Contacts of the helix formed by residues 495 - 509 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B ALA 5.6 0.2 - - - +
355B ILE 5.7 0.7 - - - -
357B SER* 5.3 2.0 - - - -
360B ALA* 4.9 0.9 - - - -
493B PRO 3.4 1.4 + - - -
494B CYS* 1.3 80.1 - - - +
496B GLN* 1.3 64.0 + - - +
497B VAL* 2.9 7.9 + - - +
498B GLU* 2.9 21.7 + - - +
499B SER* 2.8 28.0 + - - -
523B LEU* 4.3 12.1 - - - +
524B ALA 3.3 17.5 - - - +
525B GLN* 3.6 10.5 - - - +
526B GLN* 2.9 21.7 + - - +
528B ARG* 2.9 31.8 + - - -
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Residues in contact with GLN 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B LEU* 3.5 43.5 + - + +
351B ASN 3.2 21.8 + - - -
353B ALA* 3.5 24.2 + - - +
355B ILE* 3.7 24.2 + - + +
360B ALA* 3.5 26.3 - - + +
363B ASN* 4.6 5.2 + - - +
495B ASP* 1.3 77.8 - - - +
497B VAL* 1.3 59.3 + - + +
499B SER* 3.5 2.0 - - - -
500B ALA* 3.1 21.0 + - - +
523B LEU 5.5 0.6 + - - -
525B GLN* 2.8 29.0 + - - +
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Residues in contact with VAL 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ILE* 4.2 15.2 - - + +
348B LEU* 4.0 9.4 - - + -
349B GLN* 3.4 37.2 - - + +
495B ASP* 2.9 5.6 + - - +
496B GLN* 1.3 73.4 - - - +
498B GLU* 1.3 67.0 + - - +
499B SER 3.1 0.9 - - - -
500B ALA* 3.2 4.7 + - - +
501B VAL* 3.1 25.0 + - - +
525B GLN* 3.6 32.1 - - - +
528B ARG* 3.6 7.2 - - - +
533B LEU* 3.5 22.4 - - + -
536B ILE* 3.8 7.6 - - + -
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Residues in contact with GLU 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B TRP* 5.0 1.2 - - - -
492B ARG 4.2 0.7 - - - +
493B PRO* 3.5 13.5 - - + +
494B CYS* 2.8 38.7 + - - +
495B ASP* 2.9 9.3 + - - +
497B VAL* 1.3 75.2 - - - +
499B SER* 1.3 56.6 + - - +
501B VAL* 3.3 1.7 + - - +
502B ALA* 2.9 31.2 + - - +
528B ARG* 3.4 16.8 - - - +
536B ILE* 3.8 22.4 - - + +
541B TYR* 2.5 27.8 + - - +
558B GLY 5.2 0.2 + - - -
582B SER* 2.8 17.3 + - - -
584B PRO* 3.4 24.8 - - + +
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Residues in contact with SER 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B SER* 3.4 17.2 - - - -
360B ALA* 3.5 29.4 - - - +
361B SER* 4.6 2.9 - - - -
364B ALA* 5.3 0.9 - - - -
493B PRO* 3.3 24.8 - - - +
495B ASP 2.8 21.0 + - - -
496B GLN 3.5 1.1 - - - -
497B VAL 3.1 0.4 - - - -
498B GLU* 1.3 77.0 - - - +
500B ALA* 1.3 58.2 + - - +
502B ALA* 3.4 3.5 + - - +
503B TRP* 3.0 34.3 + - - +
516B LEU* 5.3 0.5 - - - +
518B LEU* 4.9 3.6 - - - -
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Residues in contact with ALA 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B PHE* 3.8 17.7 - - + -
345B ILE* 3.8 16.9 - - + +
348B LEU* 3.7 28.0 - - + -
360B ALA 5.3 0.6 + - - +
364B ALA* 4.5 6.7 - - + +
368B PHE* 4.2 4.3 - - + -
496B GLN 3.1 6.4 + - - +
497B VAL 3.2 6.7 + - - +
499B SER* 1.3 73.1 - - - +
501B VAL* 1.3 60.9 + - - +
503B TRP* 3.3 7.6 + - - +
504B LYS* 2.9 29.5 + - - +
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Residues in contact with VAL 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ILE* 3.9 21.8 - - + -
491B TRP* 4.5 4.7 - - + -
497B VAL 3.1 14.8 + - - +
498B GLU 3.3 2.4 + - - +
500B ALA* 1.3 74.0 - - - +
502B ALA* 1.3 57.8 + - - +
504B LYS* 3.3 3.5 + - - +
505B TYR* 2.9 27.5 + - + +
536B ILE* 3.7 35.9 - - + -
537B ALA* 3.7 23.3 - - + +
675B EDO 3.6 36.3 - - - +
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Residues in contact with ALA 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B TRP* 3.6 44.8 - - + -
493B PRO* 4.9 6.5 - - + -
498B GLU 2.9 17.7 + - - +
