Contacts of the helix formed by residues 495 - 509 (chain A) in PDB entry 2R5N
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 ASP 495 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A ILE 5.7 1.1 - - - -
357A SER* 5.2 1.3 - - - -
360A ALA* 5.0 0.7 - - - -
493A PRO* 3.4 1.3 - - - +
494A CYS* 1.3 80.6 - - - +
496A GLN* 1.3 59.0 + - - +
497A VAL* 2.9 8.3 + - - +
498A GLU* 2.8 22.5 + - - +
499A SER* 2.8 32.2 + - - -
523A LEU* 4.2 14.5 - - - +
524A ALA 3.3 16.8 - - - +
525A GLN* 3.6 12.5 - - + +
526A GLN 3.0 16.1 + - - -
528A ARG* 2.9 35.6 + - - -
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Residues in contact with GLN 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LEU* 3.4 44.0 + - + +
351A ASN 3.1 23.6 + - - -
353A ALA* 3.4 24.7 + - - +
355A ILE* 3.7 25.5 + - + +
360A ALA* 3.6 26.3 - - + +
363A ASN* 4.7 4.2 + - - -
495A ASP* 1.3 78.0 - - - +
497A VAL* 1.3 58.5 + - + +
499A SER* 3.5 2.3 - - - -
500A ALA 3.1 20.4 + - - -
523A LEU 5.4 1.0 + - - -
525A GLN* 2.8 28.6 + - - +
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Residues in contact with VAL 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ILE* 4.1 14.6 - - + +
348A LEU* 3.9 8.7 - - + -
349A GLN* 3.4 36.8 - - + +
495A ASP* 2.9 7.5 + - - +
496A GLN* 1.3 74.7 - - - +
498A GLU* 1.3 67.6 - - - +
499A SER 3.1 1.1 - - - -
500A ALA* 3.1 4.9 + - - +
501A VAL* 3.0 21.5 + - - +
525A GLN* 3.6 33.0 - - - +
528A ARG* 3.7 5.8 - - - +
533A LEU* 3.4 23.6 - - + -
536A ILE* 3.9 6.7 - - + -
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Residues in contact with GLU 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A TRP* 5.0 0.9 - - - -
492A ARG 4.2 0.5 - - - +
493A PRO* 3.4 14.2 - - + +
494A CYS* 2.8 35.0 + - - +
495A ASP* 2.8 8.4 + - - +
497A VAL* 1.3 74.4 - - - +
499A SER* 1.3 56.6 + - - +
501A VAL* 3.3 2.1 + - - +
502A ALA* 2.9 30.7 + - - +
528A ARG* 3.4 17.4 + - - +
536A ILE* 3.8 23.4 - - + +
541A TYR* 2.5 28.5 + - - +
558A GLY 5.3 0.2 + - - -
582A SER* 2.8 17.8 + - - -
584A PRO* 3.4 24.8 - - + +
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Residues in contact with SER 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A SER* 3.4 17.5 - - - -
360A ALA* 3.5 22.9 - - - +
361A SER* 4.7 2.2 - - - -
493A PRO* 3.3 25.1 - - - +
495A ASP 2.8 21.5 + - - -
496A GLN 3.5 7.2 - - - -
497A VAL 3.1 0.4 - - - -
498A GLU* 1.3 77.3 - - - +
500A ALA* 1.3 57.2 + - - +
502A ALA* 3.3 4.0 + - - +
503A TRP* 2.9 34.6 + - - +
516A LEU* 5.3 0.2 - - - +
518A LEU* 5.0 3.4 - - - -
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Residues in contact with ALA 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A PHE* 3.8 14.6 - - + -
345A ILE* 3.8 19.5 - - + +
348A LEU* 3.7 28.5 - - + -
360A ALA 5.3 1.1 + - - +
364A ALA* 4.6 6.0 - - + +
368A PHE* 4.3 4.0 - - + -
496A GLN 3.1 6.6 + - - +
497A VAL* 3.6 6.7 - - - +
499A SER* 1.3 73.4 - - - +
501A VAL* 1.3 60.6 + - - +
503A TRP* 3.3 7.2 + - - +
504A LYS* 2.9 29.5 + - - +
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Residues in contact with VAL 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ILE* 3.8 32.8 - - + -
491A TRP* 4.6 5.4 - - + -
497A VAL 3.0 18.0 + - - +
498A GLU 3.7 6.5 - - - +
500A ALA* 1.3 73.1 - - - +
502A ALA* 1.3 58.1 + - - +
504A LYS* 3.3 3.4 + - + +
505A TYR* 2.8 28.2 + - + +
533A LEU 4.8 4.0 - - - +
536A ILE* 3.6 39.0 - - + -
537A ALA* 3.9 27.6 - - + +
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Residues in contact with ALA 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A TRP* 3.6 44.2 - - + -
493A PRO* 4.9 5.2 - - + -
498A GLU 2.9 17.7 + - - +
499A SER* 3.6 7.2 - - - +
501A VAL* 1.3 75.8 - - - +
503A TRP* 1.3 57.5 + - - +
505A TYR* 3.3 4.1 + - - +
506A GLY* 2.8 27.2 + - - -
514A THR* 4.4 1.7 - - - +
516A LEU* 3.7 16.1 - - + +
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Residues in contact with TRP 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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361A SER* 2.8 33.0 + - - -
364A ALA* 3.6 23.8 - - + -
365A ILE* 3.4 32.5 - - + -
368A PHE* 3.8 18.2 - + + -
375A PHE* 3.9 13.2 - + - -
430A TYR* 4.0 22.0 - + + -
456A VAL* 3.7 21.3 - - + -
458A VAL* 3.8 16.6 - - + -
499A SER* 2.9 19.4 + - - +
500A ALA 3.7 4.7 - - - +
502A ALA* 1.3 76.2 - - - +
504A LYS* 1.3 62.7 + - - +
506A GLY* 3.2 2.4 + - - -
507A VAL* 3.0 47.9 + - + +
516A LEU* 3.3 23.7 - - + +
518A LEU* 6.1 0.2 - - + -
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Residues in contact with LYS 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A PHE* 4.3 1.8 - - + -
338A ASP* 2.8 34.3 + - - -
341A ALA* 3.7 28.3 - - + -
342A LYS* 4.1 14.5 - - + +
345A ILE* 3.8 18.6 - - + -
368A PHE* 3.8 10.7 - - + -
500A ALA 2.9 16.7 + - - +
501A VAL* 3.6 5.8 - - + +
503A TRP* 1.3 76.0 - - - +
505A TYR* 1.3 64.9 + - - +
507A VAL* 3.3 10.8 - - - +
508A GLU* 2.7 57.7 + - - +
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Residues in contact with TYR 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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489A SER* 3.3 22.5 + - - -
491A TRP* 3.4 40.8 - + + -
501A VAL* 2.8 14.4 + - + +
502A ALA 3.4 9.2 - - - +
504A LYS* 1.3 77.1 - - - +
506A GLY* 1.3 64.8 + - - +
508A GLU* 4.8 1.6 - - - -
509A ARG* 3.0 25.8 + - - +
514A THR* 4.3 5.4 - - + -
537A ALA* 4.3 18.6 - - + -
587A ASP* 4.5 3.1 + - - -
588A ALA* 4.2 14.6 - - + +
591A LYS* 4.9 4.9 + - - +
673A EDO 3.9 19.6 + - - -
674A EDO 2.8 53.6 + - - -
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Residues in contact with GLY 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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454A ARG* 4.2 5.5 - - - +
455A GLN 5.5 1.0 + - - +
456A VAL* 3.8 16.7 - - - +
502A ALA 2.8 14.2 + - - -
503A TRP* 3.2 3.7 + - - -
505A TYR* 1.3 76.9 - - - +
507A VAL* 1.3 60.7 + - - +
509A ARG* 3.2 18.0 + - - +
512A GLY 5.3 0.5 - - - +
514A THR* 3.4 30.2 + - - -
516A LEU* 5.8 0.2 - - - -
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Residues in contact with VAL 507 (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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333A MET* 3.7 17.5 - - + +
337A PHE* 3.7 33.4 - - + -
368A PHE* 4.1 2.0 - - + -
372A LEU* 4.1 3.6 - - + -
375A PHE* 4.0 10.5 - - + -
428A LEU* 3.7 24.8 - - + +
454A ARG* 3.5 21.1 + - - -
456A VAL* 4.1 5.4 - - + -
503A TRP* 3.0 43.1 + - + +
504A LYS* 3.3 15.5 - - - +
506A GLY* 1.3 76.2 - - - +
508A GLU* 1.3 57.8 + - - +
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Residues in contact with GLU 508 (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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333A MET* 4.2 24.6 - - + +
337A PHE* 3.6 18.0 - - + -
338A ASP* 4.0 11.6 + - - +
504A LYS* 2.7 59.6 + - - +
505A TYR* 4.9 1.2 + - - -
507A VAL* 1.3 77.3 - - - +
509A ARG* 1.3 59.2 + - - +
510A GLN* 3.3 20.0 + - - +
674A EDO 3.2 17.2 + - - +
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Residues in contact with ARG 509 (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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454A ARG* 3.2 24.8 - - - +
487A ASN* 2.8 46.9 + - - -
489A SER* 3.6 12.2 - - - +
505A TYR* 3.0 31.4 + - - +
506A GLY 3.2 8.3 + - - +
507A VAL 3.3 0.2 - - - -
508A GLU* 1.3 74.9 - - - +
510A GLN* 1.3 62.0 + - - +
511A ASP* 3.8 5.6 + - - +
512A GLY* 3.3 29.9 - - - +
513A PRO 2.9 25.4 + - - -
514A THR* 3.5 14.4 - - - +
591A LYS* 3.4 19.3 - - - +
673A EDO 2.9 33.0 + - - +
674A EDO 3.6 8.7 - - - -
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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
------------------------------------------------------------
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