Contacts of the strand formed by residues 193 - 198 (chain B) in PDB entry 4IXU
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 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 3.3 28.9 - - + +
141B TRP* 4.0 25.1 - - + -
164B VAL* 4.0 14.8 - - + -
168B LEU* 4.1 22.9 - - + -
188B ILE* 4.8 4.7 - - + -
190B SER* 3.9 14.4 - - - +
191B ALA 3.5 1.8 - - - -
192B SER* 1.3 80.9 + - - +
194B VAL* 1.3 71.2 + - - +
195B TYR* 3.9 26.9 - - + +
214B ILE* 3.9 22.7 - - + +
215B GLN* 3.8 10.0 + - - +
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Residues in contact with VAL 194 (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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139B VAL 3.0 6.7 + - - -
140B VAL* 3.5 5.2 - - - +
141B TRP 2.9 24.6 + - - -
191B ALA 5.5 0.7 - - - +
193B ILE* 1.3 80.3 - - - +
195B TYR* 1.3 75.4 + - - +
196B ILE* 4.1 1.7 + - + -
215B GLN* 3.4 12.3 - - + +
217B PHE* 3.7 15.5 - - + -
234B THR* 3.6 34.1 - - + +
237B LEU* 4.0 22.4 - - + -
238B LEU* 3.7 28.3 - - + -
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Residues in contact with TYR 195 (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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141B TRP* 3.2 40.8 - + + -
146B ALA* 2.8 36.4 + - + -
148B ILE* 3.7 8.0 - - + +
164B VAL* 3.5 24.4 - - - +
193B ILE* 3.9 11.7 - - + -
194B VAL* 1.3 77.4 - - - +
196B ILE* 1.3 63.2 + - - +
198B LEU* 3.8 23.8 - - + -
209B LEU* 3.6 25.4 - - + -
214B ILE* 3.7 21.8 - - + -
215B GLN 3.2 9.0 + - - -
216B TYR* 3.4 15.4 - - + -
217B PHE 2.8 28.7 + - - -
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Residues in contact with ILE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL* 3.8 26.2 - - + -
141B TRP 2.9 7.3 + - - -
142B VAL* 3.3 18.4 - - + +
143B ASP 3.1 23.8 + - - -
194B VAL* 4.6 2.0 - - + -
195B TYR* 1.3 80.1 - - - +
197B GLY* 1.3 62.5 + - - +
198B LEU 3.6 1.6 - - - -
217B PHE* 3.4 4.3 - - + +
222B ILE* 3.9 20.0 - - + -
227B ILE* 4.5 0.7 - - + -
230B VAL* 4.1 16.2 - - + -
231B MET* 3.5 31.0 - - + -
234B THR* 3.9 19.7 - - + +
271B LEU* 5.0 0.9 - - + -
279B ILE* 4.0 19.7 - - + -
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Residues in contact with GLY 197 (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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143B ASP 3.1 12.9 - - - +
196B ILE* 1.3 75.9 - - - +
198B LEU* 1.3 66.1 + - - +
199B ARG* 3.3 22.7 + - - -
217B PHE 2.9 10.5 + - - -
219B MET* 3.4 24.5 - - - +
222B ILE* 4.2 5.4 - - - +
254B ALA* 5.4 0.7 - - - -
271B LEU* 4.8 7.2 - - - -
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Residues in contact with LEU 198 (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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327A ARG 3.3 3.5 - - - +
328A GLU* 5.6 0.4 - - + -
143B ASP 3.3 7.8 + - - +
144B ALA 3.5 2.7 - - - +
145B HIS 3.3 35.7 - - - +
146B ALA* 3.7 5.4 - - + +
195B TYR* 3.8 27.4 - - + -
197B GLY* 1.3 75.8 - - - +
199B ARG* 1.3 57.9 + - - +
201B VAL* 4.1 15.9 - - + -
209B LEU* 4.0 17.9 - - + -
216B TYR* 3.7 36.3 - - + -
217B PHE 5.0 0.2 - - - +
218B SER* 3.1 21.2 - - - +
219B MET* 3.0 21.0 + - - +
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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