Contacts of the strand formed by residues 196 - 203 (chain A) in PDB entry 4JVA
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 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195A GLY* 1.3 73.5 - - - -
197A PHE* 1.3 72.4 + - - +
212A ASN* 5.2 3.4 - - - +
213A TYR 3.7 6.5 - - - -
214A ASP* 4.0 13.9 - - + +
215A ASN* 3.9 16.4 - - - +
236A ALA* 3.5 3.3 - - - +
237A THR* 2.5 54.7 + - - -
238A SER* 2.9 14.8 + - - +
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Residues in contact with PHE 197 (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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173A VAL* 3.9 20.9 - - + -
179A VAL* 3.8 24.5 - - + -
192A ILE* 4.0 22.0 - - + -
194A ARG 3.8 12.6 - - - -
195A GLY* 3.5 20.4 - - - -
196A THR* 1.3 91.5 - - - +
198A ASP* 1.3 62.1 + - - +
212A ASN* 2.8 34.2 + - - +
213A TYR* 3.0 22.7 + - + +
219A PHE* 4.3 7.6 - + - -
234A ILE* 3.7 26.9 - - + -
235A THR 3.6 4.0 - - - -
236A ALA* 3.8 20.0 - - + -
237A THR* 3.6 2.2 + - - -
242A LEU* 3.9 15.5 - - + -
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Residues in contact with ASP 198 (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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197A PHE* 1.3 80.7 - - - +
199A ILE* 1.3 62.9 + - - +
200A TYR* 3.6 26.3 + - + -
209A CYS* 3.1 25.4 - - - -
212A ASN* 3.9 10.4 + - - +
233A THR 3.5 5.5 - - - +
234A ILE* 3.6 4.2 - - - +
235A THR* 3.2 29.7 + - - +
237A THR* 2.9 31.6 + - + +
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Residues in contact with ILE 199 (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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198A ASP* 1.3 77.9 - - - +
200A TYR* 1.3 59.8 + - - +
201A VAL* 4.9 0.2 - - + -
209A CYS* 3.1 7.4 - - - -
210A VAL* 2.8 48.8 + - + -
211A GLY* 3.3 12.3 + - - +
212A ASN* 3.5 24.9 - - - +
213A TYR* 3.4 38.4 - - + -
232A ALA* 4.4 9.0 - - + -
233A THR 3.6 2.5 - - - +
234A ILE* 4.1 10.3 - - + -
377A GLN* 3.9 17.5 - - + -
501A 1OR 3.9 25.8 - - + +
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Residues in contact with TYR 200 (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 GLN* 3.8 2.5 - - - +
198A ASP* 3.6 31.9 + - + -
199A ILE* 1.3 76.8 - - - +
201A VAL* 1.3 65.8 + - - +
207A GLY* 4.1 9.2 - - - -
208A ARG* 3.3 28.0 - - - +
209A CYS* 3.3 24.7 - - + +
232A ALA* 3.6 3.3 - - - +
233A THR* 2.9 46.7 + - + +
235A THR* 4.2 22.4 - - + -
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Residues in contact with VAL 201 (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 GLN* 3.5 15.7 - - - +
199A ILE* 4.9 0.9 - - + -
200A TYR* 1.3 79.7 - - - +
202A LYS* 1.3 72.4 + - - +
203A CYS* 3.7 2.4 + - + +
206A VAL 3.5 0.7 - - - +
207A GLY* 2.9 3.4 - - - -
208A ARG* 2.8 29.9 + - - +
210A VAL* 3.5 30.8 - - + +
231A ALA 4.5 4.7 - - - +
232A ALA* 4.4 14.1 - - + -
501A 1OR 4.7 26.2 - - + +
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Residues in contact with LYS 202 (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 GLN* 3.3 31.0 + - + +
201A VAL* 1.3 82.7 - - - +
203A CYS* 1.3 59.8 + - - +
204A ASP 3.7 3.4 + - - +
205A GLY* 3.9 26.1 + - - +
206A VAL 3.2 12.6 - - - +
207A GLY* 3.8 3.8 - - - +
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Residues in contact with CYS 203 (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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201A VAL* 3.7 3.1 + - + +
202A LYS* 1.3 70.5 - - - +
204A ASP* 1.3 77.6 + - - +
205A GLY 3.1 2.9 - - - -
206A VAL* 2.5 38.9 + - + +
208A ARG* 4.4 10.5 - - + +
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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