Contacts of the strand formed by residues 126 - 132 (chain B) in PDB entry 2OT3
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 CYS 126 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B ASN 3.1 15.2 + - - +
94B GLY* 3.2 1.7 - - - -
95B ALA 2.9 25.0 + - - -
124B GLU* 4.5 7.0 - - - -
125B ILE* 1.3 69.4 - - - +
127B LEU* 1.3 59.8 + - - +
176B LEU* 3.5 25.5 - - + +
179B ARG* 3.7 43.5 - - + +
180B MET* 3.9 11.7 - - + -
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ALA* 3.7 23.8 - - + -
97B LEU* 4.3 5.8 - - + -
114B VAL* 4.0 33.0 - - + -
117B LEU* 3.9 21.8 - - + -
118B ARG* 3.4 37.4 - - + +
125B ILE* 3.4 16.3 + - + +
126B CYS* 1.3 71.6 - - - +
128B CYS* 1.3 59.4 + - - +
129B ILE* 4.2 0.9 - - + -
154B VAL* 4.2 5.8 - - + +
155B GLY 5.2 0.4 + - - -
156B ALA* 3.8 16.4 - - + +
157B LYS 3.2 9.9 + - - -
179B ARG* 2.9 30.7 + - - +
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Residues in contact with CYS 128 (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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95B ALA 2.8 10.8 + - - +
96B ILE* 4.3 3.4 - - - -
97B LEU* 2.8 36.7 + - - +
127B LEU* 1.3 73.6 - - - +
129B ILE* 1.3 59.2 + - - +
130B VAL* 4.0 3.6 - - + -
157B LYS 3.4 4.7 - - - -
159B TYR* 3.6 10.1 - - + -
172B LEU* 3.6 34.5 - - + -
176B LEU* 3.7 31.4 - - - -
179B ARG* 3.6 20.2 - - - -
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Residues in contact with ILE 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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97B LEU* 3.5 6.7 - - + +
99B TYR* 3.8 22.2 - - + -
107B PHE* 4.4 9.0 - - + -
110B VAL* 4.1 24.7 - - + -
114B VAL* 4.6 7.0 - - + -
127B LEU* 5.4 0.4 - - + -
128B CYS* 1.3 75.6 - - - +
130B VAL* 1.3 61.0 + - - +
147B ALA 5.1 0.4 - - - +
150B TYR* 3.6 29.2 - - + -
151B ALA* 3.7 12.1 - - + -
154B VAL* 4.2 2.5 - - + -
156B ALA* 3.4 28.7 - - + -
157B LYS 2.9 11.0 + - - +
158B HIS* 3.2 19.0 - - + -
159B TYR 3.0 23.4 + - - -
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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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35B LEU* 4.1 13.0 - - + -
96B ILE* 3.7 27.6 - - + -
97B LEU 2.8 13.4 + - - +
98B VAL* 3.4 6.9 - - + +
99B TYR* 2.9 34.8 + - - +
128B CYS* 4.2 4.9 - - + -
129B ILE* 1.3 76.2 - - - +
131B GLY* 1.3 59.8 + - - +
132B ASN 3.3 1.9 + - - +
159B TYR* 3.5 8.5 - - + +
161B THR* 3.5 39.5 - - + +
172B LEU* 3.8 22.7 - - + -
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Residues in contact with GLY 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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99B TYR* 3.4 30.8 - - - -
101B ILE* 3.6 9.4 - - - +
130B VAL* 1.3 68.0 - - - +
132B ASN* 1.3 60.7 + - - -
134B ILE* 3.2 24.4 - - - +
158B HIS* 3.9 4.5 + - - -
159B TYR 2.9 12.7 + - - -
160B HIS* 3.6 2.1 + - - -
161B THR* 3.2 10.4 + - - -
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Residues in contact with ASN 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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30B VAL 2.9 25.9 + - - +
31B GLY* 3.5 21.4 + - - -
35B LEU* 4.1 6.6 - - - +
98B VAL* 3.7 10.3 - - + -
99B TYR 2.8 19.0 + - - +
100B ASP* 3.9 0.3 - - - -
101B ILE* 3.2 23.4 + - - +
130B VAL 3.3 0.6 + - - +
131B GLY* 1.3 74.2 - - - +
133B LYS* 1.3 92.2 + - - +
161B THR* 2.9 24.1 + - - +
163B ALA* 3.4 23.1 + - - +
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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