499B SER* 3.5 7.0 - - - +
501B VAL* 1.3 74.0 - - - +
503B TRP* 1.3 59.7 + - - +
505B TYR* 3.2 4.0 + - - +
506B GLY* 2.9 26.3 + - - -
514B THR* 4.4 1.6 - - - +
516B LEU* 3.8 15.9 - - + +
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Residues in contact with TRP 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B SER* 2.9 32.5 + - - -
364B ALA* 3.7 22.2 - - + -
365B ILE* 3.5 25.8 - - + -
368B PHE* 3.8 18.4 - + + -
375B PHE* 3.9 12.8 - + - -
430B TYR* 3.9 25.8 - + + -
456B VAL* 3.8 21.5 - - + -
458B VAL* 3.7 20.4 - - + -
499B SER* 3.0 18.1 + - - +
500B ALA 3.7 4.7 - - - +
502B ALA* 1.3 76.5 - - - +
504B LYS* 1.3 61.2 + - - +
506B GLY* 3.1 2.9 + - - +
507B VAL* 3.0 61.2 + - + +
516B LEU* 3.3 25.3 - - + +
518B LEU* 6.1 0.7 - - + -
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Residues in contact with LYS 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B PHE* 4.2 2.7 - - + -
338B ASP* 2.7 44.5 + - - +
341B ALA* 3.8 15.5 - - + -
342B LYS* 3.8 15.3 - - - +
345B ILE* 3.7 21.1 - - + -
368B PHE* 3.7 11.1 - - + -
500B ALA 2.9 13.6 + - - +
501B VAL 3.5 8.1 - - - +
503B TRP* 1.3 75.9 - - - +
505B TYR* 1.3 61.9 + - - +
507B VAL* 3.3 10.8 - - - +
508B GLU* 2.9 57.6 + - - +
675B EDO 3.9 9.0 + - - +
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Residues in contact with TYR 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B SER* 3.3 21.3 - - - -
491B TRP* 3.3 42.2 - + + -
501B VAL* 2.9 15.3 + - + +
502B ALA 3.2 8.5 + - - +
504B LYS* 1.3 75.5 - - - +
506B GLY* 1.3 63.5 + - - +
508B GLU* 3.3 6.7 + - - -
509B ARG* 3.0 44.0 + - + +
514B THR* 4.5 1.8 - - - -
537B ALA* 4.2 18.2 - - + -
587B ASP* 4.5 2.8 + - - -
588B ALA* 4.1 17.1 - - + +
591B LYS* 4.7 14.9 + - - +
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Residues in contact with GLY 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B ARG* 4.1 8.5 - - - +
455B GLN 5.5 0.9 + - - +
456B VAL* 3.8 17.6 - - - +
502B ALA 2.9 13.4 + - - -
503B TRP* 3.1 4.4 + - - -
505B TYR* 1.3 79.2 - - - +
507B VAL* 1.3 61.0 + - - +
508B GLU 3.4 0.2 + - - -
509B ARG* 3.4 13.9 + - - +
514B THR* 3.3 29.9 + - - -
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Residues in contact with VAL 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B MET* 3.6 18.1 - - + +
337B PHE* 3.6 33.7 - - + -
368B PHE* 4.2 1.8 - - + -
372B LEU* 4.1 5.8 - - + -
375B PHE* 4.0 10.3 - - + -
428B LEU* 3.7 25.6 - - + +
454B ARG* 3.6 17.3 + - - -
456B VAL* 4.2 4.0 - - + -
503B TRP* 3.0 46.2 + - + +
504B LYS* 3.3 15.7 - - - +
506B GLY* 1.3 77.5 - - - +
508B GLU* 1.3 60.5 + - - +
509B ARG 3.4 0.4 - - - +
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Residues in contact with GLU 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B MET* 4.2 17.0 - - + +
337B PHE* 3.7 21.8 - - + -
338B ASP* 4.0 11.6 - - - +
504B LYS* 2.9 62.5 + - - +
505B TYR* 3.7 5.3 + - - +
506B GLY 3.2 0.2 - - - -
507B VAL* 1.3 76.9 - - - +
509B ARG* 1.3 65.7 + - - +
510B GLN* 3.4 15.3 + - - +
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Residues in contact with ARG 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B ARG* 3.1 28.6 - - + +
487B ASN* 2.9 45.4 + - - -
488B MET 5.0 0.2 - - - -
489B SER* 3.5 19.8 - - - +
505B TYR* 3.0 33.2 + - + +
506B GLY 3.6 9.6 - - - +
507B VAL 3.4 1.4 - - - +
508B GLU* 1.3 76.7 - - - +
510B GLN* 1.3 61.6 + - - +
511B ASP* 3.4 20.9 + - - +
512B GLY* 3.3 25.9 - - - +
513B PRO 2.8 27.9 + - - -
514B THR* 3.2 18.2 - - - +
591B LYS* 4.1 18.7 - - - +
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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