Contacts of the strand formed by residues 478 - 489 (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 ARG 478 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468A THR* 3.7 2.6 - - - +
469A HIS* 3.1 41.6 + - + +
470A LYS 5.6 0.6 + - - -
472A VAL 5.4 0.2 + - - -
475A ALA* 3.3 32.9 - - - +
476A SER 3.6 6.8 + - - +
477A GLN* 1.3 73.8 - - - +
479A ASP* 1.3 63.7 + - - +
518A CYS* 4.3 1.8 - - - -
519A VAL* 3.0 40.7 - - - +
521A ALA* 4.2 12.8 - - + -
559A PRO* 3.4 39.3 + - + +
561A GLY* 4.3 11.5 - - - -
562A TRP 4.5 10.1 + - - +
563A ALA* 5.2 4.8 - - - +
568A LEU* 5.1 10.1 - - - +
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Residues in contact with ASP 479 (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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466A TYR* 2.6 31.9 + - + +
467A GLN 3.3 12.6 - - - +
468A THR* 4.3 2.2 - - - +
469A HIS* 5.1 0.4 - - - -
478A ARG* 1.3 76.2 - - - +
480A VAL* 1.3 63.7 + - - +
515A ASN* 3.5 9.0 + - - +
518A CYS* 3.4 20.1 - - + +
519A VAL 2.8 10.5 + - - +
520A ARG* 2.8 50.9 + - - +
521A ALA* 3.0 26.9 + - - +
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Residues in contact with VAL 480 (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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465A ILE 3.8 1.0 - - - +
466A TYR* 3.6 7.0 - - - -
467A GLN* 2.9 70.7 + - + +
469A HIS* 3.7 12.8 - - + +
479A ASP* 1.3 76.8 - - - +
481A LEU* 1.3 63.8 + - - +
482A TYR* 4.0 9.9 - - + -
506A SER* 4.1 3.6 - - - +
520A ARG* 4.2 5.8 - - - +
521A ALA* 3.9 18.2 - - + +
523A ILE* 3.8 41.5 - - + -
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Residues in contact with LEU 481 (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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455A VAL* 4.5 3.6 - - + -
464A ILE* 3.8 25.6 - - + -
465A ILE 3.5 7.6 - - - +
466A TYR* 4.3 13.2 - - + -
480A VAL* 1.3 78.3 - - - +
482A TYR* 1.3 58.6 + - - +
506A SER* 3.4 9.9 - - - -
507A VAL 3.1 41.8 + - - +
508A ASP* 4.1 2.5 - - - +
509A HIS* 3.5 22.4 - - + +
512A ALA* 3.4 42.6 - - + +
520A ARG* 3.8 23.5 - - - +
521A ALA 5.0 0.4 + - - -
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Residues in contact with TYR 482 (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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442A ARG* 3.1 20.1 + - - -
464A ILE* 3.3 3.0 - - - -
465A ILE* 2.8 72.3 + - + +
467A GLN* 2.6 43.3 + - + -
480A VAL* 4.0 19.3 - - + -
481A LEU* 1.3 76.1 - - - +
483A LEU* 1.3 67.7 + - - +
484A SER* 3.7 1.7 + - - -
504A ASN* 3.7 37.6 + - + -
505A PHE 3.3 20.4 - - - +
506A SER* 4.0 1.1 - - - +
507A VAL* 4.1 5.2 - - - +
523A ILE* 3.9 15.5 - - + -
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Residues in contact with LEU 483 (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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365A HIS* 4.7 0.2 - - + -
367A PHE* 3.4 44.0 - - + -
371A VAL* 3.6 23.1 - - + -
458A LEU* 3.5 22.9 - - + -
462A ALA* 4.8 4.5 - - + -
463A ILE 3.4 6.5 - - - +
464A ILE* 4.3 4.0 - - + +
482A TYR* 1.3 71.4 - - - +
484A SER* 1.3 62.4 + - - +
485A VAL* 3.9 16.6 - - + -
503A CYS 3.4 2.3 - - - +
504A ASN* 3.3 4.0 - - - -
505A PHE* 2.8 52.8 + - + +
507A VAL* 3.8 18.8 - - + +
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Residues in contact with SER 484 (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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437A TRP* 3.0 32.0 + - - -
442A ARG* 4.9 2.9 + - - -
462A ALA* 3.5 0.2 - - - -
463A ILE* 2.8 33.9 + - - -
465A ILE* 3.9 28.0 - - - +
482A TYR* 3.7 5.9 + - - -
483A LEU* 1.3 72.5 - - - +
485A VAL* 1.3 60.2 + - - +
502A VAL* 4.0 1.0 - - - +
503A CYS 3.4 3.6 - - - -
504A ASN* 2.7 20.4 + - - -
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Residues in contact with VAL 485 (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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365A HIS* 6.0 0.2 - - - +
371A VAL* 4.0 24.7 - - + -
375A VAL* 5.1 0.2 - - + -
437A TRP* 3.9 3.4 - - - -
461A ASN* 3.2 30.5 - - - +
462A ALA* 4.1 8.5 - - + -
483A LEU* 3.9 21.3 - - + -
484A SER* 1.3 75.2 + - - +
486A ILE* 1.3 62.2 + - - +
487A ARG* 3.9 16.8 - - + +
501A ILE 3.7 0.7 - - - +
502A VAL* 3.1 6.1 - - - +
503A CYS* 2.8 57.5 + - + +
505A PHE* 4.5 0.7 - - + -
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Residues in contact with ILE 486 (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* 3.5 42.8 - - + +
434A ASN* 3.6 21.5 - - - +
437A TRP* 3.5 39.2 - - + +
461A ASN* 3.0 46.5 + - + +
485A VAL* 1.3 72.3 - - - +
487A ARG* 1.3 63.7 + - - +
500A TRP* 3.9 22.0 - - + -
501A ILE 3.4 6.7 - - - +
502A VAL* 4.4 0.9 - - + +
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Residues in contact with ARG 487 (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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362A VAL* 3.3 35.1 - - - +
371A VAL* 4.8 3.8 - - + -
372A GLU* 2.9 40.0 + - - +
375A VAL* 4.4 13.8 - - + +
461A ASN* 3.7 18.4 - - - +
485A VAL* 3.9 15.5 - - + -
486A ILE* 1.3 76.1 - - - +
488A LYS* 1.3 85.1 + - - +
489A ILE* 4.0 17.7 - - + +
490A PRO* 5.5 0.8 - - - +
500A TRP* 3.4 11.6 - - - -
501A ILE* 2.8 52.2 + - + +
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Residues in contact with LYS 488 (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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487A ARG* 1.3 91.9 + - - +
489A ILE* 1.3 65.8 + - - +
490A PRO* 3.3 27.4 - - - +
498A GLU* 3.6 36.2 + - + +
499A THR 3.5 8.3 - - - +
500A TRP* 3.6 45.6 - - + +
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Residues in contact with ILE 489 (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* 3.8 22.2 - - + -
379A MET* 4.3 33.2 - - + -
487A ARG* 4.0 27.4 - - + +
488A LYS* 1.3 81.5 - - - +
490A PRO* 1.4 82.3 - - + +
491A ALA 3.6 0.2 + - - -
498A GLU* 3.7 2.9 - - - +
499A THR* 2.7 43.7 + - - +
501A ILE* 4.2 15.5 - - + -
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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