Contacts of the helix formed by residues 225 - 233 (chain B) in PDB entry 5C1V
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 GLY 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205B GLU* 3.7 9.6 - - - -
224B TYR* 1.3 78.8 - - - +
226B PRO* 1.3 75.1 - - - +
227B MET 3.4 1.8 - - - -
228B CYS* 3.6 1.8 + - - +
229B ASP* 2.9 37.6 + - - -
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Residues in contact with PRO 226 (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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203B SER* 3.6 11.2 - - - +
205B GLU* 3.4 24.5 - - + +
206B ILE* 3.5 23.4 - - + +
215B LEU* 3.4 28.7 - - + -
222B PRO* 5.9 1.8 - - + -
225B GLY* 1.3 85.7 - - - +
227B MET* 1.3 66.3 + - + +
229B ASP* 3.4 1.9 + - - +
230B ILE* 3.2 28.6 + - - +
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Residues in contact with MET 227 (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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148B ARG* 3.4 35.0 - - - +
187B LEU* 3.8 32.3 - - + -
215B LEU* 4.3 13.6 - - + +
216B ASP 4.2 11.7 - - - +
217B ARG* 3.5 11.9 - - - +
219B LYS* 3.8 23.8 - - - +
221B PRO* 4.3 10.5 - - + -
222B PRO* 3.8 27.6 - - + -
225B GLY 3.4 0.4 - - - -
226B PRO* 1.3 80.9 - - + +
228B CYS* 1.3 67.0 + - - +
229B ASP 3.4 0.3 + - - -
230B ILE* 3.6 6.5 + - - +
231B LEU* 3.5 24.6 + - + +
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Residues in contact with CYS 228 (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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221B PRO* 5.2 1.8 - - - -
222B PRO* 3.2 32.3 - - - +
223B ALA* 3.6 16.6 - - - -
224B TYR* 3.9 12.1 - - - +
225B GLY 3.6 9.1 + - - +
227B MET* 1.3 80.1 - - - +
229B ASP* 1.3 57.4 + - - +
231B LEU* 3.3 3.6 + - - +
232B TRP* 3.0 56.0 + - - +
256B CYS* 4.3 12.1 - - - -
257B SER* 4.4 8.3 - - - -
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Residues in contact with ASP 229 (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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202B LEU 3.7 7.0 - - - +
203B SER* 2.6 38.3 + - - -
204B PRO* 3.4 10.4 - - - +
205B GLU* 4.8 1.2 - - - +
224B TYR* 5.7 0.3 - - - -
225B GLY 2.9 24.8 + - - +
226B PRO 3.6 1.1 - - - +
227B MET 3.2 0.2 - - - -
228B CYS* 1.3 74.5 - - - +
230B ILE* 1.3 60.1 + - - +
233B SER* 2.9 37.1 + - - -
257B SER* 2.8 33.3 + - - +
258B TYR* 3.5 18.8 - - - -
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Residues in contact with ILE 230 (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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187B LEU* 3.8 39.5 - - + +
188B ALA* 5.7 1.3 - - + -
198B VAL* 4.0 19.1 - - + -
199B HIS 4.7 1.8 - - - +
200B GLY* 2.6 32.2 + - - -
201B GLY 2.8 21.3 + - - +
203B SER* 5.4 0.2 - - - -
206B ILE* 3.5 27.1 - - + -
212B ILE* 4.5 12.3 - - + -
215B LEU* 3.7 20.0 - - + -
226B PRO 3.2 12.0 + - - +
227B MET* 3.8 7.2 - - - +
228B CYS 3.5 0.2 - - - -
229B ASP* 1.3 77.2 - - - +
231B LEU* 1.3 57.6 + - + +
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Residues in contact with LEU 231 (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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148B ARG* 3.0 52.9 - - + +
149B GLY* 3.9 10.3 - - - +
150B ASN* 3.6 12.3 - - + +
187B LEU* 4.8 6.5 - - + +
199B HIS* 3.2 26.7 - - + -
200B GLY* 3.9 3.1 - - - +
221B PRO* 3.9 33.0 - - + -
227B MET* 3.5 20.8 + - + +
228B CYS* 3.3 7.5 + - - +
229B ASP 3.2 0.6 - - - -
230B ILE* 1.3 85.2 - - + +
232B TRP* 1.3 67.6 + - + +
281B HIS* 3.5 4.7 + - - -
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Residues in contact with TRP 232 (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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150B ASN* 3.6 39.7 + - + +
155B HIS* 5.9 1.1 - + - -
156B LEU* 3.9 28.5 - - + -
221B PRO* 5.3 6.8 - - + +
222B PRO 5.8 0.2 + - - -
228B CYS* 3.0 37.3 + - - +
231B LEU* 1.3 90.7 - - + +
233B SER* 1.3 67.8 + - - +
234B ASP 3.8 0.5 + - - -
251B ASN* 3.9 1.4 + - - -
254B ARG* 3.9 61.9 + - + +
256B CYS* 4.0 14.1 - - - +
257B SER* 3.9 17.6 - - - -
281B HIS* 3.2 15.4 + - - -
503B PO4 5.4 1.3 - - - -
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Residues in contact with SER 233 (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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200B GLY* 3.1 21.7 - - - +
201B GLY* 2.6 44.0 - - - -
202B LEU 2.7 14.3 + - - -
229B ASP 2.9 19.1 + - - -
231B LEU 4.0 0.4 - - - -
232B TRP* 1.3 75.9 - - - +
234B ASP* 1.3 57.7 + - - +
257B SER* 3.9 8.4 + - - -
258B TYR* 3.3 18.2 - - - -
260B TYR* 3.2 9.5 - - - -
279B ARG* 3.3 6.9 + - - -
281B HIS* 3.7 0.3 - - - -
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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
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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