Contacts of the strand formed by residues 229 - 234 (chain A) in PDB entry 3CFV
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 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A GLY* 5.9 0.3 - - - -
180A TYR 5.7 0.5 + - - -
195A ALA* 3.2 27.0 - - + +
196A SER 3.2 27.3 + - - +
199A HIS 3.7 14.1 - - - +
200A THR 3.1 29.4 - - - +
201A VAL* 3.8 15.0 - - + -
225A HIS* 4.0 13.0 - - + +
227A ALA 3.2 2.8 + - - -
228A VAL* 1.3 72.0 - - - +
230A GLU* 1.3 58.5 + - - +
231A ASP 3.9 7.9 - - - +
244A SER* 4.4 0.2 - - - -
245A VAL 3.2 17.9 - - - +
246A ALA* 3.4 12.8 - - + -
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Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ARG* 5.4 0.5 + - - -
180A TYR* 4.2 16.6 + - - +
181A GLY 3.4 19.9 + - - -
195A ALA* 4.0 0.9 - - - -
197A ASP* 5.5 0.3 - - - +
228A VAL* 4.0 12.8 - - - +
229A VAL* 1.3 74.0 - - - +
231A ASP* 1.3 59.3 + - - +
245A VAL 2.6 9.0 + - - +
246A ALA 4.5 0.2 - - - -
247A ASP* 2.9 30.6 - - - +
274A GLU* 5.3 0.7 - - - +
275A VAL 3.2 26.9 - - - +
276A ASN* 3.3 31.4 - - - +
320A PHE* 5.1 8.7 - - - -
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Residues in contact with ASP 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ARG* 3.6 16.9 + - - -
181A GLY* 3.4 17.5 - - - -
182A LEU 4.2 1.6 + - - +
195A ALA* 4.2 3.4 - - - -
229A VAL* 3.7 3.0 - - - +
230A GLU* 1.3 80.2 - - - +
232A VAL* 1.3 79.5 + - - +
233A ALA* 5.3 0.2 - - - +
244A SER* 3.6 2.3 - - - -
245A VAL* 3.0 30.1 + - + +
276A ASN 3.5 16.2 - - - +
277A CYS* 3.8 13.0 - - - +
278A LEU* 3.4 34.9 + - + +
321A GLN* 4.8 4.7 + - - -
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LEU* 3.9 20.6 - - - +
183A SER* 3.6 9.5 - - - +
193A LEU* 3.8 28.7 - - + -
194A SER 3.8 22.7 - - - +
195A ALA* 3.9 13.7 - - + +
201A VAL* 3.9 18.2 - - + -
231A ASP* 1.3 87.9 + - - +
233A ALA* 1.3 66.7 + - - +
242A PHE* 3.8 9.9 - - + -
243A GLY 3.5 13.7 - - - +
244A SER* 4.5 3.1 - - - -
278A LEU* 3.9 1.8 - - - -
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A SER* 3.7 7.9 - - - +
193A LEU* 4.6 0.9 - - - -
231A ASP* 5.3 0.4 - - - +
232A VAL* 1.3 78.0 - - - +
234A TRP* 1.3 65.2 + - - +
242A PHE* 3.4 3.8 - - - -
243A GLY 2.9 35.7 + - - -
278A LEU* 4.0 29.6 - - + +
279A SER* 5.2 1.6 - - - -
280A PHE* 3.3 16.2 - - + +
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Residues in contact with TRP 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A SER* 3.2 45.1 + - - +
184A TRP 3.3 21.1 - - - +
185A ASN* 3.2 40.3 - - + +
186A SER 5.3 0.4 - - - +
188A LEU* 6.0 1.1 - - + -
191A HIS* 3.6 15.7 + - + -
193A LEU* 3.3 28.7 - - + +
203A LEU* 3.6 20.6 - - + -
233A ALA* 1.3 76.0 - - - +
235A HIS* 1.3 70.4 + - - +
236A LEU* 3.7 8.2 + - + +
239A GLU 3.4 12.3 - - - -
240A SER 4.0 11.0 - - - -
241A LEU 3.3 20.6 - - - -
242A PHE* 3.7 13.9 - + + -
256A THR* 3.9 20.2 - - + -
280A PHE* 3.4 13.2 - - - +
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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