Contacts of the strand formed by residues 229 - 233 (chain A) in PDB entry 3V9G
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ALA* 3.3 47.1 - - + +
110A LEU* 4.2 1.8 - - - +
113A ARG* 3.6 28.8 - - + +
116A TRP* 4.6 1.3 - - + -
202A GLY 3.6 20.0 + - - +
203A PHE* 3.6 8.2 - - + -
204A VAL* 2.9 24.9 + - - +
228A ASN* 1.3 74.5 - - - +
230A VAL* 1.3 65.7 + - - +
257A ASN 3.9 10.8 - - - +
258A ILE* 3.4 16.4 - - + -
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Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ALA* 5.0 1.0 - - - +
204A VAL* 3.2 14.8 - - + +
206A ALA* 3.8 22.9 - - + -
220A ALA* 3.7 29.4 - - + +
223A PRO* 4.1 19.7 - - + -
224A ALA* 4.1 8.5 - - + +
228A ASN 4.5 0.4 - - - +
229A VAL* 1.3 83.4 - - - +
231A LEU* 1.3 76.5 + - - +
232A TRP* 3.8 3.5 + - + +
258A ILE 2.8 14.3 + - - +
259A ILE* 3.5 6.8 - - + -
260A GLN* 2.9 30.3 + - - +
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Residues in contact with LEU 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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102A LEU* 3.8 28.5 - - + +
105A ALA* 3.9 22.2 - - + +
106A ILE* 3.7 31.9 - - + +
109A ALA* 4.5 5.4 - - + -
203A PHE* 4.3 13.9 - - + -
204A VAL 2.9 11.8 + - - +
205A ALA* 3.6 0.6 - - - -
206A ALA 3.0 24.4 + - - +
230A VAL* 1.3 73.0 - - - +
232A TRP* 1.3 60.2 + - - +
233A LYS 3.9 0.2 - - - -
260A GLN* 3.9 22.4 - - + -
262A VAL* 4.1 11.9 - - + -
269A PHE* 3.6 18.1 - - + -
273A VAL* 4.4 8.3 - - + -
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Residues in contact with TRP 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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206A ALA* 3.4 20.9 - - + -
208A SER* 2.8 25.3 + - - -
213A THR 5.8 0.7 - - - -
216A GLY* 3.6 33.2 + - - -
217A GLY* 4.5 3.1 - - - -
219A LEU* 5.6 0.2 - - - +
220A ALA* 4.0 18.8 - - + -
230A VAL 3.8 1.2 + - - -
231A LEU* 1.3 70.5 - - - +
233A LYS* 1.3 65.2 + - - +
234A PRO* 3.2 15.5 - - + +
242A SER* 3.6 44.9 - - - -
245A VAL* 4.6 10.1 - - + -
246A TYR* 4.0 13.7 - + + -
249A LEU* 5.9 4.0 - - + -
259A ILE* 4.0 19.5 - - + -
260A GLN 2.9 16.6 + - - +
261A PHE* 3.8 19.5 - + - -
262A VAL* 3.0 29.0 + - - +
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Residues in contact with LYS 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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206A ALA 2.9 10.2 + - - +
207A ILE* 3.8 18.9 - - + -
208A SER 3.3 25.5 + - - +
231A LEU 3.7 2.0 + - - -
232A TRP* 1.3 71.5 - - - +
234A PRO* 1.3 78.4 + - - +
235A SER* 4.8 2.8 - - - +
236A ASP* 3.7 12.3 + - - +
262A VAL 3.6 4.0 - - - +
264A ALA 3.1 41.3 + - - +
266A GLY* 4.3 17.1 - - - +
269A PHE* 3.8 45.7 - - + -
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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