Contacts of the helix formed by residues 504 - 513 (chain B) in PDB entry 5EEQ
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 ASP 504 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ILE* 4.2 29.3 - - + +
426B HIS* 5.7 1.6 - - - +
493B PHE* 3.8 16.4 - - + -
502B PHE* 3.2 8.9 - - - +
503B THR* 1.3 92.8 + - - +
505B LEU* 1.3 65.5 + - - +
506B LEU* 3.2 10.7 + - - +
507B GLN* 2.9 32.8 + - - +
508B LEU* 3.3 15.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B HIS* 3.6 43.8 + - + +
431B TRP* 4.0 8.7 - - + -
432B PHE* 4.2 1.1 - - + -
457B VAL* 3.9 15.5 - - + -
467B PHE* 3.7 38.8 - - + -
482B ILE* 4.0 37.0 - - + -
493B PHE* 4.4 11.8 - - + -
504B ASP* 1.3 74.3 - - - +
506B LEU* 1.3 60.0 + - - +
508B LEU* 3.1 8.3 + - + +
509B VAL* 2.9 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ILE* 4.3 24.7 - - + +
426B HIS* 5.0 3.6 - - - +
429B GLN* 4.2 28.5 - - + +
431B TRP* 4.0 27.5 - - + +
504B ASP* 3.2 11.3 + - - +
505B LEU* 1.3 78.1 - - - +
507B GLN* 1.3 57.5 + - - +
509B VAL* 3.2 2.1 + - + -
510B GLU* 2.8 60.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A GLN* 5.1 9.3 + - + +
510A GLU* 3.3 48.7 + - - +
511A PHE* 3.6 10.7 - - + +
514A LEU* 4.3 1.7 - - - +
501B ARG 5.0 1.6 + - - -
502B PHE* 3.4 17.4 - - + -
503B THR* 2.8 45.6 + - - +
504B ASP* 2.9 19.6 + - - +
506B LEU* 1.3 76.4 - - - +
508B LEU* 1.3 62.4 + - - +
510B GLU* 3.9 10.1 - - - +
511B PHE* 3.0 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B LEU* 4.5 11.4 - - + -
482B ILE* 3.9 42.2 - - + -
493B PHE* 4.9 5.4 - - + +
495B MET* 4.1 25.6 - - + -
502B PHE* 3.7 39.6 - - + -
504B ASP 3.3 9.0 + - - +
505B LEU* 3.1 13.4 + - + +
507B GLN* 1.3 79.6 - - - +
509B VAL* 1.3 73.9 + - + +
511B PHE* 3.3 0.5 + - - +
512B HIS* 2.8 40.7 + - + +
523B LEU* 5.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B TRP* 3.7 39.0 - - + +
455B PHE* 3.8 30.5 - - + -
457B VAL* 4.0 15.3 - - + -
469B LEU* 5.4 0.2 - - + -
505B LEU* 2.9 20.4 + - + +
506B LEU* 3.7 4.0 - - + +
508B LEU* 1.3 83.1 - - + +
510B GLU* 1.3 65.7 + - + +
512B HIS 3.1 3.1 + - - -
513B GLN* 3.0 35.5 + - - +
523B LEU* 3.9 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A THR* 5.7 1.6 - - - +
507A GLN* 3.3 25.1 + - - +
506B LEU* 2.8 50.5 + - + +
507B GLN* 4.0 7.1 - - - +
509B VAL* 1.3 78.2 - - + +
511B PHE* 1.3 64.3 + - - +
513B GLN* 3.4 28.5 + - - +
514B LEU* 4.0 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A THR* 4.0 15.7 - - + -
502A PHE* 4.1 13.0 - + - -
507A GLN* 3.6 10.2 - - + +
511A PHE* 3.4 43.7 - + + -
500B THR* 4.8 4.9 - - + -
502B PHE* 3.6 17.3 - + + -
507B GLN* 3.0 18.7 + - + +
508B LEU 3.7 1.8 - - - +
509B VAL 3.2 0.2 - - - -
510B GLU* 1.3 77.0 - - - +
512B HIS* 1.3 84.2 + + - +
514B LEU 3.2 3.5 + - - -
515B ASN* 2.9 70.8 + - + +
517B GLY* 4.9 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B MET* 3.4 26.1 - - + +
500B THR* 5.5 2.3 - - + +
502B PHE* 3.6 30.1 - + - -
508B LEU* 2.8 27.7 + - + +
509B VAL 3.1 3.5 + - - -
511B PHE* 1.3 86.0 - + - +
513B GLN* 1.3 62.3 + - - +
514B LEU 3.2 1.3 + - - -
515B ASN 3.1 17.5 - - - +
516B ARG 3.4 26.1 + - - -
517B GLY* 4.3 6.6 - - - -
518B ILE* 4.7 2.0 + - - +
519B LEU* 3.6 18.5 - - + +
522B LEU* 3.6 5.5 - - - -
523B LEU* 3.0 39.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 513 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B TRP* 5.4 1.6 - - - +
455B PHE* 4.2 13.3 - - - -
509B VAL* 3.0 33.5 + - + +
510B GLU* 3.7 24.7 - - - +
511B PHE 3.2 0.6 - - - -
512B HIS* 1.3 79.0 - - - +
514B LEU* 1.3 67.3 + - + +
522B LEU* 3.9 15.3 - - - +
523B LEU* 3.5 29.6 + - + +
524B ARG 5.8 1.6 + - - -
526B CYS* 4.6 9.5 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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