Contacts of the strand formed by residues 132 - 140 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48G VAL* 3.8 28.9 - - + -
120G LEU* 4.0 12.3 - - + -
121G ASP 3.4 16.2 - - - +
122G GLY 3.7 20.2 - - - +
123G SER* 3.8 11.2 - - - +
126G ILE* 3.9 19.7 - - + -
130G VAL* 3.9 2.9 - - + +
131G SER* 1.3 78.6 - - - +
133G GLY* 1.3 58.1 + - - +
166G LEU* 3.7 8.9 - - - +
167G TYR* 2.9 36.8 + - + -
247G SER* 3.9 2.0 - - - -
249G VAL* 4.7 2.0 - - - -
169H SER* 4.0 7.6 - - - -
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Residues in contact with GLY 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119G PRO 4.3 0.2 - - - -
120G LEU* 3.3 4.0 - - - -
121G ASP* 2.6 39.3 + - - +
132G VAL* 1.3 79.2 - - - +
134G THR* 1.3 63.0 + - - -
165G ALA 3.1 13.5 - - - -
167G TYR* 3.5 9.4 - - - -
249G VAL* 3.8 16.1 - - - +
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Residues in contact with THR 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G LEU* 5.6 4.0 - - + -
41G VAL* 4.6 10.1 - - + -
44G ILE* 3.9 2.9 - - - +
81G VAL* 4.5 15.3 - - + -
117G PHE* 5.1 4.0 - - + -
118G ASP 3.2 15.3 - - - +
119G PRO* 2.7 24.7 + - + +
133G GLY* 1.3 70.5 - - - -
135G ILE* 1.3 66.2 + - - +
136G PHE* 4.1 7.9 + - + -
164G TYR* 3.1 6.1 - - - +
165G ALA* 2.9 36.2 + - - -
167G TYR* 2.7 28.4 + - - -
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Residues in contact with ILE 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G PHE* 3.1 7.8 - - - +
118G ASP* 2.9 30.8 + - + +
121G ASP* 3.9 25.1 - - + +
134G THR* 1.3 75.2 - - - +
136G PHE* 1.3 64.2 + - - +
163G GLY 3.8 7.0 - - - +
248G MET* 3.9 17.5 - - - -
249G VAL* 3.5 27.1 - - + -
279G TYR 3.4 24.0 - - - +
280G GLU* 4.2 4.5 - - + +
283G PRO* 3.5 22.9 - - + -
284G MET* 3.5 28.9 - - + -
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Residues in contact with PHE 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G LEU* 4.3 2.2 - - + -
37G LEU* 3.5 38.4 - - + -
41G VAL* 5.8 2.7 - - + -
115G VAL* 4.7 6.3 - - + -
116G CYS 3.3 8.5 - - - +
117G PHE* 4.1 9.2 - - + -
134G THR* 4.4 8.5 - - + -
135G ILE* 1.3 78.1 - - - +
137G GLY* 1.3 58.2 + - - +
138G ILE* 3.7 23.8 - - + -
162G ALA* 3.3 7.2 - - - -
163G GLY* 2.9 66.1 + - - +
164G TYR* 3.7 12.8 - - - -
165G ALA 4.7 0.4 - - - -
173G LEU* 4.2 21.3 - - + -
175G LEU* 4.0 21.3 - - + -
283G PRO* 3.3 12.1 - - - +
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Residues in contact with GLY 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G VAL 3.9 0.3 - - - +
115G VAL* 3.5 4.5 - - - +
116G CYS* 2.8 36.0 + - - +
136G PHE* 1.3 74.3 - - - +
138G ILE* 1.3 63.6 + - - -
139G TYR* 4.2 5.3 + - - -
159G LEU* 3.6 18.8 - - - -
161G ALA 3.7 4.3 - - - -
162G ALA* 3.9 3.4 - - - -
278G LEU 5.4 0.4 - - - -
283G PRO* 3.9 9.4 - - - +
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Residues in contact with ILE 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G LEU* 4.0 14.1 - - + -
33G LEU* 3.9 16.6 - - + -
34G LEU* 3.7 30.3 - - + -
37G LEU* 4.6 0.9 - - + -
113G TYR* 3.8 30.5 - - + -
114G VAL 3.5 6.1 - - - +
115G VAL* 4.1 15.5 - - + -
136G PHE* 3.7 20.6 - - + -
137G GLY* 1.3 77.0 - - - +
139G TYR* 1.3 65.0 + - - +
159G LEU* 3.4 5.1 - - - +
160G VAL* 2.8 30.7 + - + +
161G ALA* 2.7 26.3 + - + +
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Residues in contact with TYR 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G TYR* 3.2 11.1 - - - -
114G VAL* 2.6 55.3 + - + +
116G CYS* 4.1 26.2 - - + -
137G GLY* 4.4 4.0 - - - -
138G ILE* 1.3 75.2 - - - +
140G ARG* 1.3 56.2 + - - +
151G ASP 5.5 0.2 - - - -
152G ALA 4.8 6.1 - - - -
154G GLN* 3.7 44.4 + - + +
155G PRO 3.5 19.5 - - - -
156G GLY* 3.5 19.6 - - - -
158G ASN* 3.7 17.0 - - + -
159G LEU* 3.4 33.3 - - + +
160G VAL* 4.7 0.4 - - - +
278G LEU* 4.9 5.7 + - + +
282G ASN* 3.6 14.6 + - - +
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Residues in contact with ARG 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112G LYS* 3.7 27.3 - - + +
113G TYR* 3.9 25.9 + - + -
139G TYR* 1.3 71.0 - - - +
141G LYS* 1.3 73.5 + - - +
142G LYS* 3.2 2.3 + - - +
154G GLN* 3.0 21.7 + - - +
158G ASN 5.0 2.8 + - - -
160G VAL* 3.4 34.9 - - - +
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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