Contacts of the strand formed by residues 529 - 535 (chain B) in PDB entry 6V3O
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 PHE 529 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B THR* 4.5 4.5 - - + -
308B CYS* 3.8 20.6 - - - -
452B LYS* 3.8 17.1 + - - +
453B LEU* 3.4 7.6 - - + +
455B ILE* 4.1 17.3 - - + -
521B LEU* 3.4 47.1 - - + -
524B LEU* 3.6 43.7 - - + -
525B PRO 3.9 13.7 - - - -
526B PRO* 3.3 16.6 + - + +
527B ASP 3.3 0.2 - - - -
528B SER* 1.3 84.1 - - - +
530B GLY* 1.3 62.4 + - - +
559B LEU* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 530 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B LYS* 4.0 10.7 - - - +
453B LEU 2.8 15.1 + - - +
454B ASP* 4.1 2.9 - - - -
529B PHE* 1.3 76.6 - - - +
531B PRO* 1.3 72.9 - - - +
559B LEU* 3.5 19.5 - - - +
560B PRO* 3.8 9.7 - - - +
669B ARG* 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B ASP* 3.1 21.5 - - - +
455B ILE* 3.0 27.9 + - - +
530B GLY* 1.3 88.7 - - - +
532B TYR* 1.3 60.0 + - - +
533B ILE* 3.9 9.2 - - + -
559B LEU* 4.0 3.6 - - - +
560B PRO* 3.5 13.5 - - + +
562B VAL* 3.3 26.5 - - + -
596B GLN* 4.0 16.4 - - - +
669B ARG* 3.6 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ARG* 5.6 1.4 - - - -
455B ILE* 3.4 30.3 - - + -
457B GLN* 3.3 19.2 - - + +
462B HIS* 2.8 40.3 + + - -
514B VAL* 4.9 2.3 - - - +
517B ALA* 5.9 6.3 - - + +
518B PHE* 3.4 36.7 - + - -
521B LEU* 4.1 11.4 - - + -
531B PRO* 1.3 72.0 - - - +
533B ILE* 1.3 73.8 + - - +
534B ILE* 4.1 4.0 + - + -
546B VAL* 3.9 18.4 - - + -
550B GLN* 5.2 2.9 - - - +
559B LEU* 4.0 13.7 - - + +
560B PRO 2.9 12.6 + - - +
561B VAL* 3.5 9.3 - - + +
562B VAL 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 533 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B TRP* 3.9 14.4 - - + +
454B ASP* 4.0 14.6 - - + +
455B ILE 2.6 17.0 + - - +
456B ARG* 3.3 21.4 - - + -
457B GLN 3.1 27.2 + - - +
531B PRO* 4.2 13.0 - - + -
532B TYR* 1.3 79.7 - - - +
534B ILE* 1.3 64.0 + - - +
535B SER 3.9 0.2 - - - -
562B VAL* 3.3 21.5 - - + +
564B LEU* 4.2 13.0 - - + -
598B MET* 4.1 15.7 - - + -
638B PHE* 3.7 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B GLN 3.3 2.9 - - - +
459B SER* 3.7 35.2 - - - +
462B HIS* 4.4 13.2 - - + +
532B TYR* 4.5 6.1 - - + -
533B ILE* 1.3 75.3 - - - +
535B SER* 1.3 63.3 + - - +
537B ALA* 3.6 14.6 - - + +
542B ASP* 3.1 29.4 - - + +
543B VAL* 3.7 11.9 - - + -
546B VAL* 4.3 6.3 - - + -
561B VAL* 3.5 30.5 - - + -
562B VAL 2.9 13.9 + - - +
563B PRO* 4.5 0.7 - - + -
564B LEU* 3.0 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ASP* 2.8 22.6 + - - -
456B ARG* 2.5 37.3 + - - +
457B GLN 2.8 8.4 + - - -
458B GLU* 3.6 15.7 - - - -
459B SER* 2.9 26.3 + - - -
533B ILE 3.8 1.6 + - - -
534B ILE* 1.3 71.7 - - - +
536B MET* 1.3 69.4 + - - +
564B LEU* 3.9 6.0 - - - +
566B GLU* 3.7 8.1 - - - -
----------------------------------------------------------
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