Contacts of the strand formed by residues 177 - 186 (chain B) in PDB entry 2B5I
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 GLN 177 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B LEU 4.4 0.3 - - - +
148B PRO* 3.3 29.6 - - + +
175B ASP 4.5 0.6 + - - -
176B THR* 1.3 70.8 - - - +
178B TYR* 1.3 62.3 + - - +
179B GLU* 6.3 0.2 - - - +
202B ALA* 4.8 9.1 - - - +
203B PHE* 3.6 21.4 + - - +
204B ARG* 3.3 31.2 + - + +
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Residues in contact with TYR 178 (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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145B THR* 4.0 15.5 - - + -
146B LEU 3.3 16.8 - - - +
147B SER* 3.9 22.2 - - - -
148B PRO* 4.5 0.2 - - + -
172B LEU* 3.8 19.4 - - + +
173B THR* 2.9 35.5 + - - -
176B THR* 3.4 34.1 - - + +
177B GLN* 1.3 75.9 + - - +
179B GLU* 1.3 65.1 + - - +
202B ALA* 3.4 4.9 - - - +
203B PHE* 2.8 66.8 + + + +
205B THR* 3.7 18.6 - - + -
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Residues in contact with GLU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B THR* 3.4 9.6 - - - +
146B LEU* 2.9 55.2 + - + +
152B TRP* 3.7 19.9 + - + -
178B TYR* 1.3 80.2 - - - +
180B PHE* 1.3 62.1 + - - +
200B PRO* 3.3 26.3 - - + +
201B LEU 3.2 7.0 - - - +
202B ALA* 4.2 17.0 - - + +
203B PHE* 4.5 0.2 - - - -
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Residues in contact with PHE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 3.8 18.0 - - + +
124B ILE* 3.8 31.4 - - + -
126B TRP* 3.7 25.6 - + - -
143B ALA* 3.5 34.5 - - + -
144B ARG 3.6 14.4 - - - -
145B THR* 4.0 11.7 - - - +
152B TRP* 4.1 1.3 - - - -
158B LEU* 4.9 0.4 - - + -
167B ILE* 3.5 27.1 - - + -
169B LEU* 4.2 13.2 - - + -
179B GLU* 1.3 77.5 - - - +
181B GLN* 1.3 68.7 + - - +
182B VAL* 4.1 3.4 - - + -
200B PRO* 3.3 4.9 - - - +
201B LEU* 2.8 36.5 + - + +
203B PHE* 4.2 4.5 - - + -
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Residues in contact with GLN 181 (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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143B ALA* 3.2 6.8 - - - +
144B ARG* 2.7 72.7 + - - +
152B TRP* 3.7 18.4 - - + +
180B PHE* 1.3 82.3 - - - +
182B VAL* 1.3 60.8 + - - +
197B TRP* 3.6 24.3 - - + +
198B SER* 3.0 31.3 + - - +
200B PRO* 3.5 22.1 - - + +
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Residues in contact with VAL 182 (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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109B PRO* 3.7 25.2 - - + +
112B LEU* 4.2 6.7 - - + -
126B TRP* 3.7 48.0 - - + -
141B PHE* 3.9 8.1 - - + -
142B GLU 3.3 17.3 - - - +
143B ALA* 4.2 2.2 - - + -
180B PHE* 4.1 9.0 - - + -
181B GLN* 1.3 76.4 - - - +
183B ARG* 1.3 71.8 + - - +
197B TRP* 3.7 3.1 - - - -
198B SER* 2.9 35.7 + - - +
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Residues in contact with ARG 183 (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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109B PRO* 4.0 3.1 - - - -
141B PHE* 3.2 10.6 - - - -
142B GLU* 2.7 61.5 + - + +
157B LEU* 4.5 9.3 - - - +
182B VAL* 1.3 75.6 - - - +
184B VAL* 1.3 62.2 + - - +
194B TRP* 3.7 39.3 - - + +
195B SER* 3.6 28.9 + - - +
196B PRO 3.6 6.7 - - - +
197B TRP* 3.5 48.8 - - + +
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Residues in contact with VAL 184 (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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106B LEU* 4.0 20.5 - - + +
107B MET 4.1 8.1 - - - +
109B PRO* 3.3 35.4 - - + -
128B ILE* 4.1 12.6 - - + -
139B LEU* 4.5 10.3 - - + -
140B GLU 3.3 9.9 - - - +
141B PHE* 3.3 33.4 - - + -
183B ARG* 1.3 75.1 - - - +
185B LYS* 1.3 65.1 + - - +
186B PRO* 4.6 1.4 - - - +
193B THR 4.5 0.3 - - - +
194B TRP* 3.6 3.8 - - - -
195B SER* 3.0 32.2 + - - +
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Residues in contact with LYS 185 (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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139B LEU* 3.4 5.6 - - - -
140B GLU* 2.7 63.8 + - - +
184B VAL* 1.3 77.6 - - - +
186B PRO* 1.3 81.5 + - + +
187B LEU* 3.7 2.0 + - - +
192B THR* 3.9 11.4 - - + +
193B THR* 3.6 18.4 - - - +
194B TRP* 3.3 54.2 - - + +
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Residues in contact with PRO 186 (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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104B LEU* 4.0 17.7 - - + -
106B LEU* 3.8 37.2 - - + +
135B PHE* 3.8 31.6 - - + -
138B HIS 3.7 0.7 - - - +
139B LEU* 3.7 12.3 - - + -
184B VAL 4.6 0.4 - - - +
185B LYS* 1.3 100.6 + - + +
187B LEU* 1.3 63.2 + - - +
188B GLN 3.5 7.6 + - - +
192B THR* 3.6 17.5 - - + +
193B THR 4.8 3.4 - - - +
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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