Contacts of the helix formed by residues 510 - 524 (chain B) in PDB entry 5I94
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 510 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B SER* 5.3 1.2 - - - -
482B GLY 5.5 1.2 + - - -
485B GLY* 3.4 22.3 + - - -
487B ILE* 4.0 14.3 - - - +
501B SER* 3.0 33.8 + - - -
503B PRO 3.7 7.2 - - - -
504B LEU* 3.6 6.0 - - - +
509B ASN* 1.3 71.5 - - - +
511B VAL* 1.3 57.0 + - - +
513B GLY* 3.2 16.4 + - - -
514B ILE* 2.8 31.6 + - - +
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Residues in contact with VAL 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B GLN* 3.9 30.3 - - + +
242B GLY* 3.5 36.8 - - - +
243B GLY* 3.9 3.6 - - - -
503B PRO* 3.2 15.3 + - + +
505B ASP* 3.7 29.6 - - + +
509B ASN 3.2 1.5 + - - -
510B SER* 1.3 71.6 + - - +
512B LYS* 1.3 63.7 + - + +
514B ILE* 3.3 7.1 + - - +
515B HIS* 3.1 21.3 + - - +
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Residues in contact with LYS 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ALA* 3.8 19.7 - - - +
238B LYS* 3.7 22.2 - - - +
240B GLN* 3.8 23.7 + - - +
241B SER* 5.2 3.3 - - - +
242B GLY 6.0 0.2 - - - +
257B PRO 3.4 19.2 + - - -
258B ASP* 4.4 5.0 + - - +
259B LEU 4.0 3.2 + - - -
260B TRP* 3.8 44.7 - - + -
501B SER* 2.8 26.4 + - - +
503B PRO* 4.3 9.1 + - - +
510B SER* 3.5 1.8 + - - -
511B VAL* 1.3 74.3 - - + +
513B GLY* 1.3 60.5 + - - +
515B HIS* 3.2 6.8 + - - +
516B PHE* 2.8 32.6 + - - +
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Residues in contact with GLY 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B TRP* 4.1 2.8 - - - -
487B ILE* 3.6 19.1 - - - -
499B CYS* 4.2 20.1 - - - -
510B SER* 3.2 16.6 + - - -
512B LYS* 1.3 78.9 - - - +
514B ILE* 1.3 61.0 + - - +
516B PHE* 3.4 2.3 + - - +
517B CYS* 3.1 28.1 + - - -
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Residues in contact with ILE 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B MET* 3.6 30.5 - - + -
467B PHE* 4.2 17.5 - - + -
471B PHE* 3.9 19.1 - - + -
487B ILE* 3.8 2.9 - - + +
505B ASP* 4.3 9.4 - - - +
509B ASN* 3.9 16.4 - - + +
510B SER 2.8 19.1 + - - +
511B VAL* 3.7 6.1 - - - +
512B LYS 3.2 0.2 - - - -
513B GLY* 1.3 76.2 - - - +
515B HIS* 1.3 64.4 + - - +
517B CYS* 3.2 4.1 + - - +
518B HIS* 3.1 41.8 + - + +
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Residues in contact with HIS 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B SER* 3.3 32.1 - - - -
237B ALA* 3.5 16.7 - - + -
240B GLN* 3.3 32.9 + - + -
511B VAL 3.1 13.9 + - - +
512B LYS* 3.2 10.1 + - - +
514B ILE* 1.3 78.8 - - - +
516B PHE* 1.3 63.5 + - - +
518B HIS* 3.5 6.4 + - + +
519B ASP* 3.2 35.5 + - - +
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Residues in contact with PHE 516 (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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230B ILE* 4.0 22.9 - - + -
233B LEU* 3.5 40.4 - - + -
234B TYR 3.8 7.9 - - - -
237B ALA* 4.3 5.5 - - + +
260B TRP* 4.0 21.3 - + + -
262B VAL* 3.8 23.6 - - + -
497B MET* 3.2 28.0 - - + -
499B CYS* 3.8 16.4 - - - -
512B LYS 2.8 20.1 + - - +
513B GLY* 3.6 5.2 - - - +
515B HIS* 1.3 72.9 - - - +
517B CYS* 1.3 61.5 + - - +
519B ASP* 2.9 10.2 + - - +
520B LEU* 2.9 37.7 + - + -
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Residues in contact with CYS 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B PHE* 4.0 34.5 - - + -
475B VAL* 4.1 7.7 - - + +
477B LEU* 5.5 0.6 - - - +
487B ILE* 4.5 13.7 - - - -
489B LEU* 3.7 30.1 - - - -
499B CYS* 4.6 7.9 - - - -
513B GLY 3.1 17.8 + - - +
514B ILE 3.2 5.1 + - - +
516B PHE* 1.3 81.4 - - - +
518B HIS* 1.3 59.7 + - - +
520B LEU* 3.6 4.4 + - - +
521B VAL* 3.5 27.9 + - - +
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Residues in contact with HIS 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B PHE* 4.0 25.3 - + - -
470B GLN 5.3 0.8 + - - -
471B PHE* 4.9 2.5 - + - -
474B HIS* 3.7 35.1 - + + +
475B VAL* 3.8 20.6 - - + +
514B ILE* 3.1 43.2 + - + +
515B HIS* 4.0 7.9 - - + +
517B CYS* 1.3 75.2 - - - +
519B ASP* 1.3 63.8 + - - +
521B VAL* 3.6 2.8 + - - +
522B SER* 3.0 28.6 + - - +
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Residues in contact with ASP 519 (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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233B LEU* 3.6 26.6 - - + +
236B SER* 3.2 29.1 + - - -
237B ALA* 5.8 0.2 - - - -
515B HIS* 3.2 32.1 + - - +
516B PHE* 2.9 13.1 + - - +
518B HIS* 1.3 75.9 - - - +
520B LEU* 1.3 60.3 - - - +
522B SER* 2.9 9.4 + - - -
523B LEU* 2.9 30.5 + - - +
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Residues in contact with LEU 520 (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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226B PHE* 4.9 1.6 - - + -
230B ILE* 4.3 17.7 - - + -
233B LEU* 3.6 25.1 - - + +
477B LEU* 4.9 9.2 - - + -
489B LEU* 4.1 17.9 - - + -
491B VAL* 4.9 0.7 - - + -
495B MET* 4.0 20.9 - - + -
497B MET* 4.1 13.2 - - - -
516B PHE* 2.9 21.3 + - + +
517B CYS* 3.9 5.6 - - - +
518B HIS 3.4 0.2 - - - -
519B ASP* 1.3 77.2 - - - +
521B VAL* 1.3 58.4 + - + +
523B LEU* 3.5 0.8 + - + +
524B CYS* 2.9 46.1 + - - +
526B PHE* 4.2 17.4 - - + -
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Residues in contact with VAL 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B HIS 4.4 9.2 - - - +
475B VAL* 3.6 20.6 - - + +
477B LEU* 3.8 29.4 - - + -
517B CYS 3.5 16.8 + - - +
518B HIS* 4.4 2.9 - - - +
519B ASP 3.2 0.4 - - - -
520B LEU* 1.3 79.0 - - + +
522B SER* 1.3 61.6 + - - +
523B LEU 3.3 0.4 - - - -
524B CYS 2.8 10.6 - - - +
526B PHE* 4.5 7.2 - - + -
527B HIS* 3.6 37.5 - - + +
538B LYS* 2.8 33.1 + - - +
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Residues in contact with SER 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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518B HIS* 3.0 16.5 + - - +
519B ASP* 2.9 13.0 + - - -
521B VAL* 1.3 79.1 - - - +
523B LEU* 1.3 63.0 + - - +
537B LYS* 6.1 1.0 - - - -
538B LYS* 3.7 17.8 - - - +
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Residues in contact with LEU 523 (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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226B PHE* 6.4 0.2 - - + -
229B HIS* 3.7 46.4 - - + +
233B LEU* 4.2 25.6 - - + -
519B ASP 2.9 14.0 + - - +
520B LEU* 3.9 3.6 - - + +
522B SER* 1.3 78.4 - - - +
524B CYS* 1.3 64.3 + - - +
538B LYS* 3.3 8.1 - - - -
539B LEU* 2.8 44.4 + - + -
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Residues in contact with CYS 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PHE* 4.6 5.6 - - - -
520B LEU* 2.9 27.2 + - - +
521B VAL* 2.8 23.6 - - - +
523B LEU* 1.3 94.6 - - - +
525B ASN* 1.3 57.6 + - - +
526B PHE* 2.9 36.6 + - + -
538B LYS* 3.5 4.6 + - - +
539B LEU* 3.2 13.9 - - - +
541B PRO* 3.8 23.1 - - + -
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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
------------------------------------------------------------
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