Contacts of the strand formed by residues 132 - 140 (chain D) in PDB entry 2VT5
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 132 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169C SER* 4.2 4.3 - - - -
48D VAL* 3.9 20.9 - - + -
120D LEU* 3.8 21.8 - - + -
121D ASP 3.4 7.4 - - - +
122D GLY 3.6 29.8 - - - +
123D SER* 3.8 3.6 - - - +
126D ILE* 3.9 23.3 - - + -
130D VAL* 3.7 8.7 - - + +
131D SER* 1.3 77.3 - - - +
133D GLY* 1.3 58.7 + - - +
166D LEU* 3.6 9.2 - - - +
167D TYR* 2.9 35.7 + - + +
247D SER* 3.9 2.9 - - - -
249D VAL* 4.9 1.3 - - - -
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Residues in contact with GLY 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D LEU* 3.3 3.8 - - - -
121D ASP* 2.5 42.4 + - - +
132D VAL* 1.3 77.3 - - - +
134D THR* 1.3 61.9 + - - -
165D ALA 3.1 12.8 - - - -
167D TYR* 3.6 9.1 - - - -
249D VAL* 3.9 17.4 - - - +
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Residues in contact with THR 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D LEU* 5.2 4.3 - - + -
41D VAL* 4.5 10.5 - - + -
44D ILE* 3.6 3.5 - - - +
81D VAL* 4.5 14.6 - - + -
117D PHE* 5.3 3.1 - - + -
118D ASP 3.2 11.0 - - - +
119D PRO* 2.7 25.1 + - + +
133D GLY* 1.3 72.0 - - - -
135D ILE* 1.3 69.3 + - - +
136D PHE* 4.6 7.8 - - + -
164D TYR* 3.0 7.4 - - - +
165D ALA* 2.8 36.2 + - - -
167D TYR* 2.7 29.8 + - - -
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Residues in contact with ILE 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D PHE* 3.1 7.6 - - - +
118D ASP* 2.9 31.4 + - + +
121D ASP* 3.8 27.1 - - + +
134D THR* 1.3 74.9 - - - +
136D PHE* 1.3 63.0 + - - +
163D GLY 3.6 9.0 - - - +
248D MET* 4.1 14.6 - - - -
249D VAL* 3.5 31.6 - - + -
279D TYR 3.4 24.2 - - - +
280D GLU* 4.0 14.8 - - + +
283D PRO* 3.6 22.0 - - + -
284D MET* 4.2 13.5 - - + -
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Residues in contact with PHE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D LEU* 4.3 2.9 - - + -
37D LEU* 3.7 39.0 - - + -
41D VAL* 5.9 1.6 - - + -
115D VAL* 4.4 7.0 - - + -
116D CYS 3.2 9.0 - - - +
117D PHE* 4.1 8.5 - - + -
134D THR* 4.6 8.1 - - + -
135D ILE* 1.3 78.5 - - - +
137D GLY* 1.3 57.4 + - - +
138D ILE* 3.8 22.9 - - + -
162D ALA* 3.4 7.1 - - - -
163D GLY* 3.1 64.9 + - - -
164D TYR* 3.6 12.3 - - - -
165D ALA 4.7 0.4 - - - -
173D LEU* 4.4 19.3 - - + -
174D VAL 4.5 2.2 - - - -
175D LEU* 4.2 16.6 - - + -
283D PRO* 3.3 12.7 - - - +
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Residues in contact with GLY 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D VAL 3.7 1.2 - - - +
115D VAL* 3.4 4.0 - - - +
116D CYS* 2.8 40.3 + - - +
136D PHE* 1.3 74.7 - - - +
138D ILE* 1.3 63.4 + - - -
139D TYR* 4.4 3.0 - - - -
159D LEU* 3.6 20.4 - - - -
161D ALA 3.7 3.6 - - - -
162D ALA* 4.0 2.5 - - - -
278D LEU 5.3 0.4 - - - -
283D PRO* 4.1 8.2 - - - +
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Residues in contact with ILE 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 4.2 9.4 - - + -
33D LEU* 3.8 32.8 - - + -
34D LEU* 3.7 30.5 - - + -
113D TYR* 3.7 28.7 - - + -
114D VAL 3.4 3.6 - - - +
115D VAL* 4.3 10.5 - - + -
136D PHE* 3.8 18.2 - - + -
137D GLY* 1.3 76.5 - - - +
139D TYR* 1.3 62.5 + - - +
159D LEU* 3.6 4.4 - - - +
160D VAL* 2.8 29.9 + - + +
161D ALA* 2.8 31.1 + - + +
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Residues in contact with TYR 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D TYR* 3.2 13.8 - - - -
114D VAL* 2.7 49.9 + - + +
116D CYS* 4.1 27.1 - - + -
137D GLY 4.4 3.1 - - - -
138D ILE* 1.3 75.4 - - - +
140D ARG* 1.3 58.8 + - - +
152D ALA* 4.7 5.8 - - - -
154D GLN* 3.5 50.8 + - + +
155D PRO 3.4 20.2 - - - -
156D GLY* 3.4 19.8 + - - -
158D ASN 3.7 12.8 - - - -
159D LEU* 3.5 32.3 - - + +
160D VAL* 4.3 3.8 - - - -
278D LEU* 5.1 5.6 + - + +
282D ASN* 3.9 10.4 + - - +
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Residues in contact with ARG 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D LYS* 3.9 21.8 - - + +
113D TYR* 4.0 16.4 - - + -
114D VAL* 4.7 0.2 - - - -
139D TYR* 1.3 72.5 - - - +
141D LYS* 1.3 74.5 + - - +
142D LYS* 3.5 30.6 + - - +
154D GLN* 3.0 23.3 + - - +
158D ASN 4.8 2.2 + - - +
160D VAL* 3.8 19.3 - - + +
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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