Contacts of the strand formed by residues 136 - 141 (chain B) in PDB entry 2BP1
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 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B ILE* 3.8 25.1 - - + +
105B THR* 4.2 12.6 - - + -
124B LEU* 4.2 9.2 - - + -
128B LEU* 3.8 18.8 - - + +
131B LEU* 4.1 19.3 - - + -
133B CYS* 4.3 1.6 - - - -
135B GLN* 1.3 75.2 - - - +
137B ASP* 1.3 60.3 + - - +
138B LEU 3.6 18.6 - - - +
139B PHE* 4.1 6.1 - - + -
165B LYS 3.1 9.0 + - - +
166B PHE* 3.1 25.1 - - + -
167B VAL* 3.0 27.6 + - - +
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Residues in contact with ASP 137 (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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94B LEU 4.0 8.1 - - - +
101B VAL 3.9 4.2 - - - +
102B LYS* 3.3 40.3 + - + +
103B ILE* 3.0 38.4 + - - +
135B GLN* 5.5 2.2 + - - +
136B VAL* 1.3 74.4 - - - +
138B LEU* 1.3 62.3 + - + +
167B VAL* 3.5 18.7 - - + +
168B GLU* 3.1 28.8 + - - +
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Residues in contact with LEU 138 (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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71B GLU* 4.9 6.1 - - - +
103B ILE 3.2 3.6 + - - +
104B ALA* 3.1 16.4 - - + -
105B THR 3.0 26.0 + - - -
136B VAL* 3.3 7.5 - - - +
137B ASP* 1.3 81.7 - - + +
139B PHE* 1.3 59.8 + - - +
140B TYR* 3.2 39.7 - - + +
168B GLU* 3.3 16.4 - - + +
169B LEU 3.7 2.0 - - - +
170B GLY* 3.6 29.8 - - - +
196B VAL* 3.7 34.1 - - + -
222B ARG* 5.2 2.0 - - - +
224B TYR* 4.2 11.0 - - + -
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Residues in contact with PHE 139 (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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105B THR* 3.5 12.1 - - + -
106B LYS 4.3 2.0 - - - -
107B ALA* 3.7 32.5 - - + -
120B VAL* 3.7 32.8 - - + -
123B GLN 5.6 0.2 - - - -
124B LEU* 3.9 37.7 - - + -
136B VAL* 4.1 1.8 - - + -
138B LEU* 1.3 73.9 - - - +
140B TYR* 1.3 65.3 + - - +
141B LEU* 4.7 3.8 - - + -
157B CYS* 4.3 8.5 - - - -
160B LEU* 4.8 0.7 - - + -
166B PHE* 3.5 52.7 - + + -
168B GLU 2.9 8.9 + - - -
169B LEU* 3.4 14.3 - - + +
170B GLY 2.8 23.5 + - - -
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Residues in contact with TYR 140 (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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73B ASP* 3.8 7.6 + - - -
104B ALA* 3.8 6.9 - - + +
105B THR 2.8 23.2 + - - +
106B LYS* 3.2 22.8 - - + -
107B ALA 3.0 26.5 + - - -
138B LEU* 3.2 35.4 - - + +
139B PHE* 1.3 81.6 - - - +
141B LEU* 1.3 67.3 + - - +
142B HIS* 4.8 0.2 - - - -
170B GLY* 3.3 24.5 - - - -
171B LEU 3.7 9.9 - - - -
172B SER* 4.4 2.2 - - - -
196B VAL* 3.4 11.1 - - + +
198B GLN* 3.1 51.8 + - + +
224B TYR* 3.3 18.7 - - - -
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Residues in contact with LEU 141 (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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107B ALA* 3.8 3.8 - - + +
115B LEU* 4.4 14.6 - - + -
120B VAL* 4.9 3.6 - - + -
139B PHE* 4.7 8.7 - - + -
140B TYR* 1.3 74.2 - - - +
142B HIS* 1.3 61.9 + - - +
143B ALA 3.3 1.9 + - - -
150B VAL* 5.6 2.2 - - + -
153B THR* 3.8 32.3 - - + -
154B LEU* 4.4 17.0 - - + -
157B CYS* 4.0 19.3 - - - -
169B LEU* 5.0 3.6 - - + -
170B GLY 3.1 11.8 + - - +
171B LEU* 3.8 17.3 - - + -
172B SER* 3.0 28.1 + - - +
174B TYR* 3.3 31.3 - - + +
182B ILE* 5.5 0.9 - - + -
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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