Contacts of the strand formed by residues 118 - 126 (chain B) in PDB entry 2QBX
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 THR 118 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B VAL* 5.6 0.2 - - - -
116B LYS* 4.8 2.8 - - - +
117B GLU* 1.3 86.8 + - + +
119B PHE* 1.3 61.1 + - - +
148B THR* 3.8 13.4 - - + +
149B ILE 3.1 10.8 - - - +
150B ALA* 3.6 25.6 - - + -
187B GLN 5.0 0.2 - - - +
188B ASP* 4.9 2.6 - - - +
189B TYR* 2.7 42.1 + - - -
193B MET* 3.5 16.5 - - - +
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Residues in contact with PHE 119 (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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51B TRP* 4.9 6.1 - + + -
98B MET* 4.1 12.8 - - - -
100B PHE* 3.9 30.7 - + + -
102B VAL* 5.6 1.6 - - + -
118B THR* 1.3 74.5 - - - +
120B ASN* 1.3 68.3 + - - +
148B THR* 3.5 1.4 - - - +
149B ILE* 2.6 80.6 + - + +
186B PHE* 3.8 30.1 - + + -
187B GLN 3.4 16.6 - - - +
188B ASP* 4.8 0.4 - - - -
189B TYR* 3.6 9.2 - - - -
193B MET* 3.8 26.2 - - + -
195B LEU* 4.4 14.6 - - + -
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Residues in contact with ASN 120 (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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119B PHE* 1.3 79.2 - - - +
121B LEU* 1.3 60.0 + - - +
122B TYR* 3.6 24.9 + - + -
145B LYS* 3.4 21.3 + - - +
147B ASP 3.6 3.1 - - - +
148B THR* 2.7 32.1 + - - -
185B ALA 3.5 0.7 - - - +
186B PHE* 3.3 6.8 - - - -
187B GLN* 2.8 55.8 + - - +
189B TYR* 3.3 21.0 + - - -
411B SO4 5.6 0.2 + - - -
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Residues in contact with LEU 121 (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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96B VAL* 4.4 14.1 - - + -
98B MET* 4.0 26.2 - - + -
119B PHE 4.2 0.4 + - - -
120B ASN* 1.3 73.0 - - - +
122B TYR* 1.3 68.7 + - - +
145B LYS* 3.7 5.0 - - - +
146B VAL* 2.7 58.1 + - + -
147B ASP 3.0 16.0 + - - +
149B ILE* 4.3 10.3 - - + -
172B ARG* 4.3 6.3 - - + -
174B PHE* 5.8 0.2 - - + -
184B LEU* 4.3 11.7 - - + -
185B ALA 3.4 4.3 - - - +
186B PHE* 3.4 36.3 - - + -
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Residues in contact with TYR 122 (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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80B TRP* 3.6 23.1 - + - -
120B ASN* 3.6 24.6 + - + -
121B LEU* 1.3 75.1 - - - +
123B TYR* 1.3 61.0 + - - +
140B GLU* 3.8 23.1 + - + -
143B TRP* 3.7 30.1 - - + -
144B VAL 3.1 8.3 - - - +
145B LYS* 3.4 39.7 + - + +
146B VAL* 4.1 4.5 - - - +
184B LEU* 3.3 9.4 - - - +
185B ALA* 2.8 39.0 + - + +
187B GLN* 2.8 34.4 + - + -
411B SO4 3.3 16.3 + - - -
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Residues in contact with TYR 123 (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 TYR* 1.3 74.4 - - - +
124B TYR* 1.3 68.5 + - - +
125B GLU* 3.9 30.4 + - + -
143B TRP* 3.4 5.8 - - - -
144B VAL* 2.7 72.4 + - + +
145B LYS 5.3 0.4 - - - -
146B VAL* 3.6 15.3 - - + -
174B PHE* 3.4 48.7 - + + -
175B GLY* 4.7 10.2 + - - -
176B PRO 5.2 2.8 + - - -
177B VAL* 4.6 2.0 - - + -
182B PHE* 4.9 2.7 - - + -
183B TYR 3.2 13.0 - - - +
184B LEU* 3.7 13.9 - - + -
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Residues in contact with TYR 124 (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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127A ASP* 4.1 6.6 + - - -
179A ARG* 3.2 25.6 + - + +
123B TYR* 1.3 79.2 - - - +
125B GLU* 1.3 77.2 + - - +
126B ALA* 3.8 13.0 - - + -
130B SER* 4.6 6.7 - - - -
135B PHE* 3.4 24.6 - + - -
136B PRO* 4.0 19.1 - - + -
142B PRO* 3.6 37.0 - - + +
143B TRP* 3.6 22.9 - - + -
144B VAL* 5.4 2.0 - - - -
182B PHE* 3.2 4.4 - - - -
183B TYR* 2.9 43.7 + + - -
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Residues in contact with GLU 125 (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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179A ARG* 2.9 34.4 + - - +
405A SO4 3.9 12.6 + - - +
123B TYR* 3.9 24.2 + - + -
124B TYR* 1.3 82.4 - - - +
126B ALA* 1.3 61.0 + - - +
176B PRO 4.1 5.7 - - - +
177B VAL* 3.3 29.5 - - + +
178B SER* 3.0 26.8 + - - -
179B ARG* 3.4 19.6 + - - +
181B GLY 3.3 10.2 - - - +
182B PHE* 3.9 4.5 - - + -
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Residues in contact with ALA 126 (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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127A ASP* 3.5 12.6 - - - +
179A ARG* 4.2 1.1 - - - +
85B PHE* 3.8 4.1 - - + -
124B TYR* 3.8 14.3 + - + -
125B GLU* 1.3 76.9 - - - +
127B ASP* 1.3 64.8 + - - +
128B PHE 3.3 20.0 - - - +
130B SER* 3.9 6.3 - - - +
179B ARG* 4.2 1.8 - - - +
180B SER 3.4 2.9 + - - -
181B GLY 2.8 33.2 + - - +
183B TYR* 4.1 13.2 - - + -
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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