Contacts of the strand formed by residues 153 - 163 (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 CYS 153 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLU* 3.6 3.8 - - - +
52B VAL* 2.9 41.2 + - - -
54B ALA 3.3 12.8 + - - -
56B ALA* 3.6 25.1 - - + -
59B ILE* 3.7 27.8 - - - -
145B VAL* 3.9 9.9 - - + -
146B VAL 3.1 16.2 - - - +
148B THR* 3.2 6.8 + - - -
152B SER* 1.3 77.6 - - - +
154B VAL* 1.3 66.8 + - - +
155B ILE* 4.9 0.4 - - - -
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Residues in contact with VAL 154 (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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49B GLU* 4.0 26.0 - - + +
50B LEU 3.5 9.4 - - - +
51B GLU* 3.8 22.2 - - + +
144B HIS 3.6 0.2 - - - +
145B VAL* 3.7 0.5 - - - -
146B VAL* 2.8 40.6 + - + +
148B THR* 3.5 24.0 - - + -
153B CYS* 1.3 77.5 - - - +
155B ILE* 1.3 63.5 + - - +
156B LYS* 3.5 26.4 + - + -
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Residues in contact with ILE 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS* 3.7 2.3 - - - +
49B GLU* 3.3 5.4 - - - -
50B LEU* 2.8 39.4 + - + +
52B VAL* 3.8 21.5 - - + -
59B ILE* 3.8 31.2 - - + -
63B TYR* 3.5 34.3 - - + +
143B ILE* 4.1 9.2 - - + -
144B HIS 3.9 2.5 - - - -
145B VAL* 4.6 6.5 - - + +
153B CYS* 4.2 1.1 - - - -
154B VAL* 1.3 71.4 - - - +
156B LYS* 1.3 60.4 + - - +
157B SER* 3.6 17.3 + - - +
184B ALA* 4.1 26.5 - - + +
188B SER* 4.7 3.1 - - - +
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Residues in contact with LYS 156 (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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47B HIS* 6.1 2.9 - - - -
48B HIS 3.7 5.2 - - - +
49B GLU* 3.2 25.8 + - + +
142B THR 3.8 1.4 - - - +
143B ILE* 3.6 1.0 - - - -
144B HIS* 2.8 52.6 + - + +
146B VAL* 4.0 20.2 - - + -
154B VAL* 3.8 24.0 - - + +
155B ILE* 1.3 70.0 - - - +
157B SER* 1.3 62.3 + - - +
158B SER* 5.4 0.8 + - - -
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Residues in contact with SER 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B HIS* 3.5 2.3 + - - +
48B HIS* 2.9 45.1 + - - +
63B TYR* 4.6 0.9 + - - -
142B THR 3.3 6.5 - - - -
143B ILE* 3.9 11.4 - - - +
155B ILE* 3.6 22.1 + - - +
156B LYS* 1.3 73.1 - - - +
158B SER* 1.3 63.5 + - - +
177B THR* 5.3 0.4 - - - +
180B LEU* 3.7 37.1 + - - +
184B ALA* 4.9 1.4 - - - +
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Residues in contact with SER 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 4.7 5.7 - - - +
46B ILE 3.2 14.1 - - - -
47B HIS* 3.6 23.5 - - - +
140B MSE 3.9 0.2 - - - +
141B ASP* 3.4 3.6 - - - -
142B THR* 2.8 49.3 + - - +
156B LYS 5.4 0.6 + - - -
157B SER* 1.3 76.2 - - - +
159B THR* 1.3 66.4 + - - +
177B THR* 5.7 0.7 - - - -
180B LEU* 3.5 4.7 - - - +
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Residues in contact with THR 159 (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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44B LYS 3.8 1.2 - - - +
45B VAL* 3.5 4.5 - - - -
46B ILE* 3.0 55.3 + - + +
139B TYR* 3.9 24.7 + - - +
140B MSE 3.2 5.2 - - - -
141B ASP* 3.0 24.7 - - - +
158B SER* 1.3 75.8 - - - +
160B GLU* 1.3 59.6 + - - +
161B TYR* 4.2 8.8 + - - -
175B ILE* 4.4 0.5 - - - +
176B THR 4.6 6.5 - - - +
177B THR* 4.8 4.0 - - + -
180B LEU* 3.4 15.0 - - + -
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Residues in contact with GLU 160 (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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43B THR* 4.1 9.3 - - + +
44B LYS 3.3 10.5 - - - +
45B VAL* 3.9 19.5 - - + +
138B TYR* 4.0 16.5 - - + +
139B TYR* 3.5 1.2 - - - -
140B MSE 2.8 40.5 + - + +
158B SER 4.3 0.2 - - - -
159B THR* 1.3 74.0 + - - +
161B TYR* 1.3 64.3 + - - +
162B HIS* 2.8 32.1 + - + -
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Residues in contact with TYR 161 (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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42B VAL 3.8 0.3 - - - +
43B THR* 4.2 0.3 - - - +
44B LYS* 2.8 74.4 + - + +
46B ILE* 5.0 10.7 - - + +
136B VAL* 4.1 9.2 - - + -
138B TYR* 3.1 14.6 - - - +
139B TYR* 4.0 13.7 - + + -
159B THR* 4.2 9.2 - - - -
160B GLU* 1.3 77.1 - - - +
162B HIS* 1.3 68.6 + - - +
163B VAL* 3.4 29.6 - - + -
171B VAL* 4.3 5.6 - - + -
172B GLU* 4.0 20.6 + - - +
175B ILE* 3.6 49.7 + - + +
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Residues in contact with HIS 162 (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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41B THR* 3.6 17.9 - - - +
42B VAL 3.1 4.5 - - - +
43B THR* 3.2 23.3 + - - -
136B VAL* 3.4 6.1 - - - +
137B THR* 3.0 44.0 + - - +
138B TYR* 3.1 39.2 + + + -
160B GLU* 2.8 31.9 + - + -
161B TYR* 1.3 78.2 + - - +
163B VAL* 1.3 59.7 + - - +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR* 3.2 5.5 - - - -
42B VAL* 2.7 43.9 + - + +
44B LYS* 4.7 6.5 - - + -
135B GLY 3.5 6.3 - - - +
136B VAL* 3.8 12.8 - - + -
161B TYR* 3.4 28.0 - - + -
162B HIS* 1.3 72.8 - - - +
164B LYS* 1.3 70.0 + - - +
165B PRO 3.6 0.3 - - - -
167B PHE* 4.1 10.8 - - + -
168B VAL* 3.7 20.2 - - + +
171B VAL* 3.4 29.2 - - + -
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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