Contacts of the helix formed by residues 516 - 530 (chain B) in PDB entry 5D3O
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 516 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487B SER* 5.2 1.4 - - - -
488B GLY 5.4 0.6 + - - -
491B GLY* 3.3 27.7 + - - -
492B GLY 5.4 0.4 + - - -
493B ILE* 4.2 15.8 - - - +
506B TRP* 4.7 0.5 + - - -
507B SER* 3.0 29.0 + - - -
509B PRO 3.5 8.1 - - - -
510B LEU* 3.6 8.1 - - - +
515B ASN* 1.3 71.1 - - - +
517B VAL* 1.3 57.3 + - - +
519B GLY* 3.2 16.9 + - - -
520B ILE* 2.9 30.3 + - - +
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Residues in contact with VAL 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B GLN* 4.7 20.0 - - + +
248B GLY* 4.3 22.4 - - - +
249B GLY* 3.7 19.1 - - - +
509B PRO* 3.0 13.1 + - + +
510B LEU 3.7 25.8 - - - -
511B ASP* 3.7 15.7 - - + +
515B ASN 3.1 1.1 + - - -
516B SER* 1.3 68.7 - - - +
518B LYS* 1.3 69.1 + - + +
520B ILE* 3.4 6.7 + - - +
521B HIS* 3.0 21.0 + - - +
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Residues in contact with LYS 518 (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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243B ALA* 3.2 27.6 - - - +
244B LYS* 4.0 12.6 + - - +
246B GLN* 3.4 22.1 + - - +
247B SER* 4.5 8.7 + - - +
248B GLY 5.4 2.0 + - - -
263B PRO 4.6 13.2 + - - -
264B ASP* 5.9 1.8 - - - +
265B LEU 4.4 3.8 - - - +
266B TRP* 3.7 45.8 - - + -
507B SER* 3.3 27.1 + - - +
509B PRO* 4.8 8.0 + - + +
516B SER* 3.5 1.4 + - - -
517B VAL* 1.3 80.2 - - + +
519B GLY* 1.3 58.0 + - - +
521B HIS* 3.1 9.6 + - - +
522B PHE* 2.9 28.2 + - - +
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Residues in contact with GLY 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B TRP* 3.9 15.2 - - - -
493B ILE* 3.9 17.3 - - - -
505B CYS* 4.4 6.0 - - - -
516B SER* 3.2 17.5 + - - -
517B VAL 3.2 0.6 - - - -
518B LYS* 1.3 75.8 - - - +
520B ILE* 1.3 64.8 + - - +
522B PHE* 3.3 3.0 + - - +
523B CYS* 3.0 29.1 + - - -
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Residues in contact with ILE 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B MET* 3.3 32.8 - - + -
473B PHE* 4.4 11.9 - - + -
477B PHE* 4.1 18.4 - - + -
493B ILE* 4.0 2.9 - - + +
511B ASP* 4.5 9.4 - - - +
515B ASN* 3.8 20.0 - - + +
516B SER 2.9 20.7 + - - +
517B VAL* 3.7 5.6 - - - +
519B GLY* 1.3 73.4 - - - +
521B HIS* 1.3 69.2 + - - +
522B PHE 3.3 0.5 + - - -
523B CYS* 3.4 2.1 + - - +
524B HIS* 3.2 41.2 + - + +
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Residues in contact with HIS 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LEU 5.4 0.2 + - - -
242B SER* 3.8 23.6 - - - -
243B ALA* 3.5 21.0 + - + +
246B GLN* 3.4 40.0 + - + -
517B VAL* 3.0 13.8 + - + +
518B LYS* 3.1 12.5 + - - +
520B ILE* 1.3 78.2 - - - +
522B PHE* 1.3 62.5 + - - +
524B HIS* 3.6 4.5 + - + +
525B ASP* 3.1 47.3 + - - +
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Residues in contact with PHE 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B ILE* 4.0 19.1 - - + -
239B LEU* 3.4 46.1 - - + +
240B TYR 3.8 7.2 - - - -
243B ALA* 4.3 4.0 - - + +
266B TRP* 3.8 24.2 - + + -
268B VAL* 3.8 24.2 - - + -
503B MET* 3.3 27.8 - - + -
505B CYS* 3.9 13.2 - - - -
518B LYS 2.9 12.0 + - - +
519B GLY* 3.5 9.0 - - - +
520B ILE 3.1 0.2 - - - -
521B HIS* 1.3 75.7 - - - +
523B CYS* 1.3 64.6 + - - +
525B ASP* 3.4 4.9 + - - +
526B LEU* 2.8 36.5 + - + +
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Residues in contact with CYS 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B PHE* 4.0 26.7 - - + -
