Contacts of the strand formed by residues 517 - 524 (chain B) in PDB entry 5Y7G
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 ARG 517 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B CYS* 3.7 10.5 - - - -
511B PHE* 3.6 2.3 - - - -
512B TRP* 2.9 69.5 + - + +
515B GLN* 3.0 50.1 - - + +
516B ARG* 1.3 77.0 - - - +
518B TYR* 1.3 70.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 518 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B CYS 3.2 18.6 - - - +
482B LEU* 3.6 20.4 - - + -
483B PRO* 3.3 25.4 - - + -
486B HIS* 2.4 32.1 + + - -
490B TRP* 3.5 18.5 - + - -
509B ILE* 4.9 3.8 - - + -
510B GLN 3.1 13.5 - - - +
511B PHE* 3.6 17.9 - - + -
512B TRP* 3.3 9.0 - - - -
517B ARG* 1.3 81.5 - - - +
519B ARG* 1.3 68.9 + - - +
520B MET* 4.3 16.6 - - + -
546B MET* 4.2 0.4 - - + +
547B PRO* 3.1 48.3 - - + +
548B VAL* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 519 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LEU* 4.0 24.8 - - - +
375B LEU* 4.2 10.7 - - - +
509B ILE* 4.6 1.1 - - - -
510B GLN* 2.5 60.8 + - + +
512B TRP* 3.5 19.3 - - + -
518B TYR* 1.3 77.8 - - - +
520B MET* 1.3 72.5 + - - +
521B VAL* 3.8 14.6 + - - +
547B PRO* 3.3 25.4 - - + +
548B VAL* 4.3 2.2 - - - +
549B ALA* 3.7 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 520 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ILE* 4.4 22.4 - - + -
482B LEU* 6.2 0.4 - - + -
490B TRP* 3.3 45.3 - - + +
505B LEU* 4.8 5.8 - - + -
506B PRO* 4.3 30.1 - - + -
508B LEU 3.5 10.5 - - - +
509B ILE* 4.4 13.9 - - + +
518B TYR* 4.3 13.0 - - + -
519B ARG* 1.3 74.6 - - - +
521B VAL* 1.3 62.1 + - - +
522B GLU 4.3 0.4 - - - -
541B CYS* 4.8 10.8 - - - -
547B PRO 3.0 11.0 + - - +
548B VAL* 3.5 10.6 - - + +
549B ALA 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 521 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LEU* 4.5 6.3 - - + -
371B VAL* 5.3 0.2 - - + -
375B LEU* 4.6 9.6 - - + -
506B PRO* 3.9 4.3 - - - -
507B ASP 3.6 0.2 + - - -
508B LEU* 2.8 53.2 + - + +
510B GLN* 4.0 15.5 - - + +
519B ARG* 3.8 29.8 + - + +
520B MET* 1.3 80.6 - - - +
522B GLU* 1.3 62.9 + - - +
523B VAL* 4.2 8.3 - - + -
549B ALA* 3.3 9.4 - - + +
551B CYS* 4.0 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 522 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B GLU* 4.8 0.3 - - - +
505B LEU 3.6 6.2 - - - +
506B PRO* 3.0 23.1 - - + +
507B ASP* 2.5 52.2 + - - +
520B MET 4.3 0.2 - - - -
521B VAL* 1.3 71.4 - - - +
523B VAL* 1.3 65.1 + - - +
524B LYS* 3.6 30.4 + - + -
530B LEU* 6.1 0.7 - - + -
534B GLN* 3.7 20.0 + - + +
538B LEU* 5.5 5.8 - - + +
549B ALA 3.5 5.9 + - - -
550B VAL* 3.5 20.8 - - + +
551B CYS* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 523 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B VAL* 3.5 38.4 - - + +
368B GLU* 3.6 17.3 - - + +
371B VAL* 3.8 19.3 - - + -
507B ASP* 2.8 28.3 + - - +
508B LEU* 3.6 32.1 - - + -
521B VAL* 4.2 5.8 - - + -
522B GLU* 1.3 83.2 - - - +
524B LYS* 1.3 66.4 + - - +
525B GLY 4.2 0.2 - - - -
551B CYS* 3.5 5.4 - - + -
553B VAL* 3.8 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 524 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B GLU* 3.6 24.7 + - + -
523B VAL* 1.3 82.1 - - - +
525B GLY* 1.3 65.0 + - - +
528B ASP* 3.3 44.1 + - + +
529B ARG* 3.3 23.8 + - - +
530B LEU* 3.7 9.4 - - - +
531B GLN* 4.4 3.0 - - - +
534B GLN* 2.8 33.1 + - - +
550B VAL* 4.5 16.8 - - + -
551B CYS 3.0 11.0 + - - +
552B TYR* 4.0 15.7 - - + -
553B VAL* 3.1 26.0 + - - +
----------------------------------------------------------
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