Contacts of the helix formed by residues 512 - 525 (chain B) in PDB entry 5B2R
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 SER 512 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B LEU* 3.9 11.9 - - - +
509B PRO* 3.2 25.7 + - - -
510B LYS 3.3 0.6 - - - -
511B HIS* 1.3 80.1 - - - +
513B LEU* 1.3 61.8 + - - +
514B LEU* 3.2 2.6 + - - +
515B TYR* 3.1 19.9 + - - +
516B GLU* 3.0 22.6 + - - +
617B GLU* 2.6 27.5 + - - -
620B VAL* 3.9 12.6 - - - +
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Residues in contact with LEU 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B HIS 3.5 1.0 + - - -
512B SER* 1.3 71.3 + - - +
514B LEU* 1.3 60.1 + - + +
516B GLU* 3.1 6.9 + - + +
517B TYR* 2.8 48.8 + - + -
591B LEU* 5.3 0.5 - - - +
593B THR* 3.6 17.5 - - + +
594B TYR* 3.4 46.9 - - + +
597B LEU* 4.2 12.1 - - + -
607B LEU* 4.7 5.6 - - + +
616B LEU* 3.7 42.2 - - + +
617B GLU* 3.5 9.3 + - - +
620B VAL* 4.9 4.5 - - + +
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Residues in contact with LEU 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B LEU* 4.3 2.0 - - + -
512B SER* 3.6 4.3 - - - +
513B LEU* 1.3 77.8 - - + +
515B TYR* 1.3 63.5 + - - +
517B TYR* 3.2 16.8 + - + +
518B PHE* 2.9 24.3 + - - +
613B GLU* 3.5 37.5 - - + +
617B GLU* 3.0 27.2 + - - +
664B ARG* 3.3 42.4 - - + +
667B ILE* 3.9 13.6 - - + +
668B ASN* 4.5 17.7 - - + +
680B LEU* 4.8 8.0 - - + +
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Residues in contact with TYR 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A A 3.3 8.4 + - - -
5A A 2.5 30.3 + - - -
508B LEU* 4.1 21.2 - - + +
509B PRO 3.9 15.9 - - - +
510B LYS* 3.7 34.5 - - + +
512B SER* 3.1 15.0 + - - +
514B LEU* 1.3 78.1 - - - +
516B GLU* 1.3 59.5 + - + +
518B PHE* 3.3 10.0 + + - +
519B THR* 3.0 46.0 + - + +
660B GLY* 3.8 3.1 - - - -
661B ARG* 2.8 23.0 + - - +
662B LEU* 3.8 36.7 + - + +
667B ILE* 4.2 10.3 - - + -
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Residues in contact with GLU 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B LYS 4.1 13.3 - - - +
511B HIS* 4.3 14.5 - - - -
512B SER 3.0 16.7 + - - +
513B LEU* 3.1 4.7 + - + +
515B TYR* 1.3 77.7 - - + +
517B TYR* 1.3 60.2 + - - +
519B THR* 2.7 23.8 + - + +
520B VAL* 2.9 19.2 + - - +
590B SER* 3.7 20.8 + - - +
591B LEU* 3.7 10.0 - - + -
592B GLY* 3.1 11.9 + - - -
593B THR* 2.9 41.2 + - - -
594B TYR 4.5 0.7 + - - -
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Residues in contact with TYR 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B LEU* 2.8 40.5 + - + +
514B LEU* 3.5 17.7 - - + +
516B GLU* 1.3 74.6 - - - +
518B PHE* 1.3 62.6 + - - +
520B VAL* 3.3 1.6 + - + +
521B TYR* 2.9 50.7 + + + -
549B VAL* 4.8 3.6 - - + -
554B LYS* 3.1 39.7 + - - -
591B LEU* 3.9 25.8 - - + +
594B TYR* 3.6 16.9 - + + -
607B LEU 4.6 6.3 + - - -
680B LEU* 4.3 15.9 - - + -
684B LYS* 5.7 4.3 - - - -
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Residues in contact with PHE 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A A 3.7 20.4 - - - -
514B LEU 2.9 13.3 + - - +
515B TYR* 3.3 18.2 - + - +
516B GLU 3.2 0.2 - - - -
517B TYR* 1.3 75.6 - - - +
519B THR* 1.3 67.5 + - + +
522B ASN* 2.9 40.1 + - - +
662B LEU* 3.5 28.9 - - + -
667B ILE* 3.8 34.8 - - + -
679B ILE* 4.3 4.5 - - + -
680B LEU* 4.1 13.5 - - + +
683B LEU* 3.5 27.6 - - + +
693B PHE* 3.7 36.3 - + + -
