Contacts of the helix formed by residues 505 - 515 (chain A) in PDB entry 2DW1
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 ILE 505 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A LEU* 3.8 13.7 - - + -
495A TYR* 3.4 37.7 - - + +
496A GLY* 3.9 10.1 - - - -
503A CYS* 3.4 9.6 - - - +
504A PRO* 1.3 81.3 - - - +
506A MET* 1.3 64.0 + - - +
507A TYR* 3.0 19.7 + - + +
508A HIS* 3.2 53.7 + - + +
509A GLN* 3.2 18.3 + - - +
589A THR* 4.1 3.1 - - - -
590A LYS* 5.4 1.1 - - - +
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Residues in contact with MET 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A ILE* 1.3 72.2 - - - +
507A TYR* 1.3 57.5 + - - +
509A GLN* 3.7 9.4 - - - +
510A CYS* 3.0 33.9 + - - -
520A GLU* 3.7 40.8 - - + +
526A PHE* 3.9 16.8 - - + -
554A LYS* 3.0 47.3 - - + +
558A LEU* 4.0 15.0 - - + +
585A VAL* 4.4 11.0 - - + -
589A THR* 3.6 16.2 - - + +
590A LYS 4.0 18.3 + - - +
591A CYS* 4.3 4.7 - - + +
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Residues in contact with TYR 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A ILE* 3.0 14.8 + - + +
506A MET* 1.3 75.2 - - - +
508A HIS* 1.3 89.7 + + - +
510A CYS* 3.3 5.1 + - - +
511A TYR* 3.0 31.7 + + + +
518A VAL 4.1 6.7 - - - -
519A TYR* 3.3 44.8 + + + -
520A GLU* 5.4 5.6 - - + +
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Residues in contact with HIS 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A LEU* 3.6 19.7 - - + +
503A CYS 4.6 4.7 - - - -
504A PRO* 5.9 0.4 - - + -
505A ILE* 3.2 39.4 + - + +
507A TYR* 1.3 95.4 - + - +
509A GLN* 1.3 58.6 + - + +
511A TYR* 3.1 9.4 + - + +
512A ASP* 2.8 42.1 + - - +
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Residues in contact with GLN 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A PRO* 3.9 2.0 - - + +
505A ILE 3.2 28.6 + - - +
506A MET* 3.7 7.7 - - - +
507A TYR 3.2 0.2 - - - -
508A HIS* 1.3 77.5 - - + +
510A CYS* 1.3 64.4 + - - +
512A ASP* 3.4 7.4 + - - +
513A LEU* 3.1 29.9 + - + +
558A LEU* 3.7 19.1 - - + +
584A MET 4.3 1.4 - - - +
585A VAL* 3.6 11.8 - - - +
586A LEU* 3.0 52.4 + - + +
589A THR* 2.9 24.7 + - - +
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Residues in contact with CYS 510 (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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506A MET 3.0 21.7 + - - +
507A TYR 3.3 5.1 + - - +
509A GLN* 1.3 75.2 - - - +
511A TYR* 1.3 58.6 + - - +
513A LEU* 3.1 2.7 + - - -
514A PHE* 2.8 33.6 + - - +
518A VAL* 3.8 20.3 - - + +
519A TYR* 3.6 14.4 - - - -
520A GLU* 4.0 3.1 - - - -
558A LEU* 4.0 12.1 - - - +
559A TYR 4.2 0.4 - - - -
560A CYS* 2.0 51.1 - - - -
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Residues in contact with TYR 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A TYR* 3.0 28.0 + + + +
508A HIS* 3.4 13.2 - - + +
510A CYS* 1.3 77.7 - - - +
512A ASP* 1.3 79.8 + - - +
515A GLY* 2.8 62.7 + - - -
516A ALA* 3.7 13.2 - - + -
518A VAL 4.8 1.7 + - - +
342B ASN* 4.5 18.8 + - + +
376B GLU* 5.2 1.4 + - - -
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Residues in contact with ASP 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A HIS* 2.8 28.1 + - - +
509A GLN* 3.9 6.7 - - - +
510A CYS 3.3 0.2 - - - -
511A TYR* 1.3 92.8 - - - +
513A LEU* 1.3 61.7 + - + +
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Residues in contact with LEU 513 (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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509A GLN* 3.1 22.3 + - + +
510A CYS 3.7 2.9 - - - +
511A TYR 3.1 0.2 - - - -
512A ASP* 1.3 80.4 - - + +
514A PHE* 1.3 91.3 + - + +
558A LEU* 3.9 23.3 - - + -
574A PHE* 4.1 21.2 - - + +
582A LYS* 3.9 34.8 - - + +
583A GLY* 3.9 21.5 - - - +
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Residues in contact with PHE 514 (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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510A CYS 2.8 20.2 + - - +
513A LEU* 1.3 102.6 - - + +
515A GLY* 1.3 60.1 + - - +
516A ALA 4.0 2.1 + - - +
518A VAL* 3.9 29.5 - - + +
558A LEU 5.6 0.9 - - - -
560A CYS* 3.8 18.6 - - - -
562A ASP* 5.6 0.2 - - - +
572A LYS* 3.3 50.9 - - + -
573A MET* 3.7 2.7 - - - -
574A PHE* 3.6 47.1 - + + -
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Residues in contact with GLY 515 (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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511A TYR* 2.8 51.3 + - - -
512A ASP 4.8 0.2 - - - -
513A LEU 3.9 0.4 - - - -
514A PHE* 1.3 73.8 - - - +
516A ALA* 1.3 64.0 + - - +
517A ASP 4.1 0.2 + - - -
518A VAL* 3.9 10.0 + - - +
342B ASN* 5.5 6.1 - - - -
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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
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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