Contacts of the strand formed by residues 511 - 514 (chain D) in PDB entry 3GEF
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 511 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453D ARG* 5.4 0.3 + - - -
496D THR* 3.5 6.7 - - - -
498D TRP* 2.8 31.5 + - + +
504D ALA* 5.4 0.9 - - - +
505D THR 3.4 21.3 - - - +
506D HIS* 3.6 1.6 - - - -
507D SER* 2.7 41.0 + - - +
508D PRO 3.4 2.4 - - - -
509D PRO 3.5 0.2 - - - -
510D THR* 1.3 108.8 + - - +
512D LEU* 1.3 63.2 + - - +
513D VAL 4.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 512 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481D TYR* 3.4 28.7 - - + +
483D PHE* 4.0 16.8 - - + -
484D PRO* 4.3 11.4 - - + -
487D PHE* 4.0 16.4 - - + -
495D VAL* 3.9 24.9 - - + -
496D THR 2.8 11.2 + - - +
497D ILE* 3.3 7.3 - - + +
498D TRP* 2.8 27.3 + - - +
506D HIS* 3.5 10.5 - - - +
508D PRO* 3.7 37.5 - - + -
509D PRO* 5.1 0.4 - - + -
511D ASP* 1.3 73.1 - - - +
513D VAL* 1.3 65.4 + - - +
514D TRP 3.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 513 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481D TYR* 5.6 1.2 - - - -
497D ILE* 5.6 0.2 - - - -
498D TRP* 3.6 19.3 - - + +
499D ALA 4.5 2.7 - - - +
500D ALA* 4.2 21.3 - - + +
502D ALA 6.0 0.9 - - - +
504D ALA* 4.6 6.3 - - + +
505D THR* 3.8 11.0 - - - +
506D HIS* 2.9 51.4 + - + +
512D LEU* 1.3 75.6 - - - +
514D TRP* 1.3 63.5 + - - +
515D LYS* 3.3 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 514 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479D LEU* 4.3 17.7 - - + -
480D THR 3.4 30.2 + - - -
481D TYR* 3.8 37.7 - + + +
497D ILE* 4.5 3.1 - - + +
498D TRP 2.8 17.6 + - - +
499D ALA* 4.6 3.6 - - + -
500D ALA 3.4 7.8 + - - -
512D LEU 3.8 1.2 + - - -
513D VAL* 1.3 69.8 - - - +
515D LYS* 1.3 75.7 - - + +
516D ALA* 4.6 5.9 - - + +
517D GLN* 3.3 58.8 - - + +
519D THR 4.9 0.9 - - - -
520D TRP* 3.6 51.4 - + - -
----------------------------------------------------------
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