Contacts of the strand formed by residues 128 - 133 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D VAL* 3.4 25.8 - - + -
97D ILE* 4.8 1.3 - - + -
114D ARG* 2.7 48.0 + - + +
117D ILE* 3.8 32.5 - - + -
118D ALA* 4.3 7.9 - - + -
121D LEU* 4.9 0.2 - - + -
123D CYS* 3.9 23.3 - - - -
124D ASP 4.2 3.6 - - - +
125D ILE 3.2 6.2 + - - +
126D GLU 3.4 0.6 - - - -
127D GLN* 1.3 84.0 - - - +
129D ASN* 1.3 59.4 + - - +
130D VAL* 4.3 16.8 - - + -
54F ALA* 4.3 2.8 - - - +
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Residues in contact with ASN 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D VAL 2.9 11.0 + - - +
96D ASP* 3.1 21.8 + - - +
97D ILE* 2.8 27.7 + - - +
114D ARG* 4.6 4.1 + - - +
128D VAL* 1.3 74.7 - - - +
130D VAL* 1.3 70.8 + - - +
131D LYS* 3.8 5.5 - - - +
51F GLY* 3.2 31.0 - - - +
54F ALA* 3.2 14.6 - - + -
56F GLY* 2.9 47.8 + - - -
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Residues in contact with VAL 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ILE* 3.5 13.7 - - + +
99D ILE* 3.8 16.4 - - + -
107D ARG* 5.1 0.2 + - - -
110D ILE* 3.2 38.7 - - + +
113D MSE 3.8 27.6 - - + -
114D ARG* 3.8 23.7 - - + +
117D ILE* 4.2 22.9 - - + -
128D VAL* 4.3 4.9 + - + -
129D ASN* 1.3 86.1 + - - +
131D LYS* 1.3 62.4 + - - +
56F GLY* 4.7 5.9 - - - +
57F ASP* 4.7 1.9 - - - +
60F LYS* 5.6 0.7 + - - -
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Residues in contact with LYS 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D ASP* 2.7 29.3 + - - -
97D ILE 2.9 14.0 + - - +
98D THR* 2.8 32.6 + - + +
99D ILE* 2.9 30.0 + - - +
107D ARG* 3.9 1.3 - - - +
110D ILE* 4.9 1.1 - - - -
129D ASN* 3.8 6.7 - - - +
130D VAL* 1.3 75.7 - - - +
132D ALA* 1.3 63.5 + - - +
133D THR* 5.8 1.6 - - - -
6F HIS 2.7 28.3 + - - +
7F GLY* 5.1 0.4 - - - -
8F PHE 5.5 0.4 - - - +
47F ASP* 3.7 38.6 - - + +
56F GLY 3.7 5.8 - - - +
57F ASP* 3.5 24.0 - - + +
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Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D ILE* 3.3 16.6 - - + +
101D ALA* 6.4 0.7 - - + -
103D ALA 5.9 2.7 - - - +
106D MSE 4.7 24.7 - - + -
107D ARG* 3.0 33.6 + - - +
110D ILE* 4.7 5.8 - - + -
131D LYS* 1.3 77.9 - - - +
133D THR* 1.3 60.5 + - - +
57F ASP* 4.6 2.8 - - - +
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Residues in contact with THR 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D THR* 3.8 21.5 - - + -
99D ILE 2.8 10.9 + - - +
100D ILE* 3.4 5.3 - - + -
101D ALA 2.9 26.7 + - - +
131D LYS* 5.8 2.7 - - - -
132D ALA* 1.3 76.2 - - - +
134D THR* 1.3 78.2 + - - +
8F PHE* 3.7 31.9 + - + +
9F ASP* 3.4 19.8 + - - -
47F ASP* 5.4 3.1 - - - -
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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