRO 5.8 0.2 - - - +
95E MET* 4.3 3.1 - - + -
96E ALA 3.2 5.1 + - - -
97E ALA* 3.4 23.8 - - + -
98E ALA* 2.9 26.1 + - + -
101E SER* 3.3 7.8 + - - -
120E VAL* 1.3 78.3 - - - +
122E ILE* 1.3 77.2 + - - +
123E HIS* 3.8 25.4 - - + +
172E ASP* 4.2 20.9 - - + +
173E ASN 3.2 19.5 - - - +
174E PHE* 3.6 37.5 - - + -
175E LEU* 5.4 0.2 - - - -
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Residues in contact with ILE 122 (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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98E ALA* 4.8 1.8 - - - +
101E SER* 3.4 25.1 - - - +
120E VAL* 4.5 1.3 - - + -
121E MET* 1.3 75.8 - - - +
123E HIS* 1.3 61.4 + - - +
154E LEU* 5.1 11.2 - - + -
165E ILE* 5.9 0.4 - - + -
168E ASP* 4.5 1.2 - - + +
169E THR* 3.7 24.2 - - + -
171E ARG 3.8 0.7 - - - +
173E ASN* 2.9 56.7 + - + +
175E LEU* 4.6 9.4 - - + +
183E TYR* 4.1 29.2 - - + +
185E LEU* 4.3 22.9 - - + -
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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