Contacts of the strand formed by residues 173 - 177 (chain B) in PDB entry 3F9C
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 ILE 173 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B LEU* 3.6 35.7 - - + -
84B TYR 3.5 2.0 - - - +
85B TYR* 4.1 12.8 - - + -
86B PRO* 4.1 0.9 - - + -
138B LEU* 4.3 8.7 - - + -
144B TYR* 3.8 34.0 - - + +
145B PRO 2.8 14.0 + - - +
146B LEU* 3.5 16.5 - - + +
147B VAL* 2.9 25.8 + - - -
172B PHE* 1.3 77.5 - - - +
174B VAL* 1.3 63.5 + - - +
175B ALA 4.1 0.2 - - - -
236B ILE* 5.8 0.9 - - + -
258B LEU* 4.4 9.0 - - + -
261B SER* 4.0 13.7 - - - +
262B ILE* 3.7 24.5 - - + -
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Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ARG 3.5 1.7 - - - +
83B LEU* 3.3 9.6 - - - +
84B TYR* 2.8 57.7 + - + +
147B VAL* 3.5 16.2 - - + +
149B PHE* 4.2 22.9 - - + -
164B GLY* 3.4 30.5 - - - +
167B LEU* 3.7 26.2 - - + -
168B ALA 4.1 5.4 - - - +
172B PHE* 4.3 2.7 - - + -
173B ILE* 1.3 76.8 - - - +
175B ALA* 1.3 58.5 + - - +
176B ALA* 4.5 2.5 - - + +
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 4.0 12.1 - - + -
82B ARG 3.8 3.4 - - - -
83B LEU* 4.0 11.2 - - + -
146B LEU* 4.3 8.0 - - + +
147B VAL 2.8 13.5 + - - +
148B VAL* 3.4 15.0 - - + +
149B PHE* 2.8 24.0 + - - -
173B ILE 4.1 1.0 - - - -
174B VAL* 1.3 70.5 - - - +
176B ALA* 1.3 61.7 + - - +
177B VAL* 3.3 4.1 + - + +
232B ALA* 5.5 0.4 - - + -
236B ILE* 3.9 27.1 - - + -
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 3.1 1.9 - - - -
82B ARG* 2.7 44.9 + - + +
84B TYR* 4.2 16.2 - - + -
149B PHE* 3.6 26.7 - - + +
157B ARG* 3.5 27.6 - - - +
160B TYR* 5.9 1.8 - - + -
174B VAL* 3.7 2.7 + - + -
175B ALA* 1.3 68.9 - - - +
177B VAL* 1.3 63.9 + - - +
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 5.2 1.3 - - + -
80B PHE 3.6 8.1 - - - +
81B LEU* 4.0 7.4 - - + -
148B VAL* 4.0 17.9 - - + -
149B PHE 2.9 16.7 + - - +
151B HIS* 3.2 20.6 + - - +
157B ARG* 3.9 4.5 - - - -
175B ALA 3.3 3.3 + - - +
176B ALA* 1.3 74.4 - - - +
178B GLU* 1.3 67.0 + - - +
179B HIS* 3.7 33.7 - - + +
228B GLU* 4.3 14.1 - - + +
229B CYS* 4.6 2.2 - - - -
232B ALA* 3.3 33.7 - - + -
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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