Contacts of the strand formed by residues 200 - 204 (chain A) in PDB entry 3IWW
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 200 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A PRO* 3.8 31.2 - - + +
172A GLY* 4.0 19.1 - - - +
173A ASP 3.0 7.4 + - - +
174A LEU* 3.3 16.0 - - + +
175A VAL* 2.8 24.8 + - - -
199A LYS* 1.3 74.0 - - - +
201A VAL* 1.3 64.5 + - - +
223A LYS* 4.5 7.4 - - + -
224A GLY* 3.5 16.8 - - - +
226A ILE* 3.8 28.5 - - + -
342A VAL* 3.8 17.0 - - + +
344A MET* 4.0 18.2 - - + -
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Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL* 3.1 11.4 - - + +
177A VAL* 3.8 33.2 - - + -
180A ALA* 5.6 0.7 - - + -
185A PHE* 4.8 2.0 - - + -
196A CYS* 4.5 15.9 - - + -
199A LYS 4.7 1.8 - - - +
200A ILE* 1.3 78.0 - - - +
202A ILE* 1.3 60.4 + - - +
203A ALA* 4.8 1.3 - - + +
217A ALA* 4.0 21.8 - - + -
222A ALA* 3.6 24.9 - - + -
224A GLY 2.9 8.1 + - - -
225A VAL* 3.4 16.6 - - + -
226A ILE* 2.8 25.5 + - - +
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Residues in contact with ILE 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 4.0 22.9 - - + -
175A VAL 2.8 17.9 + - - +
176A TYR* 3.3 20.6 - - + -
177A VAL* 3.1 22.1 + - - -
200A ILE 3.9 0.8 + - - -
201A VAL* 1.3 74.1 - - - +
203A ALA* 1.3 62.8 + - - +
226A ILE* 3.3 31.9 - - + +
228A TYR* 4.0 21.5 - - + -
297A ILE* 4.7 2.9 - - + -
302A ALA* 5.1 0.9 - - + -
305A LEU* 4.0 29.4 - - + -
306A LEU* 3.9 22.4 - - + -
309A MET* 4.8 1.3 - - - -
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Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A TYR* 4.8 0.4 - - - -
177A VAL* 3.6 19.3 - - + -
178A ASN 3.4 9.2 - - - +
179A TYR 4.6 0.2 - - - -
180A ALA* 3.8 15.3 - - + -
201A VAL* 4.9 4.5 - - + -
202A ILE* 1.3 75.1 - - - +
204A ARG* 1.3 64.4 + - - +
213A LYS* 4.8 0.4 - - + -
225A VAL* 5.1 2.0 - - + -
226A ILE 2.8 11.3 + - - +
227A LEU* 3.4 16.7 - - + -
228A TYR* 3.1 29.2 + - - -
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Residues in contact with ARG 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A TYR* 3.3 14.0 + - + +
178A ASN* 2.7 49.4 + - - +
179A TYR* 3.3 30.8 + - + -
203A ALA* 1.3 74.1 - - - +
205A TYR* 1.3 57.5 + - - +
213A LYS* 2.7 29.6 + - - +
227A LEU* 5.4 0.2 - - - -
228A TYR* 3.3 28.4 - - + +
230A ASP* 3.9 13.2 - - + -
232A ALA* 3.8 6.7 - - - +
233A ASP* 3.0 25.9 + - - -
318A SER 3.2 18.8 + - - -
319A TRP 3.7 4.8 - - - -
320A ARG 3.6 13.5 + - - -
321A GLY* 3.6 23.6 - - - -
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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