Contacts of the helix formed by residues 630 - 639 (chain A) in PDB entry 4OSI
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 THR 630 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A CYS* 3.4 6.7 - - - -
628A GLY 5.6 0.4 - - - +
629A LEU* 1.3 76.6 - - - +
631A PRO* 1.3 73.8 - - - +
632A GLU* 2.8 29.4 + - - +
633A GLN* 3.1 37.6 + - + +
634A VAL* 3.2 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 631 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A HIS 4.6 9.6 - - - +
595A LEU* 4.3 17.7 - - + -
599A GLN* 5.5 1.6 - - - +
620A LEU* 4.1 17.5 - - + -
624A CYS* 3.3 18.8 - - - -
629A LEU 4.7 0.2 - - - +
630A THR* 1.3 87.5 - - - +
632A GLU* 1.3 76.5 + - - +
633A GLN 3.1 0.2 + - - -
634A VAL* 3.3 2.8 + - + +
635A VAL* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 632 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A GLN* 4.2 20.4 - - - +
630A THR* 2.8 17.6 + - - +
631A PRO* 1.3 93.8 - - - +
633A GLN* 1.3 58.2 + - + +
635A VAL* 3.4 4.0 + - - +
636A ALA* 2.9 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 633 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A LEU* 3.2 25.8 - - + +
630A THR* 3.1 34.6 + - + +
632A GLU* 1.3 74.0 - - + +
634A VAL* 1.3 59.6 + - - +
635A VAL 3.0 1.1 - - - -
636A ALA* 2.7 28.0 + - + +
637A ILE* 2.9 17.7 + - + +
666A GLN* 4.3 23.9 + - - +
669A VAL* 3.9 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 634 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A VAL* 4.4 15.9 - - + -
620A LEU* 3.6 38.8 - - + +
623A LEU* 3.7 37.7 - - + -
624A CYS* 4.7 2.9 - - - -
629A LEU* 4.7 7.8 - - + +
630A THR 3.2 10.1 + - - +
631A PRO 3.5 7.2 - - - +
633A GLN* 1.3 75.3 - - - +
635A VAL* 1.3 58.3 + - + +
637A ILE* 3.2 12.9 + - + +
638A ALA* 2.9 28.4 + - - +
647A LEU* 4.0 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 635 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A LEU* 3.9 22.9 - - + -
599A GLN* 3.5 52.3 - - + +
602A ALA* 5.3 1.8 - - + -
603A ILE* 4.5 7.2 - - + -
616A VAL* 5.8 0.4 - - + -
620A LEU* 5.2 0.2 - - + -
631A PRO 2.9 21.2 + - - +
632A GLU 3.4 7.9 - - - +
634A VAL* 1.3 80.2 - - + +
636A ALA* 1.3 59.4 + - - +
638A ALA* 3.3 6.2 + - - +
639A SER* 2.9 44.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A GLU 2.9 13.0 + - - +
633A GLN* 2.7 18.4 + - + +
635A VAL* 1.3 73.6 - - - +
637A ILE* 1.3 54.5 + - - +
639A SER* 3.7 5.5 + - - -
640A HIS* 3.0 31.2 + - - -
669A VAL* 5.1 3.1 - - + -
673A SER* 3.4 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 637 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A LEU* 5.5 0.2 - - + -
629A LEU* 4.5 11.0 - - + -
633A GLN 2.9 21.4 + - - +
634A VAL* 3.6 17.9 - - + +
636A ALA* 1.3 73.8 - - - +
638A ALA* 1.3 65.6 + - - +
639A SER 3.2 0.8 + - - -
640A HIS* 4.1 8.7 - - - +
643A GLY* 3.8 11.1 - - - -
646A ALA* 3.6 29.3 - - + +
647A LEU* 3.9 24.2 - - + +
650A VAL* 4.6 12.1 - - + -
669A VAL* 4.4 20.9 - - + -
672A ALA* 3.9 19.7 - - + +
673A SER* 3.9 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 638 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A ILE* 4.0 16.0 - - + +
606A ASN* 4.6 1.6 + - - -
612A ALA* 3.8 12.1 - - + +
616A VAL* 3.4 32.5 - - + -
634A VAL 2.9 13.2 + - - +
635A VAL* 3.9 4.7 - - - +
637A ILE* 1.3 76.1 - - - +
639A SER* 1.3 57.5 + - - +
640A HIS 2.8 21.3 + - - +
643A GLY* 3.5 13.5 - - - -
647A LEU* 3.6 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 639 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A ALA* 3.9 29.4 - - - +
603A ILE* 4.0 4.3 + - - +
606A ASN* 3.2 20.8 + - - +
635A VAL* 2.9 27.6 + - - +
636A ALA* 3.7 9.6 + - - -
637A ILE 3.2 2.4 - - - -
638A ALA* 1.3 73.1 - - - +
640A HIS* 1.3 71.8 + - - +
----------------------------------------------------------
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