Contacts of the strand formed by residues 145 - 152 (chain B) in PDB entry 2G9I
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 GLY 145 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B GLY* 5.4 0.4 - - - -
34B ASP 2.9 11.8 + - - -
35B VAL* 3.3 4.5 - - - +
36B LEU* 2.8 31.4 + - - +
144B VAL* 1.3 73.3 - - - +
146B VAL* 1.3 58.1 + - - +
168B SER 3.4 10.5 - - - -
169B GLY 4.0 9.3 + - - -
170B VAL* 3.7 19.5 - - - -
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Residues in contact with VAL 146 (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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36B LEU* 3.3 18.8 - - + +
38B VAL* 4.9 4.7 - - + -
129B ALA* 3.7 30.7 - - + +
132B LEU* 4.3 22.0 - - + -
133B ARG* 3.8 30.3 - - + +
136B ILE* 4.7 0.7 - - + -
144B VAL* 4.4 6.3 - - + -
145B GLY* 1.3 77.4 - - - +
147B ILE* 1.3 73.9 + - - +
148B ILE* 4.3 3.8 - - + -
167B ILE* 3.2 3.8 - - - +
168B SER 2.7 37.8 + - - +
170B VAL* 4.2 0.9 - - - +
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Residues in contact with ILE 147 (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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35B VAL* 4.0 10.1 - - + -
36B LEU 2.9 9.7 + - - +
37B VAL* 3.4 7.4 - - + +
38B VAL 2.8 25.5 + - - -
146B VAL* 1.3 78.9 - - - +
148B ILE* 1.3 69.4 + - - +
149B THR* 3.9 14.8 - - + -
164B ALA* 3.7 26.9 - - + -
166B GLY 3.4 4.5 - - - +
167B ILE* 3.8 11.2 - - + -
170B VAL* 4.1 13.2 - - + -
195B ALA* 3.7 24.2 - - + +
198B ILE* 3.7 33.9 - - + -
199B ALA* 4.3 3.6 - - + -
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Residues in contact with ILE 148 (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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38B VAL* 3.2 13.0 - - + +
40B SER* 3.8 28.0 - - - -
43B ILE* 3.8 31.4 - - + -
122B PRO* 5.3 0.7 - - + -
125B PRO* 3.7 13.2 - - + +
128B SER* 3.8 6.5 - - - -
129B ALA* 3.5 36.1 - - + +
132B LEU* 5.3 0.2 - - + -
146B VAL* 4.3 7.0 - - + -
147B ILE* 1.3 76.3 - - - +
149B THR* 1.4 58.0 + - - +
164B ALA* 3.4 3.5 - - - -
165B ILE* 2.6 41.1 + - + -
166B GLY* 2.8 17.7 + - - +
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Residues in contact with THR 149 (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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37B VAL* 3.4 24.0 - - + +
38B VAL 2.8 13.7 + - - -
39B CYS* 3.7 10.8 + - - -
40B SER* 2.8 35.4 + - - -
147B ILE* 3.9 2.7 - - + -
148B ILE* 1.4 76.0 - - - +
150B ASP* 1.3 65.2 + - - +
162B GLY* 5.1 2.5 - - - -
163B PHE 3.2 9.4 - - - +
165B ILE* 4.4 1.3 - - - -
199B ALA* 3.4 37.0 - - + +
202B ALA* 5.3 0.4 - - + +
203B ASN* 5.0 5.6 + - - +
206B MSE 4.2 12.0 - - - -
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Residues in contact with ASP 150 (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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39B CYS* 6.0 1.8 - - - -
40B SER* 3.9 15.9 + - - +
41B THR* 5.6 4.5 - - - +
99B PHE* 4.8 6.6 - - - -
101B ASN* 5.1 0.5 + - - -
103B CYS* 5.6 0.2 - - - -
107B GLY* 4.2 20.3 - - - +
149B THR* 1.3 76.4 - - - +
151B THR* 1.3 78.1 + - - +
152B ASN* 3.7 15.9 + - - +
162B GLY* 3.5 1.6 - - - -
163B PHE* 2.9 29.1 + - - +
165B ILE* 4.0 22.8 - - + +
203B ASN* 5.5 0.2 - - - -
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Residues in contact with THR 151 (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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150B ASP* 1.3 83.5 + - - +
152B ASN* 1.3 73.8 + - - +
160B VAL* 4.0 23.0 - - + +
161B VAL 3.1 10.1 - - - +
203B ASN* 3.1 43.5 - - - +
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Residues in contact with ASN 152 (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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101B ASN* 2.7 29.9 + - - -
102B VAL 5.2 2.7 - - - +
103B CYS* 3.8 22.1 - - + +
104B VAL* 5.2 5.8 + - + +
107B GLY* 5.4 3.0 - - - -
150B ASP* 3.7 19.4 + - - +
151B THR* 1.3 90.8 + - - +
153B GLY* 1.3 69.7 + - - +
154B ARG* 4.3 0.7 - - - -
160B VAL* 3.2 7.7 - - - -
161B VAL 3.0 27.0 + - - -
163B PHE* 3.4 27.8 - - + +
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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