Contacts of the strand formed by residues 130 - 135 (chain E) in PDB entry 1VQ7
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 130 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E MET 3.6 3.4 - - - +
85E GLU* 4.7 15.2 - - + +
125E GLU 4.0 0.2 - - - +
126E ILE* 3.2 5.1 - - - +
127E ASP* 2.6 47.9 + - + +
128E GLY 3.2 1.2 - - - -
129E GLU* 1.3 85.3 - - + +
131E LEU* 1.3 64.5 + - - +
170E ARG* 5.6 6.9 + - - -
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Residues in contact with LEU 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E GLY* 3.6 3.3 - - - -
84E MET* 2.7 54.1 + - + +
86E VAL* 5.2 6.7 - - + -
95E VAL* 4.2 22.2 - - + -
97E VAL* 5.3 1.8 - - + -
102E VAL* 5.3 2.5 - - + -
124E VAL* 3.8 26.0 - - + -
125E GLU 3.5 2.0 - - - -
126E ILE* 3.4 33.4 - - + -
130E GLU* 1.3 77.4 - - - +
132E THR* 1.3 61.4 + - - +
133E VAL 4.1 0.7 - - - -
148E ILE* 4.5 3.8 - - + -
166E VAL* 3.4 33.0 - - + -
170E ARG* 5.0 0.9 + - - -
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Residues in contact with THR 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E GLU* 3.7 27.3 + - - +
82E TYR 3.3 9.0 + - - -
123E ASP 3.3 9.5 - - - +
124E VAL* 4.7 0.4 - - - -
125E GLU* 2.8 49.5 + - + +
131E LEU* 1.3 76.4 - - - +
133E VAL* 1.3 63.1 + - - +
134E SER* 3.6 4.2 + - - +
170E ARG* 4.0 14.4 + - - -
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Residues in contact with VAL 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E GLU* 3.1 2.9 - - - -
82E TYR* 2.6 46.0 + - + +
84E MET* 3.4 38.6 - - + -
122E THR* 3.3 28.3 - - + -
123E ASP 3.3 5.2 - - - +
124E VAL* 4.3 7.6 - - + +
132E THR* 1.3 71.6 - - - +
134E SER* 1.3 58.8 + - - +
141E VAL* 3.7 13.6 - - + +
144E THR* 3.8 19.7 - - + -
145E ALA* 4.0 7.0 - - + +
148E ILE* 3.9 8.5 - - + -
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Residues in contact with SER 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E TRP 3.1 15.0 - - - -
81E GLU* 3.3 25.4 + - - -
122E THR* 3.3 3.3 - - - -
123E ASP* 2.5 58.8 + - - +
125E GLU* 5.4 3.8 + - - +
132E THR* 3.9 6.0 + - - +
133E VAL* 1.3 75.7 - - - +
135E GLY* 1.3 58.6 + - - +
141E VAL* 3.8 8.1 - - - -
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Residues in contact with GLY 135 (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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26E ASN* 4.2 5.8 - - - -
80E TRP* 3.0 36.1 + - - +
122E THR* 4.5 4.7 - - - -
123E ASP* 4.5 6.5 - - - -
134E SER* 1.3 75.5 - - - +
136E PRO* 1.3 69.8 - - - +
137E ASP 3.5 2.2 - - - -
141E VAL* 3.5 12.3 - - - +
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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
------------------------------------------------------------
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