Contacts of the helix formed by residues 638 - 648 (chain A) in PDB entry 3SXS
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 SER 638 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A ARG* 4.3 1.1 - - - +
636A LEU 3.8 3.0 + - - -
637A ALA* 1.3 75.8 - - - +
639A ASP* 1.3 58.9 + - - +
640A THR* 3.4 9.0 + - - -
641A ILE* 3.1 38.3 + - - +
642A TYR* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 639 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A ARG* 4.4 10.4 - - - +
638A SER* 1.3 73.6 - - - +
640A THR* 1.4 58.3 + - - +
642A TYR* 3.3 10.3 + - - +
643A GLN* 2.9 57.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 640 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A SER* 3.2 8.1 + - - -
639A ASP* 1.4 78.5 + - - +
641A ILE* 1.3 61.7 + - - +
643A GLN* 3.3 9.5 + - - +
644A ILE* 3.2 27.4 + - + +
669A LEU* 3.9 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 641 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A PRO* 5.7 1.3 - - + +
514A LEU* 4.0 25.8 - - + -
602A MET* 3.9 12.4 - - + +
606A PHE* 3.6 47.6 - - + -
637A ALA* 4.1 10.3 - - + -
638A SER* 3.1 27.3 + - - +
640A THR* 1.3 71.5 - - - +
642A TYR* 1.3 66.3 + - - +
644A ILE* 3.2 10.8 + - + +
645A MET* 3.0 23.0 + - + +
669A LEU* 4.1 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A LEU 2.7 25.9 + - - -
632A TYR* 3.7 8.5 - - - -
633A ARG* 3.5 53.2 - - + -
634A PRO* 4.2 0.4 - - + -
637A ALA* 4.6 1.3 - - + +
638A SER 3.0 17.0 + - - +
639A ASP* 3.3 7.2 + - - +
641A ILE* 1.3 76.6 - - - +
643A GLN* 1.3 75.6 + - - +
645A MET* 3.2 26.7 + - + +
646A TYR* 2.8 59.9 + + - +
649A TRP* 4.3 6.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 643 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A ASP* 2.9 46.3 + - - +
640A THR* 3.3 10.3 + - + +
642A TYR* 1.3 91.9 - - - +
644A ILE* 1.3 56.8 + - + +
646A TYR* 3.8 15.4 - - - +
647A SER* 3.0 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A MET* 4.1 18.4 - - + -
640A THR* 3.2 17.5 + - + +
641A ILE* 3.5 11.0 - - + +
642A TYR 3.2 0.4 - - - -
643A GLN* 1.3 73.3 - - + +
645A MET* 1.3 65.0 + - - +
647A SER* 2.7 24.6 + - - -
648A CYS* 3.6 6.8 + - - -
662A LEU* 3.6 25.6 - - + -
665A SER* 4.2 23.6 - - - +
666A ILE* 4.3 17.3 - - + -
669A LEU* 3.7 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A GLY* 3.8 17.5 - - - +
602A MET* 3.9 37.5 - - + +
603A TRP* 3.9 31.4 - - - -
606A PHE* 4.4 2.0 - - + -
634A PRO* 4.1 14.6 - - + -
637A ALA* 4.3 3.8 - - + -
641A ILE* 3.0 33.1 + - + +
642A TYR* 3.3 31.0 - - + +
644A ILE* 1.3 77.1 - - - +
646A TYR* 1.3 65.1 + - - +
648A CYS* 3.0 21.3 + - - +
649A TRP* 3.6 21.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A GLY 4.8 3.8 + - - -
630A ARG* 3.6 34.3 - - + +
642A TYR* 2.8 55.3 + + + +
643A GLN* 3.8 17.9 - - - +
645A MET* 1.3 73.2 - - - +
647A SER* 1.3 58.0 + - - +
649A TRP* 3.0 40.5 + + + +
650A HIS 4.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 647 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A GLN 3.0 15.3 + - - -
644A ILE* 2.7 21.9 + - - -
646A TYR* 1.3 76.3 - - - +
648A CYS* 1.3 60.4 + - - +
649A TRP 3.2 0.9 + - - -
650A HIS* 3.9 7.3 + - - +
655A LYS 4.3 3.8 - - - +
656A ARG* 3.8 8.0 - - - -
657A PRO* 3.4 33.3 - - - +
662A LEU* 4.4 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 648 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A VAL* 3.2 42.0 - - - +
596A TRP* 3.3 11.4 - - - -
598A PHE* 4.2 4.9 - - - -
599A GLY* 3.8 18.4 - - - -
602A MET* 5.3 0.2 - - - -
644A ILE 3.6 15.3 - - - -
645A MET* 3.0 13.4 + - - +
647A SER* 1.3 77.1 - - - +
649A TRP* 1.3 60.7 + - + +
650A HIS 3.5 0.9 - - - -
656A ARG* 3.2 22.6 + - - -
657A PRO* 4.5 1.3 - - - -
662A LEU* 4.0 21.8 - - - -
----------------------------------------------------------
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