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Residues in contact with THR 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A A 4.8 0.7 - - - +
5A A 3.7 38.1 - - - +
510B LYS* 6.1 0.7 - - - -
515B TYR* 3.0 25.1 + - + +
516B GLU* 2.7 27.7 + - + +
518B PHE* 1.3 87.9 - - + +
520B VAL* 1.3 62.5 + - - +
522B ASN* 3.5 4.2 + - - +
523B GLU* 3.3 18.4 + - - +
589B ALA* 3.6 24.3 - - - +
590B SER 4.6 2.3 + - - -
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Residues in contact with VAL 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B GLU 2.9 19.0 + - - +
517B TYR* 3.9 3.6 - - - +
519B THR* 1.3 76.9 + - - +
521B TYR* 1.3 62.2 + - + +
523B GLU* 3.3 3.7 + - - +
524B LEU* 2.9 28.6 + - + +
549B VAL* 4.2 15.9 - - + -
553B PHE* 3.8 41.7 - - + -
587B PHE* 5.7 0.3 - - - -
589B ALA* 3.8 7.0 - - + -
590B SER 3.7 28.3 - - - +
591B LEU* 3.6 22.4 - - + -
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Residues in contact with TYR 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B TYR* 2.9 46.8 + + - +
518B PHE 4.3 1.3 - - - +
520B VAL* 1.3 77.3 - - + +
522B ASN* 1.3 61.9 + - - +
524B LEU* 3.9 5.8 - - + +
525B THR* 2.9 34.0 + - - -
545B LYS* 4.3 21.8 - - + -
546B LYS* 4.2 14.3 - - - +
549B VAL* 3.6 40.0 - - + +
680B LEU* 4.2 6.5 - - + -
683B LEU* 3.8 22.2 - - + +
684B LYS* 3.7 54.8 - - + +
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Residues in contact with ASN 522 (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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4A A 4.8 20.4 + - - -
518B PHE* 2.9 30.7 + - + +
519B THR* 3.9 5.8 - - - +
520B VAL 3.3 0.2 - - - -
521B TYR* 1.3 77.2 - - - +
523B GLU* 1.3 62.3 + - - +
525B THR* 3.5 13.0 - - - +
526B LYS* 4.2 5.4 + - - +
683B LEU* 3.4 14.9 - - + +
692B ASN* 3.2 17.9 + - - +
693B PHE* 2.8 43.6 + - - +
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Residues in contact with GLU 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A A 4.7 1.8 + - - -
519B THR 3.3 13.1 + - - +
520B VAL 3.8 2.5 - - - +
522B ASN* 1.3 78.8 - - - +
524B LEU* 1.3 64.5 + - - +
526B LYS* 3.3 14.5 + - - +
527B VAL* 3.7 9.6 + - - +
582B GLY 4.8 11.5 - - - +
583B VAL* 4.1 8.7 - - - +
587B PHE* 3.5 24.5 - - + +
588B ASN* 2.9 34.8 + - - +
589B ALA* 2.8 33.3 + - + +
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Residues in contact with LEU 524 (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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520B VAL* 2.9 19.1 + - + +
521B TYR* 3.9 7.9 - - + +
523B GLU* 1.3 77.5 - - - +
525B THR* 1.3 62.6 + - - +
526B LYS 3.1 0.2 - - - -
527B VAL* 3.0 24.8 + - + +
540B LEU* 3.5 33.1 - - + +
545B LYS* 3.6 45.5 - - + +
548B ILE* 4.3 16.2 - - + -
549B VAL* 4.1 15.7 - - + -
553B PHE* 4.3 12.6 - - + -
564B LEU* 5.7 0.4 - - + -
587B PHE* 3.9 26.7 - - + -
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Residues in contact with THR 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B TYR 2.9 15.3 + - - +
522B ASN* 3.5 17.3 - - - +
524B LEU* 1.3 75.7 - - - +
526B LYS* 1.3 60.1 + - + +
527B VAL 3.5 0.7 - - - -
539B PHE* 3.5 4.9 - - - -
545B LYS* 2.9 26.2 + - - +
682B PHE 4.9 0.5 + - - -
683B LEU* 3.5 15.2 + - + -
690B ASN* 2.9 60.8 + - - +
691B ARG 4.2 2.5 - - - +
692B ASN* 4.1 19.7 - - + -
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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