Contacts of the helix formed by residues 223 - 232 (chain B) in PDB entry 3VRY
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 THR 223 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B PHE* 3.8 10.5 - - - -
221B PHE* 3.6 6.1 - - - +
222B SER* 1.3 89.4 - - - +
224B LEU* 1.3 65.5 + - - +
225B GLN* 3.6 10.4 + - - +
226B GLU* 3.2 40.6 + - - +
227B LEU* 3.4 5.0 + - - +
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Residues in contact with LEU 224 (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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144B LEU* 4.0 35.9 - - + -
149B TRP* 3.9 14.6 - - + -
175B ILE* 4.1 30.2 - - + +
185B TYR* 4.1 18.2 - - + -
205B ILE* 4.2 15.7 - - + -
213B PHE* 3.6 42.8 - - + -
223B THR* 1.3 72.1 - - - +
225B GLN* 1.3 60.3 + - - +
227B LEU* 3.2 9.2 + - + +
228B VAL* 2.8 31.2 + - - +
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Residues in contact with GLN 225 (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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147B GLU* 3.5 13.3 - - - +
149B TRP* 3.1 40.5 + - + +
223B THR* 3.2 10.8 + - - +
224B LEU* 1.3 76.7 - - - +
226B GLU* 1.3 54.0 + - + +
228B VAL* 3.1 9.3 + - - +
229B ASP* 2.8 65.3 + - - +
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Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PHE* 3.6 16.6 - - + +
222B SER* 2.8 44.7 + - - -
223B THR* 3.2 20.3 + - - +
225B GLN* 1.3 74.4 - - + +
227B LEU* 1.3 59.2 + - - +
229B ASP* 3.1 8.6 + - - +
230B HIS* 2.8 32.1 + - - +
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Residues in contact with LEU 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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175B ILE* 4.8 7.2 - - + -
187B LEU* 4.9 7.0 - - + -
205B ILE* 4.0 36.1 - - + -
213B PHE* 4.2 13.0 - - + -
215B ILE* 4.0 25.1 - - + +
221B PHE* 3.6 37.9 - - + -
223B THR 3.4 4.9 + - - +
224B LEU* 3.2 14.7 + - + +
226B GLU* 1.3 79.4 - - - +
228B VAL* 1.3 66.5 + - + +
230B HIS* 3.3 0.7 + - - +
231B TYR* 3.2 46.9 + - + -
242B LEU* 5.6 0.9 - - + -
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Residues in contact with VAL 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B TRP* 4.0 20.9 - - + -
173B PHE* 3.7 38.8 - - + -
175B ILE* 3.7 22.9 - - + -
187B LEU* 5.8 0.4 - - + -
224B LEU 2.8 20.2 + - - +
225B GLN* 3.1 22.4 + - - +
227B LEU* 1.3 73.0 - - + +
229B ASP* 1.3 63.9 + - - +
231B TYR 3.6 0.5 + - - -
232B LYS* 3.1 33.2 + - + +
242B LEU* 3.7 11.0 - - + +
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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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225B GLN* 2.8 47.9 + - - +
226B GLU* 3.1 7.5 + - - +
228B VAL* 1.3 74.1 - - - +
230B HIS* 1.3 63.7 + - - +
232B LYS* 3.2 31.5 + - - +
233B LYS* 3.6 20.8 + - - +
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Residues in contact with HIS 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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219B SER* 4.7 6.3 + - - -
221B PHE* 3.4 42.9 - + + -
226B GLU 2.8 9.5 + - - +
227B LEU 3.5 3.1 - - - +
229B ASP* 1.3 76.2 - - - +
231B TYR* 1.3 76.4 + + - +
233B LYS* 2.7 48.1 + - + +
234B GLY 3.7 2.6 + - - -
236B ASP* 2.9 31.7 + - + +
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Residues in contact with TYR 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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187B LEU* 5.4 0.2 - - + -
215B ILE* 4.1 24.2 - - + +
216B SER* 4.3 12.5 + - - -
219B SER* 4.4 13.3 - - - -
221B PHE* 4.1 8.2 - + - -
227B LEU* 3.2 49.6 + - + +
230B HIS* 1.3 99.0 - + - +
232B LYS* 1.3 56.1 + - - +
233B LYS 3.2 0.4 - - - -
234B GLY 3.4 9.5 - - - +
235B ASN 3.4 25.8 - - - -
236B ASP* 3.7 17.0 + - + -
238B LEU* 3.6 24.0 - - + -
241B LYS* 3.2 9.4 - - - +
242B LEU* 2.9 47.1 + - + -
530B ILE* 4.8 2.0 - - + +
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Residues in contact with LYS 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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173B PHE* 4.7 11.4 - - - -
228B VAL* 3.1 23.5 + - + +
229B ASP* 3.2 28.3 + - - +
230B HIS 3.0 0.4 - - - -
231B TYR* 1.3 79.1 - - - +
233B LYS* 1.3 57.0 + - + +
241B LYS* 3.1 21.6 + - - +
242B LEU* 3.5 24.3 - - + +
243B SER 3.5 21.4 + - - -
245B PRO* 5.4 5.2 - - - +
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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