Contacts of the strand formed by residues 131 - 135 (chain A) in PDB entry 2ATW
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 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A ILE* 3.9 32.5 - - + -
126A ASN* 4.6 1.6 - - - +
129A GLY 5.3 0.2 - - - +
130A LEU* 1.3 75.0 - - - +
132A VAL* 1.3 63.6 + - - +
133A VAL* 4.0 8.0 + - + -
144A GLY 3.9 0.2 - - - +
145A VAL* 3.3 5.1 - - - +
146A ILE* 2.8 59.5 + - + +
151A GLN* 3.6 27.1 - - + +
157A TYR* 3.7 26.0 - - + +
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Residues in contact with VAL 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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119A ILE* 3.5 5.7 - - - +
120A GLN* 3.0 45.5 + - + +
122A ASP* 3.8 16.8 - - + +
125A ALA* 3.5 31.4 - - + -
126A ASN* 4.6 3.1 - - - +
130A LEU 4.2 0.2 + - - -
131A VAL* 1.3 74.6 - - - +
133A VAL* 1.3 68.2 + - - +
143A GLU* 3.5 36.1 - - + +
144A GLY 3.5 5.6 - - - +
145A VAL* 4.8 9.2 - - + -
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Residues in contact with VAL 133 (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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117A GLY* 3.8 5.6 - - - +
118A VAL 3.7 24.0 - - - +
119A ILE* 4.2 6.5 - - + -
131A VAL* 4.0 18.2 - - + +
132A VAL* 1.3 82.4 - - - +
134A ARG* 1.3 64.4 + - - +
135A ILE* 3.5 19.8 + - + +
143A GLU* 3.3 5.9 - - - -
144A GLY 2.8 35.7 + - - +
146A ILE* 4.0 19.3 - - + -
163A LEU* 4.0 11.9 - - + -
165A CYS* 5.3 1.1 - - - -
181A LEU* 3.9 19.3 - - + -
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Residues in contact with ARG 134 (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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117A GLY* 3.0 1.6 - - - -
118A VAL* 2.8 55.8 + - - +
120A GLN* 4.0 35.9 + - + +
133A VAL* 1.3 71.2 - - - +
135A ILE* 1.3 59.7 + - - +
141A ALA* 4.0 24.3 - - + +
142A SER 3.3 16.4 - - - +
143A GLU* 4.4 9.6 - - - +
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Residues in contact with ILE 135 (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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109A THR* 4.1 17.7 - - + +
115A VAL* 3.9 31.6 - - + -
116A ALA 3.1 15.5 - - - +
117A GLY* 4.2 0.7 - - - -
133A VAL* 3.7 23.6 - - + +
134A ARG* 1.3 76.9 - - - +
136A GLY* 1.3 65.8 + - - +
137A THR* 4.2 5.4 - - + -
141A ALA* 3.4 9.1 - - - +
142A SER* 2.9 37.6 + - - +
144A GLY 5.0 1.6 - - - +
165A CYS* 6.2 0.2 - - - -
179A ILE* 4.3 26.0 - - + -
181A LEU* 3.8 18.2 - - + -
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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