Contacts of the helix formed by residues 430 - 443 (chain A) in PDB entry 2C31
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 ILE 430 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 3.8 25.5 - - + +
93A HIS* 3.9 20.2 - - + -
397A VAL* 4.2 7.6 - - + -
398A ASN 4.2 5.8 - - - +
399A GLU* 3.3 28.5 - - + +
421A ASP 4.3 3.8 - - - +
422A SER* 4.3 8.7 - - - +
427A VAL* 4.0 21.5 - - + +
429A GLY* 1.3 78.9 - - - +
431A GLY* 1.3 74.9 + - - +
432A MET 3.6 0.4 - - - -
433A GLY* 3.7 2.4 + - - -
434A TYR* 3.0 62.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A VAL* 3.6 3.9 - - - +
399A GLU* 3.0 24.7 + - - -
429A GLY 3.1 3.0 - - - -
430A ILE* 1.3 89.4 - - - +
432A MET* 1.3 67.6 + - - +
434A TYR* 3.2 3.3 + - - +
435A CYS* 3.1 21.7 + - - -
450A GLU* 3.6 14.8 - - - -
458A SER* 4.0 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A GLY* 1.3 76.6 - - - +
433A GLY* 1.3 61.8 + - - +
435A CYS* 3.3 11.3 + - - +
436A VAL* 3.2 27.4 + - - +
448A ALA* 4.6 0.2 - - + -
450A GLU* 3.6 32.1 - - + +
455A PHE* 4.0 16.2 - - + -
458A SER* 3.2 41.8 + - - +
459A GLY* 4.4 1.1 - - - -
461A GLU* 3.6 18.2 - - + -
462A LEU* 3.7 19.7 - - + -
465A ILE* 3.7 23.5 - - + +
474A VAL* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 4.2 9.6 - - - -
58A HIS* 3.7 29.9 - - - +
61A TYR* 4.7 3.4 - - - -
62A ALA* 3.4 18.0 - - - +
429A GLY 5.2 0.6 + - - -
430A ILE 3.7 4.6 + - - -
431A GLY 3.2 0.6 - - - -
432A MET* 1.3 76.9 - - - +
434A TYR* 1.3 63.7 + - - +
436A VAL* 3.2 2.9 + - - +
437A ALA 3.2 17.5 + - - -
458A SER* 4.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A TYR* 3.3 29.2 - - + -
64A SER* 3.9 3.8 - - - -
65A ILE* 3.7 33.0 - - + +
93A HIS* 2.8 28.8 + - - -
99A PHE* 3.8 12.6 - - - -
249A MET* 5.6 0.4 - - - -
397A VAL* 3.9 13.0 - - + -
420A LEU* 3.7 29.8 - - + -
421A ASP 3.6 22.0 + - - -
430A ILE* 3.0 44.6 + - + +
431A GLY 3.4 4.3 - - - +
433A GLY* 1.3 75.2 - - - +
435A CYS* 1.3 57.9 + - - +
437A ALA* 3.4 1.0 + - - +
438A ALA* 2.8 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A VAL* 3.9 9.0 - - - -
431A GLY 3.1 19.4 + - - -
432A MET* 3.4 17.5 - - - +
433A GLY 3.2 0.2 - - - -
434A TYR* 1.3 77.2 - - - +
436A VAL* 1.3 62.1 + - - +
438A ALA* 4.0 0.9 - - - +
439A ALA* 3.1 25.6 + - - +
446A VAL* 4.1 11.1 - - - +
448A ALA* 3.6 31.0 - - - -
465A ILE* 4.2 6.7 - - + -
472A VAL* 3.7 33.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 4.5 4.3 - - + -
51A TYR* 4.3 22.0 - - + -
53A PHE* 3.6 34.3 - - + -
432A MET* 3.2 14.2 + - + +
433A GLY 3.2 6.2 + - - +
435A CYS* 1.3 78.4 - - - +
437A ALA* 1.3 57.3 + - - +
439A ALA* 3.7 2.1 - - - +
440A ALA* 2.8 30.0 + - - +
461A GLU* 5.3 1.1 - - + +
464A THR* 4.3 13.7 - - + -
465A ILE* 4.0 21.8 - - + -
470A LEU* 3.9 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 3.8 19.1 - - - +
62A ALA* 3.1 37.2 - - + +
65A ILE* 3.4 17.0 - - + -
66A ALA* 4.3 4.7 - - + -
69A ILE* 5.0 0.2 - - - -
433A GLY 3.2 3.4 + - - +
436A VAL* 1.3 76.5 - - - +
438A ALA* 1.3 61.6 + - - +
440A ALA* 3.1 1.1 + - - -
441A VAL* 2.8 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 4.1 13.8 - - + +
395A SER* 4.0 11.0 - - - +
420A LEU* 3.9 23.1 - - + -
434A TYR 2.8 24.0 + - - +
435A CYS 4.5 0.2 - - - -
437A ALA* 1.3 71.5 - - - +
439A ALA* 1.3 56.9 + - - +
442A THR* 2.6 39.0 + - - +
446A VAL* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A CYS 3.1 19.5 + - - +
436A VAL 3.7 2.9 - - - +
438A ALA* 1.3 75.3 - - - +
440A ALA* 1.3 58.7 + - - +
442A THR* 4.0 2.9 - - - -
443A GLY* 2.8 31.0 + - - -
444A LYS 4.0 7.6 - - - +
446A VAL* 3.7 14.1 - - + +
470A LEU* 4.2 29.8 - - + -
471A PRO* 4.5 7.8 - - + +
472A VAL* 4.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 4.0 11.7 - - + +
49A ARG* 2.7 29.8 + - - +
51A TYR* 3.6 39.3 - - + +
436A VAL 2.8 19.3 + - - +
437A ALA* 3.5 4.3 - - - +
439A ALA* 1.3 79.3 - - - +
441A VAL* 1.3 57.3 + - - +
443A GLY* 4.3 3.1 + - - -
470A LEU* 5.2 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 6.2 0.7 - - + -
29A TYR* 3.6 19.5 - - - +
49A ARG* 4.2 7.0 - - - +
66A ALA* 4.0 13.0 - - + -
69A ILE* 3.9 37.0 - - + -
70A GLU* 3.6 35.2 - - + +
437A ALA 2.8 25.7 + - - +
440A ALA* 1.3 73.5 - - - +
442A THR* 1.3 67.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE* 4.6 13.2 - - + -
395A SER* 4.1 17.9 + - - +
418A LYS* 5.2 8.7 - - - +
438A ALA* 2.6 25.4 + - - +
441A VAL* 1.3 90.0 - - + +
443A GLY* 1.3 67.5 + - - +
444A LYS* 3.1 43.6 + - - +
445A PRO 5.2 0.2 + - - -
446A VAL* 5.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ALA 2.8 16.8 + - - -
440A ALA 4.3 3.0 + - - -
441A VAL 3.7 1.2 - - - -
442A THR* 1.3 78.3 - - - +
444A LYS* 1.3 61.3 + - - +
471A PRO* 5.6 3.8 - - - -
----------------------------------------------------------
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