Contacts of the strand formed by residues 591 - 594 (chain A) in PDB entry 2JIM
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 ALA 591 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A SER 3.4 14.6 - - - +
152A PHE* 3.9 11.7 - - + -
250A TYR 2.8 10.7 + - - +
251A VAL* 3.4 2.9 - - - -
252A ASN 2.8 23.9 + - - -
328A LEU* 3.7 33.2 - - + -
583A PHE* 3.6 22.3 - - + -
586A LYS* 4.6 0.9 - - - -
590A ARG* 1.3 73.1 - - - +
592A VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 592 (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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150A THR 4.1 5.8 - - - +
151A SER* 3.1 15.2 + - - -
252A ASN* 3.3 20.2 - - + +
254A MET* 3.6 26.9 - - + -
325A ASN* 4.1 2.3 - - - +
328A LEU* 3.6 13.5 - - - +
586A LYS* 3.7 22.0 - - + +
590A ARG 4.1 5.8 - - - +
591A ALA* 1.3 81.5 - - - +
593A ILE* 1.3 65.2 + - - +
594A TRP* 3.3 42.3 + - + +
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Residues in contact with ILE 593 (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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247A TRP* 5.2 0.4 - - + -
251A VAL* 3.7 14.8 - - + -
252A ASN 2.8 10.6 + - - +
253A PHE* 3.5 30.1 - - + -
254A MET 3.0 25.1 + - - -
266A TYR* 3.7 27.6 - - + -
325A ASN* 3.1 24.2 - - - +
328A LEU* 3.7 29.4 - - + -
329A ILE* 3.7 27.1 - - + +
591A ALA 4.3 0.2 - - - -
592A VAL* 1.3 74.9 - - - +
594A TRP* 1.3 62.9 + - - +
595A MET* 5.6 0.7 - - + -
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Residues in contact with TRP 594 (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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150A THR* 2.9 38.9 + - + -
151A SER* 4.3 2.2 - - - -
230A HIS* 4.4 1.4 - - - -
254A MET* 3.5 33.0 - - + -
255A ASP 5.1 1.8 - - - -
258A GLY* 3.9 20.4 - - - -
266A TYR* 5.2 0.2 - - - -
321A ASN* 4.0 17.7 - - + +
322A LEU* 4.0 1.2 - - - +
325A ASN* 3.0 27.9 + - - -
586A LYS* 4.7 6.3 - - - -
592A VAL* 3.3 29.1 - - + +
593A ILE* 1.3 72.2 - - - +
595A MET* 1.3 62.0 + - - +
596A ARG* 3.0 66.2 + - + +
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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