Contacts of the helix formed by residues 631 - 636 (chain A) in PDB entry 5CGD
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 CYS 631 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627A LEU 3.1 22.3 + - - -
628A GLY* 3.2 16.4 - - - +
629A TYR 3.1 1.0 - - - -
630A LEU* 1.3 77.8 - - - +
632A THR* 1.3 54.6 + - - +
633A PHE 3.0 0.2 - - - -
634A CYS* 2.8 30.5 + - - +
635A LEU* 3.0 19.6 + - + +
646A LEU 6.1 0.2 - - - -
647A GLN* 5.0 2.1 - - - +
650A GLY* 3.3 40.2 - - - -
651A ILE* 3.7 17.7 - - + -
806A VAL* 4.2 8.5 - - + -
4005A 51E 4.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 632 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583A ALA* 3.7 13.2 + - - +
584A VAL* 4.6 3.8 - - - +
587A ALA* 3.2 25.2 - - + +
628A GLY 4.5 4.0 - - - +
629A TYR 3.5 11.6 + - - +
630A LEU 3.3 0.4 - - - -
631A CYS* 1.3 75.4 - - + +
633A PHE* 1.3 61.8 + - - +
634A CYS 3.2 1.3 - - - -
635A LEU* 3.8 2.4 - - - +
636A ILE* 2.9 32.2 + - - +
803A CYS* 4.0 37.7 - - + +
806A VAL* 5.3 1.8 - - + -
807A SER* 3.7 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 633 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A VAL* 3.9 15.9 - - + -
587A ALA* 3.8 22.7 - - + -
588A CYS* 3.8 24.0 - - - -
591A LEU* 3.9 20.9 - - + -
629A TYR 3.7 12.3 - - - -
630A LEU* 3.1 23.5 + - + +
631A CYS 3.0 1.0 - - - -
632A THR* 1.3 79.2 + - - +
634A CYS* 1.3 60.7 + - - +
636A ILE 3.2 17.3 - - - +
637A ALA* 3.3 10.7 - - - +
643A TYR* 5.1 4.2 - - - -
4004A OLA 3.7 44.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 634 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A LEU* 3.8 14.4 - - - -
631A CYS* 2.8 12.8 + - - +
633A PHE* 1.3 81.6 - - - +
635A LEU* 1.3 55.6 + - - +
636A ILE 3.3 0.2 - - - -
637A ALA* 4.3 5.3 - - - +
643A TYR* 4.2 14.5 - - + +
646A LEU* 3.7 36.3 - - - -
647A GLN* 2.7 44.2 + - + +
731A LEU* 3.7 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 635 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A CYS* 3.0 26.1 + - + +
632A THR* 4.2 1.3 - - + +
634A CYS* 1.3 76.8 - - - +
636A ILE* 1.3 67.1 + - - +
637A ALA 3.8 0.9 - - - -
647A GLN* 3.5 31.0 - - + +
651A ILE* 4.1 17.9 - - + -
731A LEU* 3.6 18.6 + - - +
799A ILE* 3.6 29.4 - - + +
802A MET* 3.7 28.3 - - + -
803A CYS* 3.6 34.3 - - - +
806A VAL* 5.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A PRO* 4.6 2.9 - - + -
580A PRO* 4.2 28.3 - - + +
583A ALA* 4.9 5.2 - - + -
584A VAL* 4.4 13.9 - - + -
632A THR* 2.9 18.0 + - - +
633A PHE* 3.2 11.4 - - - +
635A LEU* 1.3 84.7 - - - +
637A ALA* 1.3 59.4 + - - +
729A VAL* 3.5 28.9 - - + +
730A TYR* 4.7 5.6 - - + -
799A ILE* 4.2 14.4 - - + -
800A ILE* 4.2 13.5 - - + -
803A CYS* 4.2 10.5 - - - -
4004A OLA 3.1 33.3 - - + +
----------------------------------------------------------
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