Contacts of the strand formed by residues 164 - 170 (chain A) in PDB entry 4BKR
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 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159A PRO* 3.7 28.9 - - + -
162A ASN* 3.7 4.7 - - + +
163A ALA* 1.3 80.3 - - - +
165A ASN* 1.3 76.5 + - - +
166A LEU* 3.4 17.3 + - + +
180A VAL* 3.3 6.3 - - - -
181A LEU* 2.9 36.4 + - + +
233A ASP* 4.1 34.5 - - + +
234A ILE* 6.5 0.2 - - + -
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Residues in contact with ASN 165 (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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164A VAL* 1.3 77.7 - - - +
166A LEU* 1.3 62.8 + - - +
167A ARG 4.0 1.2 + - - -
178A GLU* 3.1 49.3 + - - +
179A SER 3.8 5.4 + - - +
180A VAL* 4.5 13.0 - - + +
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Residues in contact with LEU 166 (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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164A VAL* 3.4 17.0 + - + +
165A ASN* 1.3 77.2 + - - +
167A ARG* 1.3 71.3 + - - +
168A GLY 4.0 0.2 + - - -
177A LYS 4.1 0.2 - - - +
178A GLU* 3.3 1.4 - - - -
179A SER* 2.9 38.2 + - - +
181A LEU* 3.6 22.4 - - + -
230A ILE 5.6 1.8 - - - +
233A ASP* 5.8 2.2 - - + -
234A ILE* 4.0 15.9 - - + +
283A PRO* 3.5 32.8 - - + -
284A MET* 3.9 33.2 - - + +
349A TRP* 5.3 2.5 - - + -
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Residues in contact with ARG 167 (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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165A ASN 4.0 2.6 + - - -
166A LEU* 1.3 79.5 - - - +
168A GLY* 1.3 61.9 + - - +
176A ILE* 4.0 23.5 - - + +
177A LYS 3.7 3.8 - - - +
178A GLU* 2.7 37.2 + - + +
284A MET* 3.7 12.5 + - - +
287A LEU* 3.9 13.7 - - + -
349A TRP* 2.9 69.3 + - + +
350A ASP* 3.2 26.1 + - - +
352A VAL* 4.8 2.9 + - - -
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Residues in contact with GLY 168 (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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166A LEU 4.0 0.2 + - - -
167A ARG* 1.3 77.3 - - - +
169A LEU* 1.3 61.0 + - - -
170A ASP 4.1 0.2 - - - -
176A ILE* 3.4 7.4 - - - +
177A LYS* 2.9 35.8 + - - -
284A MET* 4.6 9.2 - - - -
287A LEU* 3.8 15.5 - - - -
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Residues in contact with LEU 169 (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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168A GLY* 1.3 73.6 - - - -
170A ASP* 1.3 70.5 + - - +
171A THR* 3.3 15.7 + - + +
174A GLU* 4.3 4.3 - - - -
175A VAL 3.6 15.0 - - - +
176A ILE* 3.8 8.7 - - + -
284A MET 5.9 0.2 - - - -
286A PRO* 4.3 13.6 - - - +
287A LEU* 3.7 28.3 - - + +
290A SER* 4.2 10.5 - - - +
357A ILE* 3.7 30.1 - - + -
361A THR* 6.5 0.2 - - + -
363A PHE* 3.5 42.8 - - + -
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Residues in contact with ASP 170 (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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168A GLY 4.1 1.0 - - - -
169A LEU* 1.3 69.8 - - - +
171A THR* 1.3 53.4 + - - +
172A ASP* 3.0 23.0 + - - +
173A LYS* 3.1 22.8 + - - +
174A GLU* 2.7 35.7 + - - -
175A VAL* 3.0 17.3 + - + +
177A LYS* 2.8 42.7 + - - +
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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