Contacts of the strand formed by residues 507 - 512 (chain A) in PDB entry 6N8P
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 507 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A THR* 2.3 32.9 + - - -
389A CYS* 3.5 10.2 - - - -
441A GLY* 3.8 9.9 - - - -
442A HIS 3.0 12.9 + - - +
445A GLY 4.1 11.0 - - - +
446A THR 4.1 2.0 - - - +
447A VAL* 3.9 21.1 - - + -
465A THR* 4.1 21.8 - - + +
505A LEU 3.9 9.2 - - - +
506A GLY* 1.3 69.9 - - - +
508A GLN* 1.3 63.4 + - - +
509A LYS 3.9 2.9 - - - +
510A ILE* 3.6 34.5 - - + -
521A VAL* 4.4 12.3 - - + -
522A ALA 3.4 13.7 - - - +
523A GLY* 4.9 1.8 - - - -
527A GLN* 5.8 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A THR* 5.0 10.7 - - - +
389A CYS* 3.3 20.1 - - - +
506A GLY* 5.1 0.6 - - - -
507A ILE* 1.3 78.0 + - - +
509A LYS* 1.3 72.6 + - + +
522A ALA* 2.6 14.7 + - + +
523A GLY 3.6 25.1 - - - +
524A THR* 3.0 24.8 + - - +
590A VAL* 3.6 26.7 - - + +
591A VAL 3.6 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A CYS* 4.5 0.9 - - - -
507A ILE* 3.9 0.7 - - - +
508A GLN* 1.3 88.3 + - + +
510A ILE* 1.3 66.8 - - - +
521A VAL* 3.3 4.5 - - - -
522A ALA* 2.9 34.9 + - + +
591A VAL* 4.4 8.7 - - + +
592A THR* 3.3 30.0 + - - +
593A SER* 4.1 12.3 - - - +
594A LEU* 3.7 32.8 - - + +
714A ARG 5.8 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A CYS* 3.8 8.6 - - - +
391A HIS* 3.4 37.6 + - + +
439A LEU* 3.6 33.7 - - + +
440A THR* 4.0 2.2 - - - +
441A GLY* 3.6 33.7 - - - +
447A VAL* 3.7 21.3 - - + -
507A ILE* 3.6 12.6 - - + -
509A LYS* 1.3 80.9 - - - +
511A PHE* 1.3 65.7 + - - +
519A LEU* 4.3 9.2 - - + -
520A ALA 3.5 3.8 - - - +
521A VAL* 4.2 7.4 - - + -
594A LEU* 4.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A HIS* 4.2 13.9 - + - -
510A ILE* 1.3 78.2 - - - +
512A LEU* 1.3 74.9 + - - +
513A CYS* 4.4 8.7 - - + -
518A TYR 4.0 0.3 - - - +
519A LEU* 3.3 6.0 - - - +
520A ALA* 2.8 41.7 + - + +
594A LEU* 4.7 16.6 - - + +
595A ALA* 5.1 1.1 - - - -
596A LEU* 3.3 60.1 - - + +
598A SER* 5.1 0.7 - - - -
791A GLU* 5.5 12.1 - - + -
792A PRO* 5.2 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391A HIS* 4.0 7.1 + - - -
393A VAL* 4.3 26.8 - - + +
396A ILE* 5.5 0.7 - - + -
400A LEU* 4.7 14.1 - - + -
404A ILE* 4.8 0.9 - - + -
437A LEU* 3.7 29.4 - - + -
439A LEU* 4.2 12.6 - - + -
449A PHE* 3.9 14.6 - - + -
511A PHE* 1.3 84.6 - - - +
513A CYS* 1.3 78.3 + - - +
514A LYS* 3.5 4.2 + - - +
517A GLY 4.7 2.0 - - - -
518A TYR 3.8 10.8 - - - +
519A LEU* 3.7 17.9 - - + -
577A PHE* 4.0 22.0 - - + -
----------------------------------------------------------
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