Contacts of the helix formed by residues 431 - 442 (chain A) in PDB entry 6EJ9
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 431 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ARG* 1.