Contacts of the strand formed by residues 628 - 634 (chain A) in PDB entry 3QFR
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 HIS 628 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A ARG 4.6 3.1 - - - -
524A PRO* 3.8 31.0 - - + +
525A PHE 5.3 0.4 + - - -
529A THR* 4.1 8.2 - - + +
530A PRO 3.0 8.0 + - - +
531A VAL* 3.4 2.6 - - - -
532A ILE* 2.9 25.7 + - - +
626A GLY 3.8 8.8 + - - -
627A ALA* 1.3 71.3 - - - +
629A ILE* 1.3 62.8 + - - +
630A TYR* 3.5 36.2 - + + +
671A LYS 5.7 0.2 + - - -
672A GLY 3.3 24.7 + - - -
673A ARG* 3.3 30.6 - - + +
675A SER* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 629 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A ILE* 3.4 24.7 - - + +
623A ILE* 3.9 18.8 - - + -
627A ALA 4.9 3.4 - - - +
628A HIS* 1.3 75.5 - - - +
630A TYR* 1.3 69.8 + - - +
631A VAL* 4.2 9.0 - - + -
646A PHE* 3.7 51.4 - - + -
665A ILE* 5.3 1.1 - - + -
668A LEU* 4.6 10.3 - - + -
673A ARG 2.7 15.6 + - - +
674A TYR* 3.3 28.6 - - + -
675A SER* 2.9 26.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 630 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A PHE* 3.5 25.6 - + + -
522A ARG 2.4 34.2 + - - -
523A LEU* 3.3 0.4 - - - -
524A PRO* 3.3 19.8 - - - +
531A VAL* 3.8 19.7 - - + -
532A ILE 2.8 15.6 + - - +
533A MET* 4.4 3.6 - - + -
534A VAL* 2.8 32.8 + - - +
543A PHE* 3.5 20.9 - - + -
546A PHE* 3.7 23.3 - + - -
628A HIS* 3.5 36.6 - + + -
629A ILE* 1.3 73.6 - - - +
631A VAL* 1.3 62.9 + - - +
675A SER* 3.4 24.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 631 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A PHE* 4.2 1.3 - - - -
534A VAL* 3.3 8.3 - - + +
543A PHE* 4.6 0.4 - - - -
629A ILE* 4.2 7.2 - - + -
630A TYR* 1.3 80.1 - - - +
632A CYS* 1.3 63.0 + - - +
638A MET* 3.9 29.6 - - + -
639A ALA* 4.4 8.3 - - - +
642A VAL* 4.0 19.7 - - + -
674A TYR* 4.0 32.8 - - + +
675A SER 3.1 5.5 + - - -
676A LEU* 3.6 19.9 - - + -
677A ASP 3.0 24.8 + - - +
678A VAL* 3.8 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 632 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A PHE* 4.5 0.9 - - + -
534A VAL 2.9 7.1 + - - -
535A GLY* 3.3 13.7 - - - -
536A PRO* 3.8 0.7 - - - +
539A GLY* 3.2 34.9 - - - +
542A PRO* 3.4 30.3 - - + -
543A PHE* 3.9 8.9 - - + -
631A VAL* 1.3 76.2 - - - +
633A GLY* 1.3 57.7 + - - +
638A MET* 3.6 8.9 - - - +
677A ASP* 3.3 27.1 - - + +
678A VAL* 4.4 0.2 - - - -
679A TRP* 3.4 19.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 633 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A PRO 4.7 2.9 - - - -
538A THR* 5.7 0.2 - - - -
539A GLY* 3.8 15.0 - - - -
632A CYS* 1.3 77.7 - - - +
634A ASP* 1.3 65.0 + - - -
635A ALA 3.3 0.2 + - - -
638A MET* 3.8 5.1 - - - +
677A ASP 3.4 6.7 + - - -
678A VAL* 3.5 3.7 - - - +
679A TRP* 3.1 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 634 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A PRO 5.6 0.2 + - - -
633A GLY* 1.3 68.6 - - - -
635A ALA* 1.3 59.2 + - - +
636A ARG* 3.2 29.4 + - - +
637A ASN* 3.2 21.8 + - - +
638A MET* 3.3 26.4 + - + +
639A ALA* 3.2 23.7 + - - +
678A VAL* 4.7 0.4 - - - -
679A TRP* 3.7 6.6 - - - +
680A SER* 4.9 1.4 - - - -
753A NAP 4.8 9.6 + - + +
----------------------------------------------------------
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