Contacts of the strand formed by residues 128 - 132 (chain A) in PDB entry 1V1A
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 PHE 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A GLU 3.0 6.5 + - - +
4A VAL* 3.5 11.2 - - + -
5A VAL 3.0 13.8 + - - -
126A VAL* 2.9 19.6 - - - +
127A ARG* 1.3 127.3 - - + +
129A LEU* 1.3 60.4 + - - +
130A HIS 4.0 0.7 - - - +
158A VAL* 3.5 6.7 - - - -
159A ARG* 3.2 52.3 - - + -
160A VAL 5.6 0.2 - - - -
161A SER* 4.6 7.6 - - - -
189A LEU* 4.7 8.7 - - + -
258A LEU* 3.5 29.6 - - + -
261A ALA* 3.9 20.9 - - + -
262A VAL* 3.4 22.4 - - + -
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Residues in contact with LEU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 3.4 18.4 - - + +
7A ALA* 5.4 4.9 - - + -
118A PHE* 5.3 4.5 - - + -
123A LEU* 4.1 21.5 - - + -
128A PHE* 1.3 74.9 - - - +
130A HIS* 1.3 63.2 + - - +
131A LEU* 3.9 14.8 + - + +
145A PHE* 6.5 0.4 - - + -
149A ALA* 3.3 32.3 - - + +
150A MET* 3.6 10.1 - - + +
153A ALA* 3.3 33.7 - - + -
158A VAL* 4.0 2.9 - - + -
159A ARG 2.6 14.4 + - - +
160A VAL* 3.6 5.1 - - + +
161A SER 2.8 26.4 + - - +
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Residues in contact with HIS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 4.8 3.1 - - + -
5A VAL 2.8 10.4 + - - +
6A THR* 3.7 18.9 - - + -
7A ALA 3.4 17.8 + - - +
35A ALA 5.8 0.4 - - - -
36A GLU* 4.6 9.8 - - + +
39A VAL* 3.6 35.1 - - + +
128A PHE* 4.0 1.4 - - + -
129A LEU* 1.3 73.0 - - - +
131A LEU* 1.3 94.5 + - - +
132A SER* 4.9 3.2 - - - -
161A SER* 3.3 28.6 + - - -
163A ASP* 4.0 22.3 + - + +
165A ASN* 5.9 0.2 + - - -
191A PHE* 4.9 0.7 - + - -
254A ALA* 4.5 13.9 - - + +
258A LEU* 4.1 17.0 - - + +
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ALA* 3.5 30.3 - - + +
36A GLU* 4.4 1.1 - - - -
129A LEU* 4.5 14.8 - - + +
130A HIS* 1.3 107.9 - - - +
132A SER* 1.3 63.1 + - - +
135A THR* 5.2 5.2 - - + +
136A PRO* 6.3 0.2 - - + -
145A PHE* 4.6 9.9 - - + -
146A SER* 3.8 34.8 - - - +
149A ALA* 4.1 11.0 - - + -
150A MET* 4.2 20.9 - - + +
160A VAL* 5.6 2.7 - - + -
161A SER 2.8 9.8 + - - +
162A LEU* 3.8 15.7 - - + -
163A ASP 3.3 8.1 + - - -
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA* 4.3 3.4 - - - -
36A GLU* 2.8 29.2 + - - -
130A HIS* 4.9 2.7 - - - -
131A LEU* 1.3 79.4 - - - +
133A GLY* 1.3 57.6 + - - +
134A ILE* 2.7 23.2 + - - +
135A THR* 3.0 15.0 + - - -
136A PRO* 3.2 8.8 - - - +
162A LEU* 3.8 5.7 - - - +
163A ASP* 3.3 8.7 - - - -
165A ASN* 3.2 32.7 + - - +
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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