Contacts of the helix formed by residues 428 - 446 (chain A) in PDB entry 3J8B
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 428 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LEU 3.5 8.0 + - - +
425A GLN* 3.7 14.1 + - - +
426A GLN 3.6 1.6 - - - -
427A TYR* 1.3 77.2 - - - +
429A PRO* 1.3 57.8 - - - +
431A LEU* 3.7 4.2 - - - +
432A GLN* 2.9 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A GLN 5.4 0.8 - - - +
427A TYR 3.2 0.6 - - - -
428A VAL* 1.3 80.3 - - - +
430A GLN* 1.3 64.5 + - - +
432A GLN* 3.2 5.3 + - + +
433A ASN* 2.9 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A SER* 3.2 31.1 - - - +
427A TYR* 3.5 7.9 + - - +
429A PRO* 1.3 77.9 - - - +
431A LEU* 1.3 63.1 + - - +
433A ASN* 3.2 10.1 + - - +
434A ASN* 2.9 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU 5.7 0.4 - - - -
328A SER* 4.2 17.1 - - - +
427A TYR* 3.0 21.0 + - + +
428A VAL* 3.7 4.7 - - - +
430A GLN* 1.3 78.1 - - - +
432A GLN* 1.3 63.1 + - - +
434A ASN* 3.0 6.5 + - - +
435A THR* 3.0 24.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A VAL 2.9 19.2 + - - +
429A PRO* 3.4 6.1 - - + +
431A LEU* 1.3 75.0 - - - +
433A ASN* 1.3 57.0 + - - +
435A THR* 3.4 6.4 + - - -
436A ILE* 2.9 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A PRO 2.9 12.3 + - - +
430A GLN* 3.2 13.2 + - - +
432A GLN* 1.3 76.6 - - - +
434A ASN* 1.3 56.3 + - - +
436A ILE* 3.9 4.6 - - - +
437A LEU* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU 4.2 18.6 - - - +
328A SER 5.2 0.9 - - - +
329A ILE 4.7 10.3 - - - +
330A PRO* 5.9 2.2 - - + -
331A ILE* 5.9 2.5 - - + +
430A GLN 2.9 12.8 + - - +
431A LEU* 3.5 9.0 - - - +
433A ASN* 1.3 75.9 - - - +
435A THR* 1.3 62.9 + - - +
437A LEU* 3.2 7.8 + - - +
438A ARG* 3.0 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LEU* 6.1 6.5 - - - -
431A LEU 3.0 15.2 + - - -
432A GLN* 3.8 6.5 - - - -
434A ASN* 1.3 76.4 - - - +
436A ILE* 1.3 58.0 + - - +
438A ARG* 3.2 9.0 + - - +
439A LEU* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A GLN 2.9 18.7 + - - +
433A ASN* 4.1 3.4 - - - +
435A THR* 1.3 72.9 - - - +
437A LEU* 1.3 62.6 + - - +
439A LEU* 3.2 8.2 + - - +
440A LEU* 2.9 29.8 + - - +
459A VAL* 5.6 5.8 - - + -
460A PRO 5.3 8.5 - - - +
470A ALA* 5.3 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ILE* 5.8 8.5 - - + -
433A ASN 2.9 20.5 + - - +
434A ASN* 3.4 8.1 - - - +
436A ILE* 1.3 75.7 - - - +
438A ARG* 1.3 63.5 + - - +
440A LEU* 3.2 6.8 + - - +
441A GLN* 3.0 24.0 + - - +
474A ALA* 5.5 9.7 - - + +
479A ASP* 5.8 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LEU 5.7 5.2 - - - +
398A PHE* 6.0 6.1 - - + -
434A ASN 3.0 13.5 + - - +
435A THR* 3.5 9.6 - - - +
437A LEU* 1.3 77.1 - - - +
439A LEU* 1.3 56.9 + - - +
441A GLN* 3.3 7.2 + - - +
442A GLN* 2.9 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A PRO* 5.6 11.0 - - + +
435A THR 2.9 13.3 + - - +
436A ILE* 3.2 9.8 + - - +
438A ARG* 1.3 76.0 - - - +
440A LEU* 1.3 57.8 + - - +
442A GLN* 3.4 5.4 + - - +
443A VAL* 2.9 31.8 + - - +
459A VAL* 4.0 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A ILE 2.9 16.1 + - - +
437A LEU* 3.6 6.5 - - - +
439A LEU* 1.3 76.4 - - - +
441A GLN* 1.3 58.3 + - - +
443A VAL* 3.5 6.0 + - - +
444A SER* 2.9 28.3 + - - -
471A ILE* 5.4 11.0 - - + -
474A ALA* 4.7 17.0 - - + -
480A LEU* 4.9 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A LEU 3.0 13.7 + - - +
438A ARG* 3.6 10.1 - - - +
440A LEU* 1.3 77.2 - - - +
442A GLN* 1.3 56.4 + - - +
444A SER* 3.0 11.1 + - - -
445A GLN* 3.0 26.2 + - - +
479A ASP* 4.4 20.6 - - + +
480A LEU* 5.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A PRO* 5.0 15.7 - - + -
438A ARG 2.9 18.8 + - - +
439A LEU* 3.8 5.8 - - - +
441A GLN* 1.3 76.6 - - - +
443A VAL* 1.3 57.2 + - - +
445A GLN* 3.1 10.6 + - - +
446A ILE* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A PRO* 6.0 0.8 - - - +
439A LEU 2.9 18.6 + - - +
440A LEU* 3.8 6.7 - - - +
442A GLN* 1.3 72.5 - - - +
444A SER* 1.3 60.5 + - - +
446A ILE* 4.2 6.5 - - - +
447A TYR* 3.0 37.3 + - + +
455A LEU* 6.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A LEU 2.9 15.0 + - - -
441A GLN* 3.1 16.2 - - - -
443A VAL* 1.3 78.0 - - - +
445A GLN* 1.3 57.4 + - - +
447A TYR 3.4 13.7 - - - +
479A ASP 5.4 0.4 - - - -
480A LEU* 4.4 17.7 - - - -
481A GLN 5.8 0.9 - - - -
493A PHE* 4.1 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A GLN 3.0 11.2 + - - +
442A GLN* 3.1 11.4 + - - +
444A SER* 1.3 78.9 - - - +
446A ILE* 1.3 61.1 + - - +
447A TYR 4.5 1.8 - - - +
313M ILE* 4.3 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A GLN 2.9 14.6 + - - +
443A VAL* 3.1 8.0 + - - +
445A GLN* 1.3 78.6 - - - +
447A TYR* 1.3 60.4 + - + +
306M ASP 5.4 2.6 - - - +
309M GLU* 3.6 25.3 - - - +
310M ALA* 4.1 20.6 + - + -
313M ILE* 4.7 9.3 - - - +
----------------------------------------------------------
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