Contacts of the strand formed by residues 128 - 133 (chain B) in PDB entry 1VHA
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 VAL 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ALA* 4.3 3.8 - - - +
95B VAL* 3.8 16.8 - - + -
97B ILE* 5.2 0.2 - - + -
114B ARG* 2.7 57.0 + - + +
117B ILE* 3.9 33.7 - - + -
118B ALA* 4.2 9.0 - - + -
121B LEU* 5.4 0.2 - - + -
123B CYS* 4.0 23.6 - - - -
124B ASP 4.0 4.9 - - - +
125B ILE 3.2 7.5 + - - +
126B GLU 3.2 0.8 - - - -
127B GLN* 1.3 85.5 - - - +
129B ASN* 1.3 64.2 + - - +
130B VAL* 4.4 3.4 - - + -
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Residues in contact with ASN 129 (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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3A ARG* 6.1 0.2 - - - +
51A GLY* 3.1 39.0 - - - +
54A ALA* 3.5 13.6 - - + +
56A GLY* 3.0 40.5 + - - -
95B VAL 3.1 9.8 + - - +
96B ASP* 2.9 23.6 + - - +
97B ILE* 2.8 27.8 + - - +
114B ARG* 4.4 4.0 + - - +
128B VAL* 1.3 75.2 - - - +
130B VAL* 1.3 71.6 + - - +
131B LYS* 3.9 4.2 - - - +
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Residues in contact with VAL 130 (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 GLY* 4.6 6.9 - - - -
57A ASP* 4.8 0.7 - - - +
97B ILE* 3.5 17.7 - - + -
99B ILE* 4.1 9.9 - - + -
107B ARG* 5.2 0.5 + - - -
110B ILE* 3.6 40.0 - - + +
113B MSE 3.4 28.7 - - + -
114B ARG* 3.8 22.5 - - + +
117B ILE* 4.2 21.3 - - + -
128B VAL* 4.4 2.7 + - + -
129B ASN* 1.3 87.9 + - - +
131B LYS* 1.3 66.8 + - - +
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Residues in contact with LYS 131 (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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6A HIS 2.7 28.9 + - - +
7A GLY* 5.2 0.4 - - - -
8A PHE 5.8 0.4 - - - +
47A ASP* 3.5 40.2 - - + +
56A GLY 3.8 12.6 - - - +
57A ASP* 3.3 24.2 - - + +
96B ASP* 2.8 29.8 + - - -
97B ILE 2.9 10.6 + - - +
98B THR* 2.8 31.0 + - + +
99B ILE* 2.8 34.8 + - - +
107B ARG* 4.5 2.0 - - - +
110B ILE* 4.9 1.6 - - - -
129B ASN* 3.9 0.9 - - - +
130B VAL* 1.3 78.2 - - - +
132B ALA* 1.3 57.8 + - - +
133B THR* 6.0 2.5 - - - -
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Residues in contact with ALA 132 (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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57A ASP* 3.9 7.6 + - - +
99B ILE* 3.2 26.7 - - + +
101B ALA* 6.1 1.1 - - + +
104B PRO 5.8 2.5 - - - +
106B MSE 4.7 19.5 - - + -
107B ARG* 3.9 19.0 + - - +
110B ILE* 5.0 2.9 - - + -
131B LYS* 1.3 77.5 - - - +
133B THR* 1.3 63.7 + - - +
134B THR* 5.9 0.2 - - - -
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Residues in contact with THR 133 (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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8A PHE* 3.7 37.8 + - + +
9A ASP* 4.3 1.7 + - - -
47A ASP* 5.1 7.2 + - - -
169A MN 4.1 13.2 + - - -
98B THR* 4.0 16.8 - - + -
99B ILE 2.8 13.8 + - - +
100B ILE* 3.4 5.9 - - + -
101B ALA 3.0 25.1 + - - +
131B LYS* 6.0 2.0 - - - -
132B ALA* 1.3 75.7 - - - +
134B THR* 1.3 79.5 + - - +
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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