Contacts of the strand formed by residues 136 - 147 (chain B) in PDB entry 2VQ5
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B TYR* 3.3 29.4 + - + +
132B LEU* 3.4 35.9 - - + +
134B LEU 3.3 2.2 - - - +
135B GLY* 1.3 76.4 - - - +
137B THR* 1.3 59.5 + - - +
138B TYR 3.2 29.8 - - - +
139B TYR* 4.2 7.4 - - + -
161B TYR* 4.1 11.7 - - + -
162B HIS 3.4 7.2 - - - +
163B VAL* 3.8 20.9 - - + -
171B VAL* 4.2 5.4 - - + -
175B ILE* 4.2 15.0 - - + -
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Residues in contact with THR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR* 3.5 26.1 - - + +
132B LEU* 4.5 4.8 - - - +
135B GLY 4.2 2.7 - - - +
136B VAL* 1.3 76.5 - - - +
138B TYR* 1.3 64.5 + - - +
162B HIS* 3.0 18.8 + - - +
164B LYS* 4.0 27.1 - - - -
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Residues in contact with TYR 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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123B LYS* 5.8 2.3 + - - -
125B GLN* 4.0 17.0 - - - -
132B LEU* 4.4 2.2 - - - +
136B VAL* 3.2 8.9 - - - +
137B THR* 1.3 84.9 + - - +
139B TYR* 1.3 62.3 + - - +
140B MSE 3.2 47.1 - - + +
160B GLU* 4.0 23.1 + - - -
161B TYR* 3.1 5.2 - - - -
162B HIS* 3.1 66.5 + + + -
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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
----------------------------------------------------------
110B GLU* 4.9 2.0 - - - -
125B GLN* 3.3 10.1 + - - +
126B MSE 3.0 69.3 + - + +
131B TYR* 3.6 35.2 - + + -
132B LEU* 4.1 13.4 - - + +
136B VAL* 4.2 6.7 - - + -
138B TYR* 1.3 78.7 - - - +
140B MSE 1.3 64.0 + - - +
141B ASP* 3.5 30.4 + - - -
159B THR* 3.9 18.7 + - - +
160B GLU 3.5 3.6 - - - -
161B TYR* 4.0 14.6 - - + -
175B ILE* 4.0 24.6 - - + +
176B THR 4.6 5.0 + - - -
179B PRO* 5.4 7.3 - - - +
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Residues in contact with MSE 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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113B ILE* 3.9 23.1 - - + -
123B LYS* 4.1 20.4 - - + +
124B VAL 3.8 13.5 - - - +
125B GLN* 3.6 46.2 - - + +
138B TYR* 3.2 38.6 - - + +
139B TYR* 1.3 78.8 - - - +
141B ASP* 1.3 65.4 - - - +
142B THR* 4.1 4.3 + - - +
158B SER 3.9 0.3 - - - +
159B THR* 3.2 3.0 - - - -
160B GLU* 2.8 42.0 + - + +
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Residues in contact with ASP 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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110B GLU* 4.0 8.0 - - - +
122B LYS 3.8 0.4 - - - +
123B LYS* 3.3 6.1 - - - +
124B VAL* 2.9 40.7 + - + +
139B TYR* 3.5 20.9 + - - -
140B MSE 1.3 73.5 - - - +
142B THR* 1.3 62.0 + - - +
143B ILE* 4.3 1.1 - - - +
158B SER 3.4 2.7 - - - +
159B THR* 3.0 28.1 - - - +
180B LEU* 4.0 14.6 - - + -
1198B HBA 2.9 42.3 + - + -
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Residues in contact with THR 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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121B LEU* 4.0 31.0 - - + -
122B LYS 3.3 7.9 - - - +
123B LYS* 3.7 21.0 - - + +
140B MSE 4.1 5.7 + - - +
141B ASP* 1.3 76.9 + - - +
143B ILE* 1.3 67.7 + - - +
144B HIS* 5.0 3.1 - - + +
156B LYS 3.8 0.9 - - - +
157B SER* 3.3 2.9 - - - -
158B SER* 2.8 48.0 + - - +
180B LEU* 4.6 0.2 - - - +
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Residues in contact with ILE 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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60B TRP* 4.8 2.0 - - + -
63B TYR* 3.6 40.4 - - + -
120B ARG 3.8 0.9 - - - +
121B LEU* 3.3 5.4 - - - +
122B LYS* 2.9 49.2 + - + +
124B VAL* 5.0 0.9 - - + -
141B ASP* 4.7 2.2 - - + +
142B THR* 1.3 79.8 - - - +
144B HIS* 1.3 64.8 + - - +
145B VAL* 4.5 6.3 - - + -
155B ILE* 4.1 14.6 - - + -
156B LYS 3.6 2.9 - - - -
157B SER* 3.9 7.0 - - - +
180B LEU* 3.6 22.2 - - + -
1198B HBA 3.5 39.3 - - + -
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Residues in contact with HIS 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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119B HIS* 2.9 36.0 + - + +
120B ARG 3.4 4.7 - - - -
121B LEU* 4.0 22.1 - - + +
142B THR* 5.0 3.1 - - + -
143B ILE* 1.3 76.8 - - - +
145B VAL* 1.3 64.4 + - - +
146B VAL* 3.6 27.8 + - + +
154B VAL 3.6 0.2 - - - +
156B LYS* 2.8 51.6 + - + +
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Residues in contact with VAL 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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56B ALA* 3.5 34.8 - - + +
59B ILE* 3.9 22.7 - - + -
60B TRP* 4.1 17.0 - - + +
63B TYR* 4.1 18.2 - - + -
119B HIS 4.2 3.8 - - - +
120B ARG* 3.0 41.4 + - + +
143B ILE* 4.5 6.3 - - + -
144B HIS* 1.3 71.3 + - - +
146B VAL* 1.3 59.1 + - - +
147B PRO* 4.0 0.3 - - - +
153B CYS* 3.9 15.9 - - - -
154B VAL 3.7 4.7 - - - +
155B ILE* 4.6 5.6 - - + +
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Residues in contact with VAL 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA* 4.1 0.2 - - - -
144B HIS* 3.6 39.5 - - + +
145B VAL* 1.3 73.6 - - - +
147B PRO* 1.4 80.1 - - + +
148B THR* 5.7 2.5 - - + -
153B CYS* 3.1 3.8 - - - +
154B VAL* 2.8 43.5 + - + +
156B LYS* 4.0 22.9 - - + -
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Residues in contact with PRO 147 (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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56B ALA* 3.7 17.2 - - + +
120B ARG* 3.2 34.8 - - - +
145B VAL 4.0 0.2 - - - +
146B VAL* 1.4 97.7 - - + +
148B THR* 1.3 63.0 + - - +
149B GLY 4.3 10.5 - - - +
152B SER 3.8 4.5 - - - +
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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