Contacts of the strand formed by residues 287 - 291 (chain A) in PDB entry 2A3K
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 ILE 287 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A VAL* 2.9 19.6 + - + +
165A TYR* 3.2 23.3 - - + +
166A ILE 2.9 20.0 + - - +
190A LEU* 3.7 36.3 - - + +
192A VAL* 4.5 8.5 - - + -
274A VAL* 4.0 19.3 - - + +
285A GLY 4.7 4.3 - - - +
286A PRO* 1.3 73.2 - - - +
288A VAL* 1.3 71.3 + - - +
289A VAL* 3.4 12.5 + - + +
301A PHE* 5.4 0.7 - - + -
305A ARG* 3.7 26.7 - - - +
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Residues in contact with VAL 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ILE* 3.3 20.6 - - + +
168A THR* 4.1 13.5 - - + -
179A PHE* 3.8 30.1 - - + -
182A MET* 4.2 16.4 - - + -
183A VAL* 4.4 5.8 - - + -
188A VAL* 3.7 27.6 - - + -
190A LEU 3.0 7.9 + - - +
191A ILE* 3.3 20.9 - - + -
192A VAL 2.8 25.5 + - - -
286A PRO 3.8 1.8 + - - -
287A ILE* 1.3 71.6 - - - +
289A VAL* 1.3 64.2 + - - +
290A HIS* 4.2 3.8 - - + -
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 4.4 2.9 - - + -
166A ILE 2.8 7.2 + - - +
167A ALA* 3.4 4.9 - - - -
168A THR* 3.3 22.5 + - - +
192A VAL* 3.3 13.0 - - + +
194A LEU* 4.2 9.9 - - + -
287A ILE* 3.9 17.3 - - + +
288A VAL* 1.3 80.7 - - - +
290A HIS* 1.3 65.6 + - - +
298A THR* 3.8 31.6 - - + +
301A PHE* 3.9 38.4 - - + -
302A ILE* 4.2 13.9 - - + -
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Residues in contact with HIS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A THR* 3.1 30.5 - - + +
169A GLN 3.6 3.1 - - - +
170A GLY* 3.6 19.5 - - - -
171A PRO* 4.7 0.4 - - + -
179A PHE* 4.1 20.2 - + - -
191A ILE* 4.1 6.9 - - + +
192A VAL 3.0 14.5 + - - +
193A MET* 3.4 39.2 - - + +
194A LEU* 2.9 27.8 + - - +
207A TYR* 2.7 35.8 + + - -
288A VAL* 4.2 2.2 - - + -
289A VAL* 1.3 75.0 - - - +
291A CYS* 1.3 63.2 + - - +
298A THR* 3.5 6.1 - - - -
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Residues in contact with CYS 291 (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 THR 3.9 0.2 + - - -
170A GLY* 3.1 16.4 + - - -
193A MET* 6.1 0.4 - - - -
194A LEU* 3.3 24.2 - - + +
290A HIS* 1.3 75.2 - - - +
292A SER* 1.3 69.1 + - - +
294A GLY* 3.0 21.0 + - - -
297A ARG* 3.9 13.2 - - + +
298A THR* 2.9 38.8 + - - +
501A PO4 3.2 30.3 - - - +
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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