Contacts of the strand formed by residues 198 - 203 (chain A) in PDB entry 1BQ2
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 ASP 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A ARG* 2.8 48.8 + - + +
36A PHE 3.2 10.3 - - - +
37A ASN* 3.8 17.0 + - - +
38A LEU* 4.3 5.8 - - - +
159A LEU 4.3 0.3 - - - +
160A SER* 2.9 19.2 + - - +
161A CYS* 2.9 25.8 + - - +
185A VAL* 5.1 0.3 - - - +
197A GLY* 1.3 83.0 - - - +
199A PHE* 1.3 58.3 + - - +
200A VAL* 4.0 3.3 - - + +
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Residues in contact with PHE 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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35A ARG* 3.5 1.6 - - - -
36A PHE* 2.8 53.5 + + + +
38A LEU* 3.9 26.6 - - + +
161A CYS* 3.5 24.7 - - + -
163A LEU* 3.8 29.6 - - + -
178A ILE* 3.9 33.7 - - + -
181A TYR* 3.6 31.0 - - + -
182A ALA* 4.8 4.9 - - + -
185A VAL* 4.6 5.6 - - + -
198A ASP* 1.3 73.5 - - - +
200A VAL* 1.3 69.8 + - - +
201A TRP* 4.0 19.3 - + + -
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Residues in contact with VAL 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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33A GLN* 3.5 40.8 - - + +
34A MET 3.4 6.7 - - - +
35A ARG* 3.7 36.8 - - + +
160A SER* 5.6 2.9 - - - -
161A CYS 3.0 13.4 + - - +
162A GLN* 3.3 20.7 - - + +
163A LEU 3.1 24.6 + - - +
198A ASP* 4.4 8.1 - - + +
199A PHE* 1.3 81.6 - - - +
201A TRP* 1.3 58.0 + - - +
202A THR 4.1 0.2 - - - -
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Residues in contact with TRP 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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7A LEU* 4.6 1.6 - - + -
32A HIS* 3.9 25.8 - + + -
33A GLN* 3.1 6.1 - - - +
34A MET* 3.0 63.9 + - + +
36A PHE* 4.7 4.2 - - + -
163A LEU* 3.8 19.1 - - + -
165A GLN* 3.2 30.7 + - + +
168A CYS* 3.8 25.6 - - + -
174A LEU* 3.4 21.0 - - + +
177A ALA* 5.0 1.6 - - + -
178A ILE* 4.9 3.1 - - + -
199A PHE* 4.0 19.6 + + + -
200A VAL* 1.3 71.9 - - - +
202A THR* 1.3 65.4 + - - +
203A GLY* 3.7 20.6 - - - -
206A THR* 3.6 31.9 - - + -
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Residues in contact with THR 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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32A HIS 3.3 9.6 - - - +
33A GLN* 3.2 14.6 + - + +
162A GLN* 2.7 30.3 + - - +
163A LEU 2.9 14.6 + - - +
164A TYR* 3.2 28.4 - - + -
165A GLN* 2.8 27.7 + - - +
201A TRP* 1.3 80.3 - - - +
203A GLY* 1.3 63.3 + - - +
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Residues in contact with GLY 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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31A GLY* 3.0 26.5 - - - -
32A HIS 3.1 10.8 + - - -
164A TYR* 4.7 7.1 + - - -
165A GLN 3.1 9.6 - - - -
168A CYS* 5.8 0.2 - - - -
201A TRP* 3.7 22.8 - - - -
202A THR* 1.3 78.5 - - - +
204A GLY* 1.3 61.8 + - - -
206A THR* 4.0 3.4 - - - -
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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