Contacts of the strand formed by residues 222 - 227 (chain C) in PDB entry 4BVH
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 LEU 222 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138C GLN 5.5 0.2 - - - -
140C VAL 3.7 10.1 - - - +
142C VAL* 3.6 32.1 - - + -
213C LEU* 4.2 9.2 - - + +
216C LEU* 3.5 11.5 + - + -
217C HIS* 3.7 39.6 - - + +
220C GLY 3.7 1.2 - - - -
221C LEU* 1.3 78.2 - - - +
223C LEU* 1.3 60.0 + - - +
224C ARG 3.8 16.4 - - - +
225C LEU* 4.4 12.3 - - + +
239C ILE* 4.4 12.3 - - + -
243C LYS* 2.8 49.2 + - + +
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Residues in contact with LEU 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B GLN* 5.7 2.5 - - - +
198B GLU* 6.1 0.7 - - - +
139C ARG* 3.9 29.6 - - + +
140C VAL 2.8 17.0 + - - +
141C VAL* 3.6 13.0 - - + -
221C LEU 3.5 3.2 + - - -
222C LEU* 1.3 75.3 - - - +
224C ARG* 1.3 77.9 + - - +
243C LYS* 3.9 11.0 - - - +
308C ASP* 3.6 42.0 - - - +
311C MET* 3.7 22.0 - - + -
312C ALA 4.1 4.5 - - - +
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Residues in contact with ARG 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B ASN* 5.8 1.6 + - - -
140C VAL 3.5 1.0 + - - -
141C VAL* 3.4 7.5 - - + +
142C VAL 3.0 24.8 + - - +
222C LEU* 3.6 9.7 - - - +
223C LEU* 1.3 94.0 + - - +
225C LEU* 1.3 62.3 + - - +
226C TYR* 3.6 18.2 - - + -
242C SER* 2.7 30.9 + - - -
243C LYS* 3.4 25.4 - - - +
245C VAL* 3.8 18.8 - - + -
301C ARG* 4.5 0.4 - - - +
304C LEU* 4.0 25.1 - - - +
307C VAL* 5.2 1.8 - - - +
308C ASP* 2.8 48.0 + - + +
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Residues in contact with LEU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C VAL* 3.6 10.8 - - + +
144C VAL* 3.9 24.9 - - + -
213C LEU* 3.8 24.5 - - + -
222C LEU* 4.4 12.3 - - + -
224C ARG* 1.3 72.7 - - - +
226C TYR* 1.3 76.8 + - - +
227C THR* 4.2 5.6 - - - -
234C GLU* 3.8 14.8 - - + -
239C ILE* 3.3 35.4 - - + -
243C LYS 2.8 13.8 + - - +
244C LEU* 3.4 9.4 - - + +
245C VAL 2.9 24.8 + - - -
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Residues in contact with TYR 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C VAL* 4.0 7.0 - - + -
142C VAL 2.8 17.8 + - - +
143C MET* 3.4 6.5 - - + -
144C VAL 3.0 24.4 + - - -
224C ARG* 3.6 14.6 - - + -
225C LEU* 1.3 75.2 - - - +
227C THR* 1.3 60.6 + - - +
245C VAL* 3.5 34.5 - - + -
302C PHE* 4.0 19.5 - + - -
304C LEU* 3.1 4.9 - - - +
305C HIS* 3.0 28.9 + - + -
308C ASP* 2.6 31.7 + - + -
309C PHE* 3.6 26.0 - + - -
327C PHE* 3.6 19.6 - + + -
330C LEU* 4.4 12.1 - - + -
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Residues in contact with THR 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C VAL* 3.3 14.2 - - - +
225C LEU* 3.8 2.7 + - - -
226C TYR* 1.3 74.6 - - - +
228C GLN* 1.3 61.4 + - - +
229C ASN* 3.0 24.3 + - - +
234C GLU* 2.7 36.8 + - - +
244C LEU* 4.2 5.6 - - + -
245C VAL 2.8 20.0 + - - +
246C GLU* 3.7 25.1 - - + -
247C ALA* 2.9 32.2 + - - +
248C HIS 3.9 0.5 + - - -
327C PHE* 4.1 2.2 - - - -
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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