Contacts of the helix formed by residues 430 - 443 (chain B) in PDB entry 2JI8
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TYR* 3.8 26.9 - - + +
93B HIS* 3.9 9.0 - - + -
397B VAL* 4.2 7.2 - - + -
398B ASN 4.3 7.2 - - - +
399B GLU* 3.5 25.8 - - + +
420B LEU 4.6 0.2 - - - +
421B ASP 4.0 9.9 - - - +
422B SER* 4.1 2.7 - - - +
427B VAL* 3.7 30.7 - - + +
429B GLY* 1.3 77.2 - - - +
431B GLY* 1.3 71.8 + - - +
432B MET 3.7 0.4 - - - -
433B GLY* 4.2 1.7 - - - -
434B TYR* 3.0 68.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B VAL* 3.5 5.9 - - - +
399B GLU* 2.9 23.3 + - - -
429B GLY 3.3 2.6 - - - -
430B ILE* 1.3 85.2 - - - +
432B MET* 1.3 63.3 + - - +
435B CYS* 3.1 29.5 + - - -
450B GLU* 3.5 15.0 - - - -
458B SER* 3.9 2.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B GLY* 1.3 76.1 - - - +
433B GLY* 1.3 60.2 + - - +
435B CYS* 3.2 10.2 + - - +
436B VAL* 3.0 34.0 + - - +
448B ALA* 4.4 0.2 - - + -
450B GLU* 3.6 37.9 - - + +
455B PHE* 4.0 14.6 - - + -
458B SER* 3.2 32.7 + - - +
461B GLU* 3.4 24.7 - - + -
462B LEU* 3.9 21.5 - - - +
465B ILE* 3.8 23.5 - - + +
474B VAL* 3.9 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE* 4.0 10.3 - - - -
58B HIS* 3.6 33.4 + - - +
61B TYR* 4.9 2.2 - - - -
62B ALA* 3.3 18.3 - - - +
430B ILE 3.9 3.3 + - - -
431B GLY 3.4 0.4 - - - -
432B MET* 1.3 74.0 - - - +
434B TYR* 1.3 63.8 + - - +
436B VAL* 3.3 1.7 + - - +
437B ALA 3.1 19.2 + - - -
458B SER* 4.9 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B TYR* 3.3 29.8 - - + -
64B SER* 3.8 4.3 - - - -
65B ILE* 3.5 41.8 - - + +
93B HIS* 2.9 28.8 + - - -
99B PHE* 3.9 6.4 - - - -
249B MET* 5.8 0.2 - - - -
397B VAL* 3.9 13.9 - - + -
420B LEU* 3.8 20.4 - - + -
421B ASP 3.4 26.2 + - - -
430B ILE* 3.0 49.9 + - + +
431B GLY 3.5 3.8 - - - +
433B GLY* 1.3 74.6 - - - +
435B CYS* 1.3 56.6 + - - +
437B ALA* 4.1 0.2 - - - +
438B ALA* 2.9 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B VAL* 4.0 9.6 - - - -
431B GLY 3.1 24.6 + - - -
432B MET* 3.4 17.5 - - - +
433B GLY 3.1 0.4 - - - -
434B TYR* 1.3 76.4 - - - +
436B VAL* 1.3 56.4 + - - +
438B ALA* 4.0 1.0 - - - +
439B ALA* 3.0 31.4 + - - +
446B VAL* 4.0 10.1 - - - +
448B ALA* 3.7 25.8 - - - -
465B ILE* 4.1 7.0 - - + -
472B VAL* 3.6 35.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR* 4.6 2.7 - - + -
51B TYR* 4.2 23.6 - - + -
53B PHE* 3.6 34.1 - - + -
432B MET* 3.0 15.7 + - + +
433B GLY 3.3 5.8 + - - +
435B CYS* 1.3 76.8 - - - +
437B ALA* 1.3 57.1 + - - +
439B ALA* 3.7 1.6 - - - +
440B ALA* 2.9 27.7 + - - +
461B GLU* 5.2 1.1 - - + +
464B THR* 4.4 14.8 - - + -
465B ILE* 3.8 21.3 - - + +
470B LEU* 3.9 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR* 3.8 19.1 - - - +
62B ALA* 3.1 33.2 - - + +
65B ILE* 3.6 15.9 - - + -
66B ALA* 4.3 4.0 - - + -
433B GLY 3.1 11.2 + - - +
436B VAL* 1.3 75.0 - - - +
438B ALA* 1.3 61.4 + - - +
440B ALA 3.1 0.3 + - - -
441B VAL* 2.9 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 4.6 1.2 - - - +
69B ILE* 4.1 13.2 - - + -
395B SER* 3.8 14.8 - - - +
420B LEU* 3.8 22.7 - - + -
434B TYR 2.9 20.4 + - - +
435B CYS 4.0 0.4 - - - +
437B ALA* 1.3 76.6 - - - +
439B ALA* 1.3 55.9 + - - +
441B VAL* 4.2 0.2 - - - -
442B THR* 2.6 39.2 + - - +
446B VAL* 3.9 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B CYS 3.0 19.6 + - - +
436B VAL 3.7 4.0 - - - +
438B ALA* 1.3 77.9 - - - +
440B ALA* 1.3 57.3 + - - +
443B GLY* 3.0 30.7 + - - -
444B LYS 4.2 6.0 + - - +
446B VAL* 3.7 14.7 - - + +
470B LEU* 4.1 26.0 - - + -
471B PRO* 4.5 9.0 - - + +
472B VAL* 4.1 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TYR* 4.1 10.8 - - - +
49B ARG* 3.0 25.5 + - - +
51B TYR* 3.2 42.6 - - + +
436B VAL 2.9 19.1 + - - +
437B ALA* 3.7 3.8 - - - +
439B ALA* 1.3 77.3 - - - +
441B VAL* 1.3 60.6 + - - +
443B GLY* 4.1 4.2 + - - -
470B LEU* 5.0 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B THR* 6.0 0.9 - - + -
29B TYR* 3.5 19.1 - - - +
49B ARG* 4.5 8.7 - - - +
66B ALA* 4.1 10.3 - - + -
69B ILE* 4.0 38.4 - - + -
70B GLU* 3.9 35.8 - - + +
437B ALA 2.9 25.7 + - - +
438B ALA 3.9 4.7 - - - +
440B ALA* 1.3 72.9 - - - +
442B THR* 1.3 64.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ILE* 4.6 13.5 - - + -
395B SER* 4.2 15.3 + - - +
418B LYS* 5.0 11.0 - - + +
438B ALA* 2.6 25.1 + - - +
441B VAL* 1.3 86.9 - - + +
443B GLY* 1.3 63.4 + - - +
444B LYS* 3.1 42.7 + - - +
445B PRO 5.0 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B ALA 3.0 17.5 + - - -
440B ALA 4.1 4.1 + - - -
441B VAL 3.6 1.4 - - - -
442B THR* 1.3 77.2 - - - +
444B LYS* 1.3 61.0 + - - +
471B PRO* 5.4 4.1 - - - +
----------------------------------------------------------
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