Contacts of the helix formed by residues 516 - 530 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487A SER* 5.3 1.2 - - - -
488A GLY 5.5 0.6 + - - -
491A GLY* 3.4 21.2 + - - -
493A ILE* 4.3 10.0 - - - +
507A SER* 2.7 34.4 + - - -
509A PRO 3.5 8.1 - - - -
510A LEU* 3.4 8.7 - - - +
515A ASN* 1.3 70.3 - - - +
517A VAL* 1.3 62.8 + - - +
519A GLY* 3.2 20.7 + - - -
520A ILE* 3.0 28.8 + - - +
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Residues in contact with VAL 517 (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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246A GLN* 4.3 26.0 - - + +
248A GLY* 3.9 20.4 - - - +
249A GLY* 3.5 31.4 - - - +
509A PRO* 3.0 14.5 + - + +
511A ASP* 3.6 25.6 - - + +
515A ASN 3.1 2.1 + - - -
516A SER* 1.3 71.4 - - - +
518A LYS* 1.3 58.7 + - + +
520A ILE* 3.7 5.1 - - - +
521A HIS* 3.1 26.2 + - - +
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Residues in contact with LYS 518 (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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243A ALA* 3.5 18.9 - - + +
244A LYS* 3.7 21.5 - - - +
246A GLN* 3.6 23.6 + - + +
247A SER* 4.8 9.4 + - - +
248A GLY 5.3 2.0 + - - +
263A PRO 3.6 22.4 + - - -
264A ASP* 5.2 2.4 - - - +
265A LEU 4.9 1.2 + - - -
266A TRP* 3.7 38.0 - - + -
507A SER* 3.7 27.2 + - - +
509A PRO* 4.4 7.9 + - + +
516A SER* 3.4 0.8 + - - -
517A VAL* 1.3 79.7 - - + +
519A GLY* 1.3 65.3 + - - +
521A HIS* 3.4 6.9 + - - +
522A PHE* 3.0 26.0 + - - +
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Residues in contact with GLY 519 (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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266A TRP* 4.1 12.3 - - - -
493A ILE* 3.8 15.0 - - - -
505A CYS* 4.2 12.5 - - - -
516A SER* 3.2 19.3 + - - -
518A LYS* 1.3 77.4 - - - +
520A ILE* 1.3 57.5 + - - +
522A PHE* 3.5 2.8 + - - +
523A CYS* 3.1 33.8 + - - -
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Residues in contact with ILE 520 (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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470A MET* 3.9 27.1 - - + -
473A PHE* 4.4 10.3 - - + -
477A PHE* 4.1 20.0 - - + -
493A ILE* 3.9 6.9 - - + +
511A ASP* 4.4 9.6 - - - +
515A ASN* 3.7 20.6 - - + +
516A SER 3.0 20.7 + - - +
517A VAL* 3.7 5.6 - - - +
519A GLY* 1.3 73.4 - - - +
521A HIS* 1.3 68.4 + - - +
523A CYS* 3.1 12.9 + - - +
524A HIS* 3.2 33.5 + - + +
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Residues in contact with HIS 521 (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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242A SER* 4.0 23.1 - - - -
243A ALA* 3.6 18.9 + - + +
246A GLN* 3.1 45.5 + - + -
517A VAL 3.1 14.9 + - - +
518A LYS* 3.6 7.0 - - - +
520A ILE* 1.3 80.2 - - - +
522A PHE* 1.3 57.4 + - - +
524A HIS* 3.4 6.2 + - - +
525A ASP* 3.0 49.3 + - - +
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Residues in contact with PHE 522 (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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236A ILE* 3.8 18.2 - - + -
239A LEU* 3.5 44.6 - - + +
240A TYR* 3.7 10.8 - - + -
243A ALA* 4.3 5.1 - - + +
266A TRP* 3.9 22.2 - + + -
268A VAL* 3.9 22.0 - - + -
503A MET* 3.3 28.3 - - + -
505A CYS* 3.9 14.4 - - - -
518A LYS 3.0 17.8 + - - +
519A GLY 3.5 4.7 - - - +
521A HIS* 1.3 77.3 - - - +
523A CYS* 1.3 62.0 + - - +
525A ASP* 3.5 6.7 + - - +
526A LEU* 3.0 34.7 + - + +
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Residues in contact with CYS 523 (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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477A PHE* 4.1 25.4 - - + -
481A VAL* 3.9 17.9 - - + +
493A ILE* 4.5 17.9 - - - -
495A LEU* 4.0 29.6 - - + -
505A CYS* 4.7 4.9 - - - -
519A GLY 3.1 26.8 + - - +
520A ILE 3.1 5.5 + - - +
522A PHE* 1.3 81.1 - - - +
524A HIS* 1.3 65.1 + - - +
526A LEU* 3.5 7.5 + - - +
527A VAL* 3.5 13.3 + - - +
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Residues in contact with HIS 524 (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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473A PHE* 4.0 26.4 - + - -
476A GLN 5.0 1.0 + - - -
477A PHE* 5.0 2.2 - + - -
480A HIS* 3.6 36.8 - + + +
481A VAL* 3.9 18.4 - - + +
520A ILE* 3.2 41.5 + - + +
521A HIS* 3.8 7.7 - - - +
523A CYS* 1.3 73.2 - - - +
525A ASP* 1.3 67.6 + - - +
527A VAL* 3.1 4.4 + - - +
528A SER* 2.9 26.5 + - - +
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Residues in contact with ASP 525 (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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239A LEU* 3.2 30.7 - - + +
242A SER* 3.8 15.8 + - - -
521A HIS* 3.0 43.5 + - - +
522A PHE* 3.5 9.0 - - - +
524A HIS* 1.3 76.6 - - - +
526A LEU* 1.3 63.0 + - - +
528A SER* 3.2 11.2 + - - -
529A LEU* 3.1 23.2 + - - +
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Residues in contact with LEU 526 (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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232A PHE* 5.1 1.6 - - + -
236A ILE* 4.6 13.9 - - + -
239A LEU* 3.8 23.3 - - + +
483A LEU* 4.6 11.2 - - + -
495A LEU* 3.8 28.5 - - + -
501A MET* 4.1 19.7 - - + -
503A MET* 4.3 5.6 - - - -
522A PHE* 3.0 22.5 + - + +
523A CYS* 3.7 7.9 - - - +
524A HIS 3.2 0.2 - - - -
525A ASP* 1.3 76.9 - - - +
527A VAL* 1.3 59.6 + - + +
529A LEU* 3.5 1.4 + - - +
530A CYS* 3.0 34.2 + - - +
532A PHE* 4.2 21.2 - - + -
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Residues in contact with VAL 527 (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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480A HIS 4.0 12.3 - - - +
481A VAL* 3.5 38.4 - - + +
483A LEU* 3.8 24.2 - - + -
523A CYS 3.5 4.6 + - - +
524A HIS 3.1 6.6 + - - +
526A LEU* 1.3 78.0 - - + +
528A SER* 1.3 65.9 + - - +
529A LEU 3.1 0.9 - - - -
530A CYS 3.1 10.2 - - - +
532A PHE* 4.4 5.6 - - + -
533A HIS* 3.7 23.6 - - + +
544A LYS* 2.9 38.9 + - - +
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Residues in contact with SER 528 (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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524A HIS* 2.9 16.3 + - - +
525A ASP* 3.3 14.6 - - - -
527A VAL* 1.3 76.9 - - - +
529A LEU* 1.3 61.2 + - - +
544A LYS* 3.5 19.5 - - - +
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Residues in contact with LEU 529 (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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235A HIS* 3.7 42.0 - - + +
239A LEU* 4.3 23.8 - - + -
525A ASP 3.1 12.9 + - - +
526A LEU* 3.7 4.5 - - - +
527A VAL 3.1 0.4 - - - -
528A SER* 1.3 81.6 - - - +
530A CYS* 1.3 68.6 + - - +
544A LYS* 3.4 7.8 - - - -
545A LEU* 3.0 42.3 + - + +
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Residues in contact with CYS 530 (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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232A PHE* 4.6 6.7 - - - -
235A HIS* 6.0 0.4 - - - -
526A LEU* 3.0 17.7 + - - +
527A VAL* 3.1 21.5 - - - +
529A LEU* 1.3 89.8 - - - +
531A ASN* 1.3 53.7 + - - +
532A PHE* 2.8 45.0 + - + -
536A ASP* 4.0 0.3 - - - +
544A LYS* 3.5 3.9 - - - +
545A LEU* 3.2 28.0 - - - +
547A PRO* 3.8 17.7 - - + -
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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
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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