Contacts of the strand formed by residues 176 - 180 (chain B) in PDB entry 3IFS
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 176 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ILE* 3.4 12.1 - - + +
142B VAL* 4.6 3.1 - - + -
156B PHE* 4.0 20.2 - - + -
160B ARG* 4.1 17.3 - - + -
163B LEU* 3.3 31.4 - - + -
164B GLU* 5.6 0.4 - - - +
172B ALA* 3.3 10.9 + - + +
173B ARG 3.6 6.6 + - - +
174B LYS 3.6 0.7 - - - -
175B ARG* 1.3 78.3 - - - +
177B TYR* 1.3 74.2 + - - +
178B ALA 4.2 0.2 - - - -
196B TYR* 3.6 70.8 - - + +
197B GLU* 3.7 7.1 + - - +
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Residues in contact with TYR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B CYS* 3.8 29.8 - - + -
69B LYS* 3.2 38.5 + - + +
70B ILE* 3.6 33.2 - - + +
73B ASP* 4.8 0.2 + - - -
139B SER* 4.2 4.6 + - - -
140B ILE 2.9 16.9 + - - +
141B ASN* 2.9 23.6 + - + +
142B VAL* 2.9 14.2 + - - +
174B LYS 3.3 7.6 + - - -
175B ARG* 3.8 19.7 - - - -
176B ILE* 1.3 76.3 - - - +
178B ALA* 1.3 60.4 + - - +
197B GLU* 3.5 31.0 - - + +
199B PHE* 4.5 6.3 - + + -
218B LEU* 4.0 21.8 - - + -
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Residues in contact with ALA 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 3.4 20.9 - - + +
176B ILE 4.2 0.6 - - - -
177B TYR* 1.3 73.4 - - - +
179B THR* 1.3 62.0 + - - +
180B THR* 4.0 3.7 + - + +
187B LEU* 4.6 9.4 - - + -
191B ALA* 3.9 27.8 - - + -
196B TYR* 4.7 7.0 - - + -
197B GLU 2.9 13.1 + - - +
198B THR* 3.0 10.6 - - + +
199B PHE* 2.8 24.4 + - - +
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Residues in contact with THR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ASN* 3.4 18.5 + - - -
142B VAL 2.9 11.3 + - - +
143B ILE* 3.3 9.8 - - + -
144B SER 3.0 24.9 + - - -
178B ALA* 1.3 73.1 - - - +
180B THR* 1.3 63.1 + - - +
187B LEU* 4.3 0.2 - - - +
199B PHE* 3.4 23.6 - - + +
200B VAL 4.8 0.2 - - - -
201B ILE* 3.8 20.3 - - + +
214B PRO* 4.0 15.8 + - + +
215B VAL* 3.9 27.6 - - + +
218B LEU* 4.9 1.2 - - - +
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Residues in contact with THR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B SER 2.8 21.9 + - - -
145B LYS 4.1 2.4 + - - -
147B GLY* 4.1 11.1 - - - -
178B ALA* 4.8 7.2 - - + +
179B THR* 1.3 77.7 - - - +
181B ASP* 1.3 83.2 + - - +
184B ARG 4.4 2.3 + - - -
187B LEU* 3.8 17.3 - - + +
188B LYS* 3.9 32.2 + - + +
191B ALA* 5.6 0.7 - - + -
198B THR* 5.7 1.8 - - - -
199B PHE 3.1 12.9 + - - +
200B VAL* 3.4 0.9 - - - -
201B ILE* 3.0 27.3 + - - -
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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
------------------------------------------------------------
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