Contacts of the strand formed by residues 675 - 680 (chain A) in PDB entry 6DBU
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 675 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585A ALA* 3.1 33.3 + - - +
588A ASP* 4.4 3.8 + - - +
589A LEU* 6.1 3.2 - - - +
643A SER* 3.2 1.5 - - - -
644A PHE* 2.9 57.2 + - + +
645A THR* 4.6 5.6 - - - -
646A ILE* 4.9 7.0 - - - +
673A SER* 4.6 8.5 - - - +
674A CYS* 1.3 75.9 - - - +
676A PRO* 1.3 68.4 - - - +
677A LEU 3.7 0.2 + - - -
1014A TRP* 3.2 52.1 - - + -
1017A THR* 2.5 45.6 + - - +
1018A SER* 3.6 20.8 + - - +
1019A LYS* 5.2 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 676 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A PHE* 4.4 1.9 - - - -
641A ARG* 4.7 6.3 - - - -
642A PHE 3.7 6.5 - - - +
643A SER* 3.9 5.6 - - - -
674A CYS 3.3 10.3 - - - +
675A ARG* 1.3 85.7 - - + +
677A LEU* 1.3 60.3 + - - +
679A LEU* 4.2 19.3 - - + -
1010A LEU* 4.1 12.9 - - + +
1013A HIS* 3.3 44.9 - - + +
1014A TRP* 3.7 25.0 - - - +
1017A THR* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 677 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A ARG* 3.1 18.4 - - - +
576A PHE* 3.1 24.5 + - + +
578A TYR* 3.4 52.5 - - + +
581A ALA* 3.9 11.0 - - + -
642A PHE* 2.9 29.7 + - + +
643A SER* 5.0 0.2 - - - -
644A PHE* 3.6 35.0 - - + -
675A ARG 4.5 0.4 - - - +
676A PRO* 1.3 76.3 - - - +
678A CYS* 1.3 66.5 + - + +
697A VAL* 4.2 11.0 - - + -
1010A LEU* 4.9 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 678 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A GLY* 6.5 0.2 - - - -
573A SER* 5.5 0.9 - - - -
574A ARG 3.8 1.1 - - - -
575A ARG* 3.5 32.8 - - + -
640A VAL 4.1 0.2 - - - +
641A ARG* 3.7 0.3 - - - -
642A PHE* 3.0 42.6 + - + +
677A LEU* 1.3 86.8 - - + +
679A LEU* 1.3 74.9 + - - +
680A MET* 3.7 31.6 - - - -
693A ILE* 5.1 3.1 - - - -
694A LEU* 4.7 8.1 - - - -
697A VAL* 4.8 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 679 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A SER* 3.1 5.2 - - - -
574A ARG* 2.9 38.3 + - + +
639A ALA* 6.3 0.9 - - + -
640A VAL 3.6 9.6 - - - +
641A ARG* 4.2 16.4 - - + -
676A PRO* 4.2 24.5 - - + -
678A CYS* 1.3 87.4 - - - +
680A MET* 1.3 61.7 + - - +
990A PHE* 3.3 40.8 - - + -
1006A LEU* 3.6 25.2 - - + +
1009A ILE* 4.4 6.1 - - + -
1010A LEU* 4.4 18.8 - - + +
1013A HIS* 5.8 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 680 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A ILE 3.8 0.4 - - - -
573A SER* 3.6 18.6 - - - -
639A ALA* 3.5 3.1 - - - +
640A VAL* 2.9 63.2 + - + +
642A PHE* 6.3 0.7 - - + +
678A CYS* 3.7 13.5 - - - -
679A LEU* 1.3 82.0 - - - +
681A PHE* 1.3 59.8 + - - +
682A VAL* 3.0 20.9 + - + -
690A LEU* 3.6 15.9 - - + -
693A ILE* 3.4 26.5 - - + -
694A LEU* 3.2 36.3 - - + -
1006A LEU* 5.0 1.5 - - - +
----------------------------------------------------------
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