481B VAL* 4.0 9.0 - - + +
483B LEU* 5.5 0.2 - - - +
493B ILE* 4.2 20.9 - - - -
495B LEU* 4.0 28.3 - - + -
505B CYS* 4.8 9.9 - - - -
519B GLY 3.0 21.4 + - - +
520B ILE* 4.1 3.4 - - - +
522B PHE* 1.3 78.5 - - - +
524B HIS* 1.3 63.7 + - - +
526B LEU* 3.3 8.8 + - - +
527B VAL* 3.3 24.1 + - - +
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Residues in contact with HIS 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B PHE* 4.0 32.7 - + - -
476B GLN 5.1 0.2 + - - -
477B PHE* 4.9 2.2 - + - -
480B HIS* 3.7 38.2 - + + +
481B VAL* 4.1 17.0 - - + +
520B ILE* 3.2 29.7 + - + +
521B HIS* 3.8 8.9 - - + +
523B CYS* 1.3 75.3 - - - +
525B ASP* 1.3 69.4 + - - +
527B VAL* 3.2 4.6 + - - +
528B SER* 3.0 24.0 + - - -
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Residues in contact with ASP 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LEU* 3.5 25.8 - - + +
242B SER* 3.8 19.4 + - - -
521B HIS* 3.1 36.1 + - - +
522B PHE* 3.7 5.4 - - - +
524B HIS* 1.3 82.7 - - - +
526B LEU* 1.3 64.1 + - - +
528B SER* 3.2 9.1 + - - -
529B LEU* 3.0 24.1 + - - +
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Residues in contact with LEU 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PHE* 5.1 0.9 - - + -
236B ILE* 4.6 10.5 - - + -
239B LEU* 3.8 25.3 - - + +
483B LEU* 4.7 8.7 - - + -
495B LEU* 4.0 21.8 - - + -
501B MET* 3.7 27.8 - - + -
503B MET* 4.2 7.0 - - - -
522B PHE* 2.8 27.3 + - + +
523B CYS* 3.5 5.8 - - - +
524B HIS 3.2 0.4 - - - -
525B ASP* 1.3 74.1 - - - +
527B VAL* 1.3 58.8 + - + +
529B LEU* 3.3 1.7 + - - +
530B CYS* 3.0 32.0 + - - +
532B PHE* 4.0 26.4 - - + -
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Residues in contact with VAL 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B HIS 4.1 11.0 - - - +
481B VAL* 3.4 33.0 - - + +
483B LEU* 3.6 26.9 - - + -
523B CYS 3.3 6.0 + - - +
524B HIS 3.2 4.6 + - - +
526B LEU* 1.3 73.9 - - + +
528B SER* 1.3 58.3 + - - +
529B LEU 3.1 2.2 - - - -
530B CYS 2.8 14.4 - - - +
532B PHE* 4.4 4.5 - - + -
533B HIS* 3.4 39.5 - - + +
544B LYS* 2.7 34.0 + - - +
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Residues in contact with SER 528 (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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524B HIS 3.0 17.5 + - - -
525B ASP* 3.2 10.5 + - - -
527B VAL* 1.3 78.4 - - - +
529B LEU* 1.3 60.3 + - - +
544B LYS* 3.5 21.7 - - - +
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Residues in contact with LEU 529 (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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235B HIS* 4.0 41.5 - - + +
238B GLU* 5.7 1.1 - - - +
239B LEU* 4.0 25.6 - - + -
525B ASP 3.0 14.9 + - - +
526B LEU 3.5 3.6 - - - +
528B SER* 1.3 79.5 + - - +
530B CYS* 1.3 71.8 + - - +
544B LYS* 3.2 10.3 - - - +
545B LEU* 3.0 45.0 + - + +
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Residues in contact with CYS 530 (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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232B PHE* 4.8 4.7 - - - -
235B HIS* 6.1 0.4 - - - -
526B LEU* 3.0 14.0 + - - +
527B VAL* 2.8 23.3 - - - +
529B LEU* 1.3 102.7 - - - +
531B ASN* 1.3 59.3 + - - +
532B PHE* 2.8 39.5 + - + -
544B LYS* 3.7 3.1 - - - +
545B LEU* 3.0 17.5 - - - +
547B PRO* 3.7 22.9 - - + -
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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