Contacts of the strand formed by residues 136 - 149 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A TYR* 3.2 32.1 + - + +
132A LEU* 3.3 34.6 - - + +
135A GLY* 1.3 78.2 - - - +
137A THR* 1.3 60.6 + - - +
138A TYR 3.2 30.7 - - - +
139A TYR* 4.3 7.2 - - + -
161A TYR* 4.0 11.7 - - + -
162A HIS 3.3 6.5 - - - +
163A VAL* 3.5 21.1 - - + -
171A VAL* 4.2 7.2 - - + -
175A ILE* 4.2 14.4 - - + -
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Residues in contact with THR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLN* 3.5 25.2 + - + +
39A VAL* 5.7 0.2 - - - -
41A THR* 3.5 21.1 + - + +
132A LEU* 4.2 6.7 - - - +
135A GLY 4.4 2.0 - - - +
136A VAL* 1.3 75.6 - - - +
138A TYR* 1.3 63.5 + - - +
162A HIS* 2.8 22.2 + - - +
164A LYS* 3.6 24.2 - - - +
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Residues in contact with TYR 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLN* 4.0 23.1 - - - -
126A MSE 5.7 0.4 - - - -
132A LEU* 4.1 2.7 - - - +
136A VAL* 3.2 8.4 - - - +
137A THR* 1.3 84.0 + - - +
139A TYR* 1.3 60.5 + - - +
140A MSE 3.4 46.8 - - + +
160A GLU* 3.9 19.4 + - - -
161A TYR* 3.1 4.0 - - - -
162A HIS* 2.9 69.6 + + + -
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Residues in contact with TYR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A GLU* 4.8 5.6 - - - -
124A VAL 5.5 0.2 - - - -
125A GLN* 3.3 10.8 + - - +
126A MSE 3.0 71.0 + - + +
131A TYR* 3.6 28.6 - + - -
132A LEU* 4.4 3.2 - - + +
136A VAL* 4.3 3.8 - - + -
138A TYR* 1.3 77.6 - - - +
140A MSE 1.3 64.0 + - - +
141A ASP* 3.5 26.8 + - - -
159A THR* 3.4 26.2 + - + +
160A GLU 3.5 4.0 - - - -
161A TYR* 3.9 15.0 - - + -
175A ILE* 3.9 21.9 - - + +
176A THR 4.6 5.5 + - - -
179A PRO* 5.6 5.4 - - - +
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Residues in contact with MSE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ILE* 4.2 14.1 - - + -
123A LYS* 4.0 20.6 - - + +
124A VAL 3.7 20.2 - - - +
125A GLN* 3.6 43.1 - - + +
138A TYR* 3.4 42.8 - - + +
139A TYR* 1.3 75.5 - - - +
141A ASP* 1.3 68.6 + - - +
142A THR* 4.1 10.1 + - - +
158A SER 3.7 0.5 - - - +
159A THR* 3.4 2.0 - - - -
160A GLU* 2.9 42.4 + - + +
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Residues in contact with ASP 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A GLU* 4.0 13.6 - - - +
123A LYS* 3.3 5.7 - - - +
124A VAL* 2.8 48.6 + - + +
139A TYR* 3.5 21.9 + - - -
140A MSE 1.3 73.3 - - - +
142A THR* 1.3 61.9 + - - +
143A ILE* 4.9 2.9 - - + -
158A SER 3.3 2.9 - - - +
159A THR* 2.6 32.4 + - - -
180A LEU* 3.7 30.7 - - + +
1203A HBA 4.9 5.1 - - + -
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Residues in contact with THR 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LEU* 3.6 29.2 - - + -
122A LYS 3.4 6.5 - - - +
123A LYS* 2.8 33.0 + - + +
140A MSE 4.3 6.1 + - - +
141A ASP* 1.3 77.6 + - - +
143A ILE* 1.3 66.7 + - - +
144A HIS* 4.2 2.2 - - + +
156A LYS 3.5 1.6 - - - +
157A SER* 3.3 2.8 - - - -
158A SER* 2.8 49.8 + - - +
180A LEU* 4.8 0.3 - - - +
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A TRP* 4.6 1.8 - - + -
63A TYR* 3.8 25.6 - - + +
120A ARG 3.6 1.6 - - - +
121A LEU* 3.3 4.0 - - - +
122A LYS* 2.7 59.9 + - + +
124A VAL* 4.7 6.3 - - + -
141A ASP* 4.9 2.0 - - + -
142A THR* 1.3 80.8 - - - +
144A HIS* 1.3 61.4 + - - +
145A VAL* 4.2 7.9 - - + -
155A ILE* 3.8 28.0 - - + -
156A LYS 3.4 2.5 - - - -
157A SER* 4.0 12.1 - - - +
180A LEU* 4.1 22.4 - - + -
1203A HBA 4.2 26.7 - - + +
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Residues in contact with HIS 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A HIS* 2.7 37.3 + - + +
120A ARG 3.2 8.3 - - - -
121A LEU* 3.6 22.2 - - + +
142A THR* 4.2 2.4 - - + -
143A ILE* 1.3 73.2 - - - +
145A VAL* 1.3 63.3 + - - +
146A VAL* 3.5 21.9 + - + +
154A VAL 3.4 2.3 - - - +
156A LYS* 2.8 48.7 + - + +
1202A CL 3.4 25.2 - - + +
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ALA* 3.8 22.7 - - - +
59A ILE* 3.9 23.3 - - + -
60A TRP* 4.0 20.9 - - + -
63A TYR* 4.2 10.3 - - + -
119A HIS 4.3 0.9 - - - +
120A ARG* 2.9 41.4 + - + +
143A ILE* 4.4 9.9 - - + -
144A HIS* 1.3 75.3 + - - +
146A VAL* 1.3 62.7 + - - +
147A PRO* 3.9 0.9 - - - +
153A CYS* 3.7 27.1 - - - -
154A VAL 3.5 4.5 - - - +
155A ILE* 4.5 5.4 - - + -
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ALA* 4.3 0.2 - - - -
144A HIS* 3.5 38.4 - - + +
145A VAL* 1.3 75.6 - - - +
147A PRO* 1.4 80.6 - - + +
148A THR* 5.4 0.2 - - + -
153A CYS* 3.2 4.2 - - - -
154A VAL* 2.8 52.9 + - + +
156A LYS* 3.8 25.4 - - + +
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Residues in contact with PRO 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ALA* 3.8 17.0 - - + -
120A ARG* 3.3 31.9 - - - +
145A VAL 3.9 1.8 - - - +
146A VAL* 1.4 99.7 - - + +
148A THR* 1.3 62.9 + - - +
149A GLY 4.4 11.2 - - - +
152A SER 3.8 7.4 - - - +
1201A CL 4.0 10.3 - - + -
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Residues in contact with THR 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 2.8 29.8 + - - +
146A VAL* 3.5 2.0 + - + +
147A PRO* 1.3 78.6 - - - +
149A GLY* 1.3 55.1 - - - +
152A SER* 2.8 33.6 + - - -
153A CYS 3.4 1.2 + - - -
154A VAL* 3.7 30.3 - - + +
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Residues in contact with GLY 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A SER* 5.5 1.0 + - - -
56A ALA 5.7 0.3 + - - -
147A PRO* 3.5 10.9 - - - +
148A THR* 1.3 80.9 + - - +
150A LYS* 1.3 66.6 + - - +
151A ASP 3.3 2.9 - - - -
152A SER* 3.1 18.7 + - - +
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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