Contacts of the strand formed by residues 131 - 138 (chain A) in PDB entry 2W9T
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 TRP 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A ILE* 3.6 27.1 - - + +
103A ASP* 5.5 1.8 - - - -
105A VAL* 3.9 11.4 - - + -
106A ASP 4.2 6.5 - - - -
107A ASP* 4.2 4.3 - - - -
108A MET* 3.8 34.5 - - + -
125A PRO 5.4 0.2 + - - -
126A TYR* 3.6 24.7 - - + +
127A THR 3.3 19.4 + - - +
128A PHE* 3.5 24.3 - - - +
130A ASP* 1.3 96.0 + - + +
132A GLU* 1.3 62.6 + - - +
154A LEU* 4.1 22.9 - - + -
155A VAL 3.4 7.2 - - - -
156A ARG* 3.4 62.6 - - + -
157A ARG* 3.6 5.5 - - - -
22B TRP* 4.3 5.6 - - + -
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Residues in contact with GLU 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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131A TRP* 1.3 76.4 - - - +
133A VAL* 1.3 80.6 + - - +
134A GLU* 3.4 3.9 + - - +
154A LEU* 3.2 9.2 - - - -
155A VAL* 3.0 47.0 + - + +
157A ARG* 4.1 15.5 - - + -
22B TRP* 4.9 1.1 - - - -
144B LYS* 4.5 9.0 + - - -
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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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132A GLU* 1.3 81.3 - - - +
134A GLU* 1.3 57.3 + - - +
135A SER* 3.3 31.4 - - - +
136A SER* 3.8 14.8 - - - -
152A LEU* 5.6 0.2 - - + -
153A HIS 3.8 3.1 - - - -
154A LEU* 4.0 6.1 - - + -
22B TRP* 3.4 42.2 - - + +
25B PRO* 4.0 19.3 - - + -
28B LEU* 4.0 13.0 - - + -
144B LYS* 3.3 26.3 + - + -
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Residues in contact with GLU 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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132A GLU* 3.4 7.0 + - - +
133A VAL* 1.3 72.7 - - - +
135A SER* 1.3 80.5 + - - +
153A HIS* 2.8 48.4 + - + +
155A VAL* 3.9 19.1 - - + -
144B LYS* 4.2 15.0 - - - +
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Residues in contact with SER 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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133A VAL* 3.3 12.6 - - - +
134A GLU* 1.3 101.0 - - - +
136A SER* 1.3 62.0 + - - +
137A VAL* 4.2 14.2 - - - +
151A PHE 4.2 2.8 + - - -
152A LEU* 3.5 2.1 - - - -
153A HIS* 2.8 35.5 + - - +
143B GLU 6.4 0.2 - - - -
144B LYS* 4.6 4.7 - - - -
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Residues in contact with SER 136 (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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133A VAL* 3.8 10.1 - - - +
135A SER* 1.3 77.2 + - - +
137A VAL* 1.3 63.2 + - - +
138A GLU 4.5 0.3 + - - -
150A THR* 3.5 6.6 - - - +
151A PHE 3.4 7.0 - - - -
152A LEU* 3.9 2.1 - - - +
22B TRP 3.1 24.7 + - - -
23B HIS* 3.3 20.5 + - - +
25B PRO* 3.9 12.1 - - - -
143B GLU 3.8 7.7 + - - +
144B LYS* 3.4 21.6 - - - +
146B THR* 5.9 0.5 - - - +
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Residues in contact with VAL 137 (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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135A SER* 4.2 15.0 - - - +
136A SER* 1.3 79.9 + - - +
138A GLU* 1.3 72.0 + - - +
150A THR* 3.2 6.1 - - - +
151A PHE* 2.8 51.6 + - + +
143B GLU 4.9 7.6 - - - +
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Residues in contact with GLU 138 (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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136A SER 4.5 0.2 + - - -
137A VAL* 1.3 81.2 - - - +
139A GLY* 1.3 74.5 + - - +
140A GLN* 3.7 0.9 + - - +
141A LEU* 6.0 1.6 - - - +
149A HIS 3.8 8.7 - - - +
150A THR* 4.3 8.7 - - + +
16B TYR* 5.7 1.3 - - - +
116B LYS 5.3 4.5 - - - +
118B GLN* 5.6 5.9 + - - +
146B THR* 5.6 2.2 + - - +
147B ILE* 4.2 25.6 - - + +
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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