Contacts of the strand formed by residues 176 - 185 (chain B) in PDB entry 1BQU
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 GLU 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B THR* 3.3 7.1 - - - -
146B LYS* 2.9 63.5 + - + +
175B THR* 1.3 79.4 - - - +
177B TYR* 1.3 67.3 + - - +
178B VAL* 5.6 0.2 - - + -
200B SER* 4.0 16.5 - - - -
201B GLY 3.5 11.0 - - - +
202B ILE* 3.9 28.1 - - + +
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Residues in contact with TYR 177 (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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122B LEU* 3.9 14.1 - - + -
143B TYR* 4.5 9.4 - + - -
144B ARG* 3.3 23.1 - - - +
145B THR* 3.6 21.8 - - + -
171B LEU* 3.8 38.6 - - + +
172B LYS* 2.9 41.9 + - - +
175B THR* 3.5 29.8 - - + -
176B GLU* 1.3 74.1 - - - +
178B VAL* 1.3 62.0 + - - +
179B PHE* 3.5 22.8 - - + -
200B SER* 3.1 7.3 - - - -
201B GLY 2.8 31.9 + - - -
203B THR* 4.3 1.1 - - + -
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Residues in contact with VAL 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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143B TYR* 3.2 4.9 - - - +
144B ARG* 2.8 60.5 + - + +
146B LYS* 3.9 24.9 - - + +
151B TRP* 3.6 12.4 - - + -
176B GLU* 5.6 0.2 - - + -
177B TYR* 1.3 78.0 - - - +
179B PHE* 1.3 64.2 + - - +
198B GLU* 3.5 37.0 - - + +
199B ALA 3.4 4.0 - - - +
200B SER* 3.7 17.3 - - - +
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Residues in contact with PHE 179 (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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110B LEU* 4.0 6.1 - - + +
112B VAL* 3.5 35.9 - - + -
122B LEU* 3.9 22.4 - - + -
124B LEU* 3.6 33.9 - - + -
141B ILE* 5.1 0.4 - - + -
142B GLN 3.3 8.1 - - - +
143B TYR* 3.4 28.0 - + + -
151B TRP* 4.1 2.9 - - - -
168B VAL* 3.7 24.0 - - + -
171B LEU* 4.4 4.7 - - + -
177B TYR* 3.5 33.9 - - + -
178B VAL* 1.3 75.6 - - - +
180B ARG* 1.3 61.6 + - - +
198B GLU* 3.2 9.7 - - - +
199B ALA 2.7 35.1 + - - +
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Residues in contact with ARG 180 (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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403A SO4 5.0 1.2 + - - -
110B LEU* 4.1 2.9 - - - -
124B LEU* 6.1 0.4 - - - -
141B ILE* 3.7 2.6 - - - +
142B GLN* 2.8 61.1 + - + +
151B TRP* 3.5 44.5 - - + +
179B PHE* 1.3 77.4 - - - +
181B ILE* 1.3 64.6 + - - +
195B TRP* 3.5 46.7 - - + +
196B SER* 3.8 15.9 - - - +
198B GLU* 4.4 13.5 + - + -
405B SO4 3.0 46.5 + - - -
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Residues in contact with ILE 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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107B PRO* 3.9 19.3 - - + +
110B LEU* 4.1 19.7 - - + -
124B LEU* 5.9 2.0 - - + -
126B TRP* 3.6 29.8 - - + -
139B TYR* 3.5 25.4 - - + -
140B ASN 3.3 13.7 - - - +
141B ILE* 3.6 21.3 - - + -
180B ARG* 1.3 78.5 - - - +
182B ARG* 1.3 71.0 + - - +
195B TRP* 3.7 3.8 - - - -
196B SER* 2.9 42.9 + - - +
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Residues in contact with ARG 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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133A SER* 3.7 14.6 - - - -
403A SO4 2.9 42.7 + - - -
107B PRO* 4.2 2.5 - - - -
139B TYR* 3.2 8.5 - - - +
140B ASN* 2.9 53.9 + - + -
142B GLN* 5.9 0.2 - - - +
153B GLN* 5.3 0.8 + - - -
181B ILE* 1.3 79.0 - - - +
183B CYS* 1.3 62.0 + - - +
192B TRP* 3.6 36.6 - - + +
193B SER* 3.6 29.4 + - - +
194B ASP 3.8 3.8 - - - +
195B TRP* 3.6 42.5 - - + +
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Residues in contact with CYS 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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104B PRO* 3.8 15.4 - - - +
105B ASN 3.8 22.2 - - - -
107B PRO* 3.9 13.2 - - + -
129B PRO* 4.0 13.0 - - - -
137B LEU* 4.1 10.3 - - + -
138B LYS 3.2 14.6 - - - +
139B TYR* 3.6 18.2 - - + -
182B ARG* 1.3 77.7 - - - +
184B MET* 1.3 61.2 + - - +
192B TRP* 3.6 4.7 - - - -
193B SER* 2.8 37.2 + - - -
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Residues in contact with MET 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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104B PRO* 3.9 11.4 - - - -
137B LEU* 3.4 10.5 - - - -
138B LYS* 2.8 47.9 + - - +
183B CYS* 1.3 78.2 - - - +
185B LYS* 1.3 70.1 + - - +
188B GLY* 3.3 37.5 - - - +
189B LYS 3.7 2.2 - - - +
190B GLY* 3.5 29.2 - - - +
191B TYR 3.4 14.4 - - - +
192B TRP* 3.7 41.7 - - + -
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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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99B VAL* 3.5 27.1 - - - +
100B TYR* 3.7 20.3 - - + -
102B VAL* 5.5 3.6 + - + +
104B PRO* 4.8 0.8 - - - +
134B VAL 5.6 0.2 - - - -
135B ILE* 3.8 41.1 - - + +
136B ILE 3.5 7.5 - - - +
138B LYS* 3.7 1.9 - - - +
184B MET* 1.3 86.9 - - - +
186B GLU* 1.3 74.5 + - + +
187B ASP* 2.6 37.1 + - - +
188B GLY* 3.0 12.6 + - - -
189B LYS 3.5 20.6 - - - +
190B GLY* 5.3 1.1 - - - -
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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