Contacts of the helix formed by residues 505 - 515 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492B LEU* 3.4 17.9 - - + -
495B TYR* 3.3 37.2 - - + +
496B GLY* 3.6 12.1 - - - +
503B CYS 3.4 10.1 - - - +
504B PRO* 1.3 80.4 - - - +
506B MET* 1.3 64.4 + - - +
507B TYR* 4.3 12.3 - - + +
508B HIS* 3.4 49.0 - - + +
509B GLN* 3.2 26.0 + - - +
589B THR* 4.1 3.4 - - - -
590B LYS* 5.2 1.6 - - + +
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Residues in contact with MET 506 (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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505B ILE* 1.3 71.0 - - - +
507B TYR* 1.3 64.7 + - - +
509B GLN* 3.8 7.6 - - - +
510B CYS* 3.0 29.1 + - - -
520B GLU* 3.3 38.4 - - + +
526B PHE* 3.8 18.2 - - + -
554B LYS* 3.1 42.4 - - + +
558B LEU* 3.8 16.8 - - + -
585B VAL* 4.0 15.3 - - + -
589B THR* 3.7 13.8 - - + +
590B LYS 3.9 19.9 + - - +
591B CYS* 4.3 4.0 - - - -
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Residues in contact with TYR 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B ILE* 3.2 13.4 - - + +
506B MET* 1.3 77.3 - - - +
508B HIS* 1.3 82.5 + + - +
510B CYS* 3.3 5.0 + - - +
511B TYR* 3.0 39.6 + + + +
516B ALA* 6.1 0.2 - - - -
517B ASP 5.6 2.5 + - - -
518B VAL 3.4 13.7 - - - -
519B TYR* 3.3 45.1 + + - -
520B GLU* 4.9 9.0 - - + +
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Residues in contact with HIS 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B LEU* 3.9 18.4 - - + +
503B CYS 5.1 1.3 - - - -
505B ILE* 3.4 34.4 + - + +
506B MET 3.4 0.2 - - - -
507B TYR* 1.3 101.1 - + - +
509B GLN* 1.3 61.8 + - + +
511B TYR* 3.2 10.4 + - - +
512B ASP* 2.7 41.0 + - - +
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Residues in contact with GLN 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B PRO* 4.1 0.8 - - + -
505B ILE 3.2 30.8 + - - +
506B MET* 3.8 5.4 - - - +
508B HIS* 1.3 77.4 - - + +
510B CYS* 1.3 63.7 + - - +
512B ASP* 3.3 9.6 + - - +
513B LEU* 3.0 29.3 + - + +
558B LEU* 3.8 19.2 - - + +
584B MET 4.1 1.9 - - - +
585B VAL* 3.5 11.4 - - - +
586B LEU* 3.0 51.2 + - + +
589B THR* 2.9 28.4 + - - +
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Residues in contact with CYS 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B MET 3.0 21.8 + - - +
507B TYR 3.5 8.7 - - - +
508B HIS 3.2 0.2 - - - -
509B GLN* 1.3 76.1 - - - +
511B TYR* 1.3 58.1 + - - +
513B LEU* 3.0 3.0 + - - -
514B PHE* 2.8 34.0 + - - +
518B VAL* 4.0 17.0 - - + +
519B TYR 3.8 12.8 - - - -
520B GLU* 4.0 2.9 - - - -
558B LEU* 3.8 8.0 - - - +
559B TYR 3.9 4.7 - - - -
560B CYS* 2.0 54.5 - - + -
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Residues in contact with TYR 511 (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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342A ASN* 5.0 13.7 + - - +
376A GLU* 5.6 0.7 + - - -
507B TYR* 3.0 33.3 + + + +
508B HIS* 3.4 15.0 - - - +
510B CYS* 1.3 76.5 - - - +
512B ASP* 1.3 74.3 + - - +
515B GLY* 2.7 49.0 + - - -
516B ALA* 3.5 27.7 + - + +
518B VAL 4.5 1.7 + - - -
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Residues in contact with ASP 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B HIS* 2.7 31.6 + - - +
509B GLN* 3.3 8.6 + - - +
511B TYR* 1.3 86.6 - - - +
513B LEU* 1.3 61.8 + - + +
515B GLY 5.1 0.2 + - - -
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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
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509B GLN* 3.0 20.5 + - + +
510B CYS 3.5 3.1 - - - +
512B ASP* 1.3 81.5 - - + +
514B PHE* 1.3 90.3 + - + +
515B GLY 3.9 0.4 - - - -
558B LEU* 3.9 24.2 - - + +
574B PHE* 4.2 20.7 - - + +
582B LYS* 3.9 33.9 - - + -
583B GLY* 4.0 20.4 - - - +
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Residues in contact with PHE 514 (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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510B CYS 2.8 20.1 + - - +
513B LEU* 1.3 101.6 - - + +
515B GLY* 1.3 62.1 + - - +
516B ALA 4.5 0.7 - - - +
518B VAL* 3.8 31.4 - - + +
558B LEU 6.0 0.2 - - - -
560B CYS* 3.6 25.6 - - + -
562B ASP* 5.5 0.4 - - - +
564B SER* 5.7 1.9 + - - -
572B LYS* 3.5 46.7 - - + -
573B MET* 4.0 2.7 - - - -
574B PHE* 3.9 39.9 - + + -
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Residues in contact with GLY 515 (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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342A ASN* 5.9 0.4 - - - -
511B TYR* 2.7 44.7 + - - -
512B ASP 4.8 0.2 - - - -
513B LEU 3.9 0.4 - - - -
514B PHE* 1.3 71.2 - - - +
516B ALA* 1.3 68.4 + - - +
518B VAL* 3.3 17.5 + - - +
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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