Contacts of the strand formed by residues 167 - 171 (chain J) in PDB entry 3EXG
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 167 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112J ILE* 3.2 8.7 + - - +
113J VAL* 3.2 5.6 - - + +
114J PHE* 2.9 26.6 + - - +
143J LYS* 3.4 31.2 - - + +
145J VAL* 4.8 11.4 - - + -
160J ALA* 3.4 31.0 - - + +
163J ASP* 4.1 20.0 - - + +
165J ASN 3.2 18.4 - - - +
166J PRO* 1.3 74.5 - - - +
168J VAL* 1.3 71.6 + - - +
169J VAL* 4.5 3.8 - - + -
195J ILE* 4.8 3.8 - - + -
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Residues in contact with VAL 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83J PHE* 3.7 26.0 - - + -
93J VAL* 4.6 2.5 - - + -
114J PHE* 3.4 23.3 - - + -
136J TYR* 4.2 19.7 - - + -
142J LEU* 3.9 31.9 - - + -
143J LYS 2.9 10.5 + - - +
144J VAL* 3.9 7.8 - - + +
145J VAL* 3.2 26.0 + - - +
167J VAL* 1.3 76.7 - - - +
169J VAL* 1.3 60.1 + - - +
170J LEU* 4.1 15.5 - - + -
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Residues in contact with VAL 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J ILE* 6.0 0.7 - - + -
83J PHE* 3.2 16.5 - - - -
113J VAL* 4.3 9.2 - - + -
114J PHE 2.6 14.6 + - - +
115J ARG* 3.5 10.9 - - + -
116J GLY 3.4 9.4 + - - +
145J VAL* 3.6 25.1 - - + -
147J PRO* 4.2 12.8 - - + -
156J LEU* 5.9 0.4 - - + -
157J ILE* 4.1 31.2 - - + +
160J ALA* 4.3 12.1 - - + -
167J VAL* 4.5 0.7 - - + -
168J VAL* 1.3 73.1 - - - +
170J LEU* 1.3 61.6 + - - +
171J GLU* 3.2 28.5 + - + +
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Residues in contact with LEU 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83J PHE* 3.7 35.0 - - + -
116J GLY 4.2 1.8 - - - -
118J ASN* 3.7 24.5 - - - +
132J PHE* 4.4 8.5 - - + +
133J ALA* 3.6 31.6 - - + +
136J TYR* 4.7 1.6 - - + -
144J VAL* 3.5 27.4 - - + -
145J VAL 2.9 14.1 + - - +
146J SER* 3.6 16.2 + - - +
147J PRO* 3.5 17.9 - - - +
168J VAL* 4.1 11.2 - - + -
169J VAL* 1.3 70.7 - - - +
171J GLU* 1.3 62.7 + - - +
212J HIS* 6.2 0.2 - - + -
213J SER* 4.8 1.9 + - - -
241J ILE* 4.8 3.1 - - + -
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Residues in contact with GLU 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J ILE* 3.3 28.0 - - + +
115J ARG* 2.5 41.8 + - - +
116J GLY* 3.1 23.3 + - - +
117J PRO* 3.7 0.4 - - - -
118J ASN* 2.5 36.7 + - - +
147J PRO* 4.6 9.9 - - + -
157J ILE* 5.2 0.9 - - - +
169J VAL* 3.9 19.0 - - + +
170J LEU* 1.3 76.5 - - - +
172J ASN* 1.3 57.0 + - - +
176J TYR* 2.3 42.1 + - + +
213J SER* 5.0 0.9 - - - -
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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