Contacts of the strand formed by residues 193 - 200 (chain B) in PDB entry 5ICN
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 VAL 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ILE* 6.0 0.2 - - + -
160B ILE* 3.9 17.9 - - + -
164B LEU* 3.8 22.7 - - + -
170B VAL* 3.2 15.3 - - + +
172B TYR* 4.7 9.2 - - + -
187B PHE* 3.9 43.4 - - + +
190B THR* 3.8 9.4 - - + +
191B ASP 3.3 1.3 - - - -
192B ARG* 1.3 86.7 - - + +
194B MET* 1.3 64.4 + - - +
195B THR* 4.0 12.0 + - + +
222B TYR* 4.0 1.8 - - - +
252B PHE* 3.9 2.5 - - - -
403B K 3.2 21.3 - - - -
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Residues in contact with MET 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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170B VAL 3.2 7.1 + - - -
171B LEU* 3.4 3.4 - - + +
172B TYR 2.8 28.8 + - - +
193B VAL* 1.3 72.3 - - - +
195B THR* 1.3 61.8 + - - +
196B VAL* 4.0 10.1 - - + -
221B TYR 4.0 10.8 - - - +
222B TYR* 3.2 24.7 - - + +
224B VAL* 4.1 13.9 - - + -
248B VAL* 3.7 21.8 - - - -
252B PHE* 3.3 55.6 - - + -
370B LEU* 4.2 12.1 - - + -
373B LEU* 3.7 17.7 - - + -
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Residues in contact with THR 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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172B TYR* 3.5 20.9 - - + -
180B GLY 5.7 0.9 - - - -
183B VAL* 3.9 23.1 - - + +
184B GLU* 3.5 33.6 + - - +
187B PHE* 4.5 6.3 - - + -
193B VAL* 4.3 20.6 - - + +
194B MET* 1.3 73.6 - - - +
196B VAL* 1.3 62.8 + - - +
197B SER* 5.4 1.3 - - - -
222B TYR 3.1 8.3 + - - -
223B ALA* 3.6 6.2 - - - +
224B VAL 2.8 26.3 + - - +
225B ASN* 4.8 0.2 + - - -
403B K 4.7 3.8 - - - -
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Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 3.8 24.7 - - + -
172B TYR* 2.9 12.0 + - - +
173B ILE* 4.3 3.0 - - - +
174B ASP* 3.0 26.5 + - - +
194B MET* 4.0 9.9 - - + -
195B THR* 1.3 73.1 - - - +
197B SER* 1.3 65.1 + - - +
198B PHE* 3.7 27.6 - - + -
224B VAL* 3.3 33.4 - - + -
226B TYR* 6.5 0.4 - - + -
244B VAL* 4.6 2.7 - - + -
245B MET* 3.9 15.9 - - + -
248B VAL* 4.2 10.8 - - + -
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Residues in contact with SER 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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172B TYR* 6.0 0.2 - - - -
174B ASP* 3.6 11.8 - - - +
179B HIS* 3.6 11.0 - - - -
180B GLY* 3.6 7.0 + - - -
184B GLU* 5.4 0.4 - - - -
195B THR* 5.1 1.8 - - - -
196B VAL* 1.3 78.1 - - - +
198B PHE* 1.3 57.9 + - - +
199B HIS* 3.0 15.7 + - - -
224B VAL 3.2 7.0 + - - -
225B ASN* 3.4 18.0 - - - -
226B TYR 2.7 32.7 + - - -
402B K 2.9 19.5 - - - -
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Residues in contact with PHE 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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173B ILE* 4.5 3.6 - - + -
174B ASP 3.3 13.0 + - - +
175B ILE 3.6 6.9 - - - +
176B ASP 3.0 19.4 - - - +
177B ILE* 4.6 0.5 - - - -
196B VAL* 3.7 29.6 - - + -
197B SER* 1.3 74.8 + - - +
199B HIS* 1.3 61.4 + - - +
226B TYR* 3.5 31.9 - + + -
228B LEU* 4.4 5.6 - - + -
237B TYR* 3.3 28.6 + + + +
240B ILE* 3.6 35.7 - - + -
241B PHE* 3.5 35.4 - + - -
244B VAL* 4.1 9.2 - - + -
245B MET* 4.0 9.2 - - - -
274B PHE* 4.8 2.5 - - - -
402B K 3.1 0.9 - - - -
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Residues in contact with HIS 199 (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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177B ILE 3.0 20.9 - - - +
179B HIS* 3.5 28.5 - + + +
197B SER* 3.0 34.8 + - - -
198B PHE* 1.3 73.9 - - - +
200B LYS* 1.3 72.7 + - - +
201B TYR* 4.3 5.4 - + + -
209B GLY* 2.5 33.1 + - - -
225B ASN* 3.5 18.6 - - + -
226B TYR 3.1 11.4 + - - -
227B PRO* 4.0 6.9 - - + +
228B LEU* 2.8 27.2 + - - +
274B PHE* 3.8 10.1 - - - -
402B K 4.0 1.8 - - - -
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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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177B ILE* 3.1 10.4 + - + +
179B HIS* 5.2 1.2 + - - +
199B HIS* 1.3 91.1 - - - +
201B TYR* 1.3 71.5 + - - +
202B GLY 3.0 26.0 + - - -
203B GLU 4.9 0.9 - - - -
204B TYR* 3.3 52.8 - - + +
205B PHE 5.1 2.3 - - - +
206B PRO* 6.2 0.2 - - - +
228B LEU 3.2 12.6 + - - +
229B ARG* 4.4 7.3 - - - +
230B ASP* 2.8 33.9 + - - +
273B CYS* 3.5 13.7 - - - -
274B PHE* 3.4 20.7 - - + -
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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