Contacts of the strand formed by residues 530 - 535 (chain B) in PDB entry 1O94
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 530 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B LYS* 1.3 76.1 - - + +
531B VAL* 1.3 61.4 + - - +
532B VAL* 5.7 0.4 - - + -
555B GLU* 3.6 31.2 - - + +
600B GLY 5.3 0.2 + - - -
634B GLU* 3.3 40.7 + - - +
635B PHE* 3.8 18.6 + - - -
636B ASP* 2.8 65.0 + - - +
637B SER 2.9 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 531 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B ILE* 3.6 20.4 - - + -
528B GLY 3.4 24.2 - - - +
529B LYS 4.0 1.1 - - - +
530B ARG* 1.3 74.9 - - - +
532B VAL* 1.3 70.1 + - - +
533B ILE* 4.2 6.1 - - + -
549B LEU* 3.7 24.0 - - + -
554B HIS* 3.8 13.5 - - + +
555B GLU 2.9 12.6 + - - +
556B VAL* 3.4 10.7 - - + -
557B THR* 3.1 23.7 + - - +
637B SER* 3.2 8.5 - - - +
639B VAL* 3.9 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 532 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B ARG* 4.2 0.6 - - + -
531B VAL* 1.3 79.3 - - - +
533B ILE* 1.3 66.5 + - - +
557B THR* 3.3 14.4 - - - +
559B VAL* 3.9 23.8 - - + -
602B MET* 3.6 30.7 - - + -
633B ILE* 4.3 13.7 - - + -
634B GLU 3.9 10.5 - - - +
635B PHE* 3.7 21.5 - - + -
637B SER 3.0 6.7 + - - -
638B LEU* 3.4 8.6 - - + +
639B VAL* 2.8 26.0 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
531B VAL* 4.2 7.6 - - + -
532B VAL* 1.3 77.7 - - - +
534B LEU* 1.3 62.8 + - - +
535B ASN 3.6 0.2 + - - -
542B ALA* 3.9 20.0 - - + +
545B LEU* 4.1 8.5 - - + +
546B ALA* 3.6 43.1 - - + +
549B LEU* 4.7 5.6 - - + -
556B VAL* 3.8 11.2 - - + -
557B THR 2.8 12.6 + - - +
558B ILE* 3.5 9.5 - - + +
559B VAL* 2.9 28.1 + - - +
639B VAL* 3.4 19.1 - - + +
641B VAL* 3.6 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 534 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B ILE* 3.8 29.4 - - + -
532B VAL 4.0 1.0 - - - -
533B ILE* 1.3 75.3 - - - +
535B ASN* 1.3 56.8 + - - +
559B VAL* 3.5 23.3 - - + +
593B PHE* 3.7 25.1 - - + -
594B CYS* 3.9 27.1 - - + -
597B ILE* 4.9 2.7 - - + -
602B MET* 4.2 6.5 - - + -
638B LEU* 4.0 15.5 - - + -
639B VAL 2.8 11.7 + - - +
640B LEU* 4.4 12.3 - - + -
641B VAL* 2.9 29.5 + - - +
642B THR* 3.9 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 535 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B ILE 4.6 0.2 - - - +
534B LEU* 1.3 75.5 - - - +
536B ALA* 1.3 61.2 + - - +
537B ASP* 2.9 41.5 + - - +
542B ALA* 3.3 29.2 - - + +
558B ILE* 4.1 9.9 - - + -
559B VAL 2.8 15.3 + - - +
560B SER* 3.0 24.2 + - - +
561B GLY 3.0 26.9 + - - -
562B VAL* 3.9 2.8 - - - +
564B LEU* 3.8 14.1 - - - +
593B PHE* 4.0 4.8 - - - -
641B VAL* 3.3 7.7 - - - +
642B THR* 5.0 0.2 - - - -
----------------------------------------------------------
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