Contacts of the helix formed by residues 469 - 475 (chain A) in PDB entry 6J95
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 VAL 469 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A PRO* 3.6 11.0 - - + -
441A PRO 4.1 8.5 - - - +
442A PRO 2.9 15.6 + - - +
444A LEU* 3.8 35.7 - - + +
467A ILE* 3.1 6.8 + - + +
468A SER* 1.3 68.8 - - - +
470A TRP* 1.3 60.9 + - - +
472A LEU* 3.2 7.5 + - - -
473A HIS* 2.8 64.1 + - + +
507A LEU* 4.1 23.1 - - + +
601A HEM 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A PHE* 3.4 44.0 - + + -
130A ILE* 3.7 21.8 - - + +
133A TYR* 4.3 14.9 - + + +
437A LEU 3.2 21.1 - - - -
438A TYR* 4.0 12.8 - + - -
439A PRO* 3.9 22.2 - - + +
442A PRO* 3.1 14.6 + - + +
468A SER* 3.8 7.4 - - - +
469A VAL* 1.3 76.3 - - - +
471A ASN* 1.3 77.3 + - - +
473A HIS* 3.8 1.6 - - - +
474A ARG* 3.0 71.3 + - - +
550A MET* 3.7 22.9 - - + -
556A ILE* 4.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A PHE 4.4 0.7 - - - +
132A LEU* 3.4 15.5 + - - +
133A TYR* 3.3 31.1 + - - +
136A PHE* 3.4 31.0 - - + +
154A ILE* 4.8 1.4 - - - +
156A SER* 3.0 33.6 + - - +
468A SER* 3.0 30.0 + - - +
470A TRP* 1.3 77.1 - - - +
472A LEU* 1.3 61.1 + - - +
475A SER* 2.8 34.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A VAL 5.1 0.4 - - - +
156A SER 3.2 28.5 - - - +
157A ASP 3.7 0.7 - - - -
158A PRO* 3.4 34.1 - - + -
161A ALA* 4.0 7.2 - - + -
467A ILE* 3.7 30.1 - - + -
468A SER 3.0 15.1 + - - +
469A VAL* 3.2 8.7 + - - +
471A ASN* 1.3 78.0 - - - +
473A HIS* 1.3 60.6 + - + +
474A ARG 3.4 0.3 + - - -
475A SER* 3.7 7.7 + - - -
479A TRP* 3.0 20.4 + - - -
504A PHE 3.9 5.8 - - - +
505A SER* 3.1 20.2 + - - +
507A LEU* 3.8 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A LEU 3.2 17.7 + - - -
436A ARG* 2.9 63.7 + - + +
439A PRO* 3.8 8.1 - - + +
469A VAL* 2.8 42.5 + - + +
470A TRP* 3.8 5.2 - - - +
472A LEU* 1.3 74.6 - - + +
474A ARG* 1.3 58.0 + - + +
479A TRP* 3.1 16.1 + - - +
505A SER 3.4 16.6 - - - -
506A TYR* 3.6 11.1 - + - -
507A LEU 2.8 27.3 + - - -
508A PRO* 4.0 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A TYR* 3.8 20.3 + - + -
436A ARG* 4.4 8.5 - - - +
437A LEU* 2.8 57.5 + - + +
438A TYR* 3.8 15.6 + - - -
470A TRP* 3.0 64.4 + - - +
471A ASN 3.6 1.1 - - - -
473A HIS* 1.3 83.1 - - + +
475A SER* 1.3 64.9 + - - +
476A PRO* 3.1 9.4 - - - +
482A ALA* 3.4 22.5 - - + +
483A GLU* 4.4 22.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PHE* 3.7 23.3 - - - -
156A SER 5.5 1.3 - - - -
158A PRO* 6.5 0.4 - - - -
471A ASN 2.8 16.7 + - - -
472A LEU* 3.7 11.4 + - - -
473A HIS 3.6 2.0 - - - -
474A ARG* 1.3 74.7 - - - +
476A PRO* 1.3 67.8 - - - +
477A LEU* 3.4 21.0 + - - +
478A HIS* 3.1 24.2 + - - -
479A TRP* 3.1 16.1 + - - +
482A ALA* 4.5 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