Contacts of the strand formed by residues 643 - 648 (chain D) in PDB entry 3GUT
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 LYS 643 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D LYS* 5.4 5.5 - - - +
550D ILE* 3.4 49.9 + - + +
551D VAL 5.9 0.2 - - - -
552D ARG* 6.4 1.1 - - - +
553D MET* 4.1 12.6 - - + -
556D THR* 5.9 4.5 - - + -
628D PHE* 4.1 2.0 - - - -
629D VAL* 2.8 54.3 + - + +
641D GLU* 2.9 19.1 + - - +
642D PRO* 1.3 73.5 - - - +
644D PRO* 1.3 73.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 644 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D MET* 6.0 0.7 - - - +
556D THR* 4.3 15.8 - - - +
626D SER* 5.9 4.9 - - - +
627D VAL 3.7 9.4 - - - +
628D PHE* 4.0 15.5 - - + -
629D VAL* 4.6 1.4 - - - +
642D PRO 3.9 7.2 - - - +
643D LYS* 1.3 96.4 - - + +
645D PHE* 1.3 59.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 645 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D MET* 4.6 12.3 - - + -
555D ARG 4.2 9.2 - - - -
556D THR* 3.6 15.9 - - - -
557D ALA 3.3 30.1 - - - -
558D GLY* 3.4 10.8 - - - -
566D ILE* 5.2 5.8 - - + -
582D PHE* 3.9 21.1 - + - -
611D PHE* 6.1 0.2 - + - -
613D THR* 4.1 18.2 - - + -
626D SER* 3.4 5.8 - - - -
627D VAL* 2.9 43.1 + - + +
629D VAL* 4.2 14.1 - - + -
644D PRO* 1.3 75.3 - - - +
646D LEU* 1.3 92.9 + - - +
647D TYR* 4.0 26.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 646 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556D THR 3.2 13.2 + - - +
557D ALA* 3.0 7.8 - - + +
558D GLY 2.7 32.1 + - - +
624D PRO* 3.3 20.6 - - + -
625D ALA* 3.1 20.2 - - - +
626D SER* 2.9 28.0 - - - +
645D PHE* 1.3 79.8 - - - +
647D TYR* 1.3 72.0 + - - +
648D TYR* 3.7 11.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 647 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558D GLY 3.0 7.9 - - - -
559D CYS 3.3 26.9 - - - -
560D VAL* 3.7 19.3 - - + +
582D PHE* 4.1 7.2 - + - -
592D TRP* 3.8 10.2 - + - -
613D THR* 3.4 11.9 - - + +
614D PRO* 2.5 47.4 + - - +
616D TYR* 3.7 37.9 - + + -
621D ILE* 5.3 0.3 - - - +
624D PRO* 3.1 2.8 - - - +
625D ALA* 2.9 39.2 + - + +
627D VAL* 3.9 33.0 - - + -
645D PHE* 4.2 9.9 - + - -
646D LEU* 1.3 73.4 - - - +
648D TYR* 1.3 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 648 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555D ARG* 3.6 33.8 + - - -
557D ALA* 4.0 7.0 - - + -
558D GLY* 2.8 30.6 + - - -
559D CYS* 3.1 27.4 + - + -
560D VAL* 3.0 27.3 + - - -
564D GLU* 3.7 8.7 + - - -
624D PRO* 4.0 5.2 - - + -
646D LEU* 4.0 13.5 - - + -
647D TYR* 1.3 73.8 - - - +
649D PRO* 1.3 81.1 - - + +
650D GLU* 5.7 0.4 - - + -
----------------------------------------------------------
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