Contacts of the strand formed by residues 161 - 167 (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 ALA 161 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30G LEU* 4.8 7.9 - - + -
34G LEU* 5.0 2.0 - - + -
137G GLY* 3.7 0.2 - - - -
138G ILE* 2.7 51.0 + - + +
159G LEU* 3.6 2.8 - - - +
160G VAL* 1.3 86.9 - - + +
162G ALA* 1.3 58.5 + - - +
175G LEU* 4.7 6.5 - - + -
176G ALA 3.4 14.4 - - - +
177G MET* 4.1 14.6 - - + -
286G TYR* 4.2 4.7 + - - -
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Residues in contact with ALA 162 (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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136G PHE* 3.3 27.3 - - - +
137G GLY* 3.9 6.7 - - - -
159G LEU* 4.3 3.6 - - + -
161G ALA* 1.3 77.6 - - - +
163G GLY* 1.3 54.5 + - - +
175G LEU* 3.8 1.7 - - - +
176G ALA* 2.7 39.6 + - - +
283G PRO* 4.0 19.1 - - + +
286G TYR* 3.7 21.9 - - + -
287G VAL* 4.4 1.6 - - - -
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Residues in contact with GLY 163 (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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135G ILE* 3.8 4.6 - - - +
136G PHE* 2.9 41.1 + - - +
162G ALA* 1.3 77.0 - - - +
164G TYR* 1.3 66.5 + - - +
174G VAL 3.0 13.0 - - - -
283G PRO* 4.5 1.7 - - - +
287G VAL* 3.8 15.9 - - - +
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Residues in contact with TYR 164 (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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134G THR 3.1 14.4 - - - +
135G ILE* 4.2 2.7 - - - -
136G PHE* 3.7 8.4 - - - -
163G GLY* 1.3 79.0 - - - +
165G ALA* 1.3 61.2 + - - +
166G LEU* 4.3 4.5 - - + -
173G LEU* 3.4 3.4 - - - +
174G VAL* 2.7 67.7 + - + +
249G VAL* 3.3 22.7 - - + -
252G VAL* 4.4 4.1 - - + -
253G HIS* 2.7 50.6 + + + -
256G LEU* 3.5 15.6 - - - +
284G MET* 3.5 40.4 - - + -
287G VAL* 4.2 13.5 - - + -
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Residues in contact with ALA 165 (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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41G VAL* 3.6 38.1 - - + -
133G GLY* 3.1 6.5 - - - -
134G THR* 2.9 31.0 + - - -
136G PHE* 4.7 1.8 - - - -
164G TYR* 1.3 74.2 - - - +
166G LEU* 1.3 59.3 + - - +
167G TYR* 3.7 18.2 - - + +
171G THR* 5.0 1.1 - - + -
172G MET 3.2 10.8 - - - +
173G LEU* 4.3 3.8 - - + +
249G VAL* 3.6 4.7 - - - +
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Residues in contact with LEU 166 (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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131G SER* 4.0 15.7 - - - -
132G VAL 3.7 14.1 - - - +
164G TYR* 4.1 7.1 - - + -
165G ALA* 1.3 71.9 - - - +
167G TYR* 1.3 61.3 + - - +
168G GLY 3.9 6.5 - - - +
170G ALA 3.4 2.8 - - - +
171G THR* 3.1 6.4 - - - +
172G MET* 2.8 39.9 + - + +
249G VAL* 3.8 11.4 - - + -
250G ALA* 3.8 31.0 - - - +
253G HIS* 3.6 36.8 - - + -
128H CYS 3.9 3.4 - - - +
129H LEU* 3.9 25.6 - - + +
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Residues in contact with TYR 167 (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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41G VAL* 3.8 14.8 - - + +
44G ILE* 3.5 24.9 - - + +
45G SER* 3.8 26.7 - - - -
48G VAL* 4.0 21.5 - - + -
49G ARG* 3.8 5.4 - - - +
120G LEU* 3.9 4.5 - - + -
131G SER* 3.7 3.5 - - - -
132G VAL* 2.9 50.6 + - + +
133G GLY* 3.5 15.3 - - - -
134G THR* 2.7 32.5 + - - -
165G ALA* 3.7 15.7 - - + +
166G LEU* 1.3 68.7 - - - +
168G GLY* 1.3 63.4 + - - +
171G THR* 3.7 30.5 - - + +
169H SER* 3.7 9.7 - - - -
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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