Contacts of the strand formed by residues 211 - 215 (chain B) in PDB entry 5HVP
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 211 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A PHE* 4.9 0.7 - - + -
203B ILE* 4.4 11.2 - - + -
209B PRO 4.6 1.1 - - - +
210B LEU* 1.3 79.0 - - - +
212B THR* 1.3 62.0 + - - +
213B ILE* 3.9 11.2 - - + -
221B GLU* 3.2 10.3 - - - -
222B ALA* 2.8 38.5 + - + +
224B LEU* 3.7 44.0 - - + -
266B ILE* 3.8 17.0 - - + -
267B CYS* 3.8 24.9 - - - -
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Residues in contact with THR 212 (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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211B VAL* 1.3 76.9 - - - +
213B ILE* 1.3 64.0 + - - +
219B LEU* 5.3 17.8 - - + +
220B LYS 3.2 7.6 - - - -
221B GLU* 3.1 17.5 - - - +
265B GLU 4.1 0.2 - - - +
267B CYS* 3.4 29.6 + - - -
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Residues in contact with ILE 213 (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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211B VAL* 3.9 18.4 - - + -
212B THR* 1.3 80.8 - - - +
214B LYS* 1.3 61.6 + - - +
215B ILE* 4.6 6.7 - - + -
218B GLN 3.7 0.2 - - - +
219B LEU* 3.4 6.9 - - - +
220B LYS* 2.7 57.0 + - + +
222B ALA* 3.9 20.4 - - + -
233B LEU* 3.8 25.6 - - + -
264B ILE* 3.6 26.9 - - + -
265B GLU 3.1 8.5 - - - +
266B ILE* 4.0 18.6 - - + -
283B ASN* 4.8 0.4 - - + -
285B ILE* 4.0 5.8 - - + -
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Residues in contact with LYS 214 (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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213B ILE* 1.3 73.2 - - - +
215B ILE* 1.3 63.4 + - - +
217B GLY* 4.2 20.6 - - - +
218B GLN 3.1 13.7 - - - +
219B LEU* 3.9 20.6 - - + -
263B LEU 4.4 0.3 - - - +
264B ILE* 3.7 4.0 - - - +
265B GLU* 2.8 58.2 + - + +
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Residues in contact with ILE 215 (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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213B ILE* 4.6 11.7 - - + -
214B LYS* 1.3 75.0 - - - +
216B GLY* 1.3 63.6 + - - +
217B GLY 3.1 0.7 - - - -
218B GLN* 2.7 31.2 + - - +
220B LYS* 3.9 24.2 - - + -
233B LEU* 3.6 25.4 - - + -
236B MET* 4.1 15.7 - - + +
238B LEU* 3.9 21.3 - - + -
262B ILE* 3.5 25.8 - - + -
263B LEU 3.9 16.2 - - - +
264B ILE* 4.4 13.0 - - + -
275B VAL* 4.9 0.7 - - + -
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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