Contacts of the strand formed by residues 499 - 506 (chain A) in PDB entry 2E3M
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 499 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379A MET* 3.8 26.9 - - + +
488A LYS* 3.5 4.3 - - - +
489A ILE* 2.7 47.4 + - + +
497A PRO 4.4 1.7 + - - -
498A GLU* 1.3 73.7 - - - +
500A TRP* 1.3 68.3 + - - +
501A ILE* 4.7 1.3 - - + +
528A ILE* 3.4 33.0 - - + -
529A CYS 3.5 7.0 - - - +
530A GLN* 2.5 30.1 + - + +
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Residues in contact with TRP 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A GLY* 3.7 9.6 - - - +
430A HIS* 3.4 67.6 - + - +
433A CYS* 3.6 18.0 - - - -
434A ASN* 5.1 0.2 - - - -
486A ILE* 3.9 29.8 - - + -
487A ARG* 3.4 17.5 - - - -
488A LYS* 3.6 46.0 - - + +
498A GLU* 4.9 9.0 + - + -
499A THR* 1.3 80.7 - - - +
501A ILE* 1.3 61.3 - - - +
528A ILE* 3.6 0.2 - - - -
529A CYS 2.8 35.4 + - - +
531A THR* 5.8 0.7 - - - -
598A PHE* 4.0 9.7 + - - -
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Residues in contact with ILE 501 (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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375A VAL* 4.4 16.2 - - + +
378A HIS* 3.8 25.1 - - + -
379A MET* 4.7 6.3 - - - -
433A CYS* 3.9 1.5 - - - -
485A VAL 3.7 0.9 - - - +
486A ILE* 3.4 3.3 - - - +
487A ARG* 2.8 59.6 + - + +
489A ILE* 4.2 19.3 - - + -
499A THR* 4.8 1.1 - - + -
500A TRP* 1.3 77.3 - - - +
502A VAL* 1.3 67.6 + - - +
503A CYS* 3.6 27.1 - - - -
526A ALA* 4.2 2.2 - - + -
527A MET 3.3 9.9 - - - +
528A ILE* 3.8 20.6 - - + -
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Residues in contact with VAL 502 (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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433A CYS* 3.4 44.0 - - + +
436A PHE* 3.6 29.7 - - + -
437A TRP* 3.8 24.7 - - + -
484A SER* 4.0 0.7 - - - +
485A VAL 3.1 10.1 - - - +
486A ILE* 4.3 4.0 - - + -
501A ILE* 1.3 75.1 - - - +
503A CYS* 1.3 61.0 + - - +
504A ASN* 3.5 20.4 + - - +
525A VAL 3.8 0.3 - - - +
526A ALA* 3.2 6.8 - - - +
527A MET* 3.1 31.2 + - + +
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Residues in contact with CYS 503 (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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374A MET* 4.6 1.1 - - + -
375A VAL* 3.5 32.8 - - + -
378A HIS* 3.9 19.3 - - + -
483A LEU 3.4 4.2 - - - +
485A VAL* 2.8 47.2 + - + +
501A ILE* 3.6 24.2 - - - -
502A VAL* 1.3 71.2 - - - +
504A ASN* 1.3 62.4 + - - +
505A PHE* 4.1 14.8 - - + -
525A VAL 3.5 4.7 - - - +
526A ALA* 4.7 0.2 - - - -
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Residues in contact with ASN 504 (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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436A PHE* 3.6 30.9 + - - -
442A ARG* 5.1 5.3 - - - +
482A TYR* 3.7 24.4 - - + -
483A LEU 3.3 4.7 - - - -
484A SER* 2.7 28.5 + - - -
502A VAL* 3.5 8.3 - - - +
503A CYS* 1.3 75.8 - - - +
505A PHE* 1.3 60.2 + - - +
523A ILE* 4.0 13.1 - - + +
524A ASN* 3.5 1.4 - - - -
525A VAL* 2.7 52.8 + - + +
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Residues in contact with PHE 505 (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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367A PHE* 5.1 1.3 - + - -
370A LYS* 3.7 27.1 - - + -
371A VAL* 3.7 26.7 - - + -
374A MET* 3.8 44.6 - - + -
482A TYR* 3.7 5.7 - - - +
483A LEU* 2.8 67.1 + - + -
485A VAL* 4.5 0.4 - - + -
503A CYS* 4.2 17.0 - - + -
504A ASN* 1.3 76.7 - - - +
506A SER* 1.3 68.4 + - - +
507A VAL* 3.6 24.9 - - + -
523A ILE* 3.3 10.8 - - - +
524A ASN* 4.3 2.7 - - + +
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Residues in contact with SER 506 (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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370A LYS* 5.2 4.0 - - - -
480A VAL* 4.1 1.9 - - - +
481A LEU 3.4 13.7 + - - -
482A TYR* 4.0 1.7 - - - +
505A PHE* 1.3 78.5 - - - +
507A VAL* 1.3 65.9 + - - +
521A ALA 3.8 5.5 + - - -
522A LYS* 3.4 37.5 + - - -
523A ILE* 2.8 40.1 + - - +
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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