Contacts of the strand formed by residues 641 - 648 (chain A) in PDB entry 3QCA
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 GLN 641 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A LYS* 3.7 32.9 - - + +
639A PHE* 3.6 2.2 - - - +
640A PRO* 1.3 91.1 - - + +
642A GLU* 1.3 69.8 + - - +
643A THR* 5.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A LYS 3.5 10.5 + - - +
576A LEU* 3.7 9.6 - - + +
577A ARG* 3.1 24.9 + - - +
617A SER* 4.2 14.4 + - - +
618A THR 5.2 4.3 - - - +
619A PHE 4.5 10.9 - - - +
620A PRO* 5.9 0.7 - - - +
622A ARG* 5.2 1.7 + - - -
637A LYS* 3.5 20.6 - - - +
638A LEU* 3.9 29.6 - - + +
639A PHE 5.1 3.5 - - - +
641A GLN* 1.3 84.7 - - - +
643A THR* 1.3 74.4 + - - +
644A LEU* 4.2 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 643 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A ARG* 3.3 31.1 + - + +
585A PHE* 4.4 16.4 - - + -
616A LEU 4.5 0.3 - - - +
618A THR* 4.6 10.2 + - - +
641A GLN 4.3 0.6 + - - -
642A GLU* 1.3 81.8 + - - +
644A LEU* 1.3 74.3 + - - +
645A PHE* 4.0 29.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A LEU* 4.8 10.5 - - + -
577A ARG 2.7 11.1 + - - +
578A ILE* 4.1 18.4 - - + -
579A ARG* 2.9 24.9 + - - +
599A VAL* 5.3 1.1 - - + -
615A LEU* 3.7 31.6 - - + -
616A LEU 3.2 14.1 - - - +
617A SER* 3.6 26.2 - - - +
624A VAL* 4.6 3.8 - - + -
638A LEU* 3.9 33.9 - - + -
642A GLU* 4.2 6.1 - - + +
643A THR* 1.3 84.6 - - - +
645A PHE* 1.3 71.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579A ARG* 3.7 27.6 - - + -
585A PHE* 5.3 2.9 - + - -
614A LYS 3.1 2.6 - - - +
615A LEU* 4.2 3.1 - - - -
616A LEU* 2.6 53.5 + - + +
618A THR* 3.6 33.9 - - + -
643A THR* 4.0 26.9 - - + -
644A LEU* 1.3 78.8 - - - +
646A LEU* 1.3 63.9 + - - +
647A GLU* 5.6 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A ILE* 3.7 24.5 - - + -
579A ARG 3.1 20.7 + - - +
580A THR* 4.6 3.8 - - - -
581A PRO* 4.7 15.7 - - + +
586A LEU* 4.6 4.5 - - + -
603A VAL* 4.5 11.2 - - + -
608A PHE* 3.6 45.8 - - + +
613A TYR* 3.8 30.3 - - + +
614A LYS 3.2 8.7 - - - +
615A LEU* 4.1 17.9 - - + -
625A THR* 6.0 0.2 - - + -
644A LEU 4.3 0.2 - - - -
645A PHE* 1.3 74.4 - - - +
647A GLU* 1.3 67.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A PRO* 5.7 1.8 - - - -
613A TYR* 3.2 9.4 - - - -
614A LYS* 2.4 48.9 + - + +
616A LEU* 4.8 20.0 - - + +
621A ARG* 5.3 4.2 + - - -
645A PHE* 4.7 6.8 - - + +
646A LEU* 1.3 79.6 - - - +
648A ALA* 1.3 65.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 648 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581A PRO* 6.0 0.4 - - - +
612A GLU 3.4 9.4 - - - +
613A TYR* 3.9 14.2 - - + -
614A LYS* 5.4 0.9 - - - -
647A GLU* 1.3 74.1 - - - +
649A LYS* 1.3 58.1 + - - +
650A GLU* 2.7 38.0 + - + +
631B LYS* 6.6 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