Contacts of the strand formed by residues 137 - 145 (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 LEU 137 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B PRO* 4.2 1.6 - - + -
128B ASN* 4.0 10.8 - - + +
129B PRO* 3.8 29.4 - - + -
131B ILE* 4.2 7.9 - - + -
132B LYS* 4.1 13.5 - - + -
135B ILE* 3.6 35.7 - - + +
136B ILE* 1.3 73.7 - - - +
138B LYS* 1.3 61.8 + - - +
139B TYR* 3.8 26.5 - - + +
160B ALA 3.8 0.5 - - - +
161B SER* 3.0 9.2 - - - -
162B THR* 2.8 35.9 + - - +
183B CYS* 4.1 17.0 - - - -
184B MET 3.4 12.3 - - - +
186B GLU* 4.3 1.8 - - - -
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Residues in contact with LYS 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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72A TYR* 5.8 2.2 - - - +
73A PHE* 3.9 21.0 - - + -
133A SER 5.0 0.8 + - - -
134A VAL* 4.0 24.0 - - - +
137B LEU* 1.3 74.5 - - - +
139B TYR* 1.3 65.9 + - - +
156B PRO* 5.8 0.4 - - + +
159B THR 3.7 5.2 - - - +
160B ALA* 3.7 22.4 - - - +
183B CYS* 3.2 7.8 - - - +
184B MET* 2.8 53.4 + - + +
185B LYS 3.7 13.2 - - - +
186B GLU* 3.6 18.7 + - - +
187B ASP 5.0 0.4 - - - -
188B GLY* 3.9 15.7 - - - +
192B TRP* 3.7 23.0 - - + +
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Residues in contact with TYR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PRO* 4.3 3.8 - - + -
126B TRP* 3.8 9.2 - + - -
128B ASN* 2.6 33.3 + - - -
137B LEU* 3.8 18.7 - - + +
138B LYS* 1.3 75.0 - - - +
140B ASN* 1.3 71.5 + - - +
141B ILE* 4.4 1.3 - - + -
156B PRO* 4.4 6.4 - - - +
159B THR* 2.8 46.4 + - - +
161B SER 3.3 23.6 - - - -
162B THR* 3.5 6.9 - - - +
163B ARG* 3.0 34.2 + - + -
181B ILE* 3.5 28.3 - - + -
182B ARG 3.2 7.9 - - - +
183B CYS* 3.6 24.9 - - + -
192B TRP* 3.9 6.0 - - - -
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Residues in contact with ASN 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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133A SER* 3.0 31.3 + - - -
139B TYR* 1.3 80.8 + - - +
141B ILE* 1.3 62.2 + - - +
142B GLN 4.0 0.2 - - - -
153B GLN* 3.5 20.1 + - - +
154B ILE 5.6 0.9 - - - -
156B PRO* 3.8 11.9 - - - +
159B THR* 4.6 0.4 - - - -
181B ILE* 3.3 5.7 - - - +
182B ARG* 2.9 70.7 + - + +
192B TRP* 3.5 11.6 - - - -
195B TRP* 3.6 7.6 - - + -
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Residues in contact with ILE 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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124B LEU* 3.7 24.2 - - + -
126B TRP* 3.9 17.7 - - + -
139B TYR* 4.1 4.0 - - + -
140B ASN* 1.3 72.6 - - - +
142B GLN* 1.3 68.1 + - - +
143B TYR* 5.4 0.2 - - + -
153B GLN* 3.5 5.0 - - - +
154B ILE* 2.9 49.8 + - + +
159B THR* 3.6 29.5 + - + -
166B PHE* 3.7 28.7 - - + -
168B VAL* 5.0 4.7 - - + -
179B PHE* 5.1 0.7 - - + -
180B ARG 3.7 7.2 - - - +
181B ILE* 3.6 20.0 - - + -
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Residues in contact with GLN 142 (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 5.3 3.6 + - - -
141B ILE* 1.3 81.9 - - - +
143B TYR* 1.3 64.0 + - - +
151B TRP* 3.5 25.6 - - + +
152B SER 3.1 11.9 - - - +
153B GLN* 3.0 31.3 + - + +
179B PHE* 3.3 7.4 - - - +
180B ARG* 2.8 68.8 + - + +
182B ARG* 5.9 0.2 - - - +
195B TRP* 3.3 26.9 - - + -
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Residues in contact with TYR 143 (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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141B ILE* 5.4 0.2 - - + -
142B GLN* 1.3 77.8 - - - +
144B ARG* 1.3 65.7 + - - +
151B TRP* 3.8 2.2 - - - -
152B SER* 2.8 67.7 + - - -
153B GLN 4.2 4.0 + - - -
154B ILE* 3.5 39.8 - - + +
168B VAL* 4.4 7.2 - - + -
169B GLN 5.6 1.3 + - - -
171B LEU* 4.0 28.3 - - + -
177B TYR* 4.5 9.6 - + + -
178B VAL 3.2 8.3 - - - +
179B PHE* 3.4 28.7 - + + -
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Residues in contact with ARG 144 (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* 1.3 79.9 - - - +
145B THR* 1.3 83.0 + - - +
146B LYS* 3.1 23.0 + - - +
148B ALA* 3.8 17.6 + - + -
149B SER 5.3 0.9 - - - -
150B THR 3.3 30.1 - - - +
151B TRP* 3.3 41.5 - - + +
152B SER* 4.7 2.9 - - - +
177B TYR* 3.3 10.7 - - - -
178B VAL* 2.8 43.9 + - + +
198B GLU* 3.9 20.4 + - - -
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Residues in contact with THR 145 (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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144B ARG* 1.3 89.7 + - - +
146B LYS* 1.3 65.9 + - - +
147B ASP* 3.6 6.2 + - - +
148B ALA* 3.1 31.2 + - + +
172B LYS* 3.9 20.4 - - - +
175B THR* 3.9 16.8 - - + -
176B GLU 3.3 10.5 - - - -
177B TYR* 3.6 23.6 - - + +
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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