Contacts of the strand formed by residues 198 - 202 (chain B) in PDB entry 1ICF
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 TYR 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 3.6 38.2 - - - +
13A VAL* 3.6 24.6 - - - +
14A THR 4.4 2.4 + - - -
16A VAL* 3.6 18.6 - - + +
146A TYR* 3.6 4.2 - - - -
168A VAL* 3.7 20.2 - - + -
184B LEU* 4.3 13.9 - - + -
185B VAL 3.3 21.8 - - - -
186B LYS* 3.4 29.4 - - + +
193B TRP* 4.0 2.0 - - - -
194B GLY* 3.9 2.1 - - - -
195B MET* 2.9 41.1 + - + +
196B GLY* 3.6 11.4 - - - -
197B GLY* 1.3 81.3 - - - +
199B VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A PHE* 4.2 16.4 - - + -
146A TYR* 3.4 34.1 - - + -
151A TYR* 4.0 15.0 - - + -
183B TRP 3.4 1.4 - - - +
184B LEU* 3.8 2.7 - - - +
185B VAL* 2.9 55.0 + - + +
187B ASN* 5.3 1.3 - - + -
193B TRP* 3.5 25.1 - - + -
195B MET* 5.4 0.7 - - - -
198B TYR* 1.3 78.7 - - - +
200B LYS* 1.3 66.9 + - - +
201B MET* 4.2 8.1 - - + -
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Residues in contact with LYS 200 (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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146A TYR* 3.2 4.6 + - - -
149A GLY* 3.5 22.8 - - - +
150A ILE* 3.3 3.8 - - + -
151A TYR* 2.8 33.3 + - - +
173A GLU* 4.8 10.4 + - - +
182B TYR* 3.6 50.7 - - + -
183B TRP 3.3 4.9 - - - -
184B LEU* 4.3 8.3 - - + -
195B MET* 3.5 34.0 - - + +
199B VAL* 1.3 75.1 - - - +
201B MET* 1.3 56.4 + - - +
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Residues in contact with MET 201 (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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136A ILE* 3.9 35.9 - - + -
143A PHE* 3.9 26.2 - - + -
150A ILE* 4.1 0.9 - - - -
151A TYR* 4.0 13.7 - - + -
182B TYR* 3.0 4.1 - - - -
183B TRP* 2.7 42.0 + - + +
185B VAL* 3.5 27.4 - - + -
199B VAL* 4.2 8.3 - - + -
200B LYS* 1.3 73.9 - - - +
202B ALA* 1.3 66.1 + - - +
208B HIS* 4.6 4.9 - - + +
209B CYS* 4.0 26.2 - - + -
211B ILE* 4.2 9.6 - - + -
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Residues in contact with ALA 202 (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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119A GLU* 4.2 2.6 - - - +
150A ILE* 3.6 18.0 - - + +
151A TYR 3.2 20.6 + - - +
152A PHE* 3.9 17.3 - - + -
179B ASN 4.3 3.8 - - - +
181B LYS 3.9 1.3 - - - -
183B TRP* 3.8 7.6 - - - -
201B MET* 1.3 73.5 - - - +
203B LYS* 1.3 60.4 + - - +
205B ARG* 3.7 22.2 - - + +
208B HIS* 4.0 22.7 - - + +
211B ILE* 5.2 1.0 - - - +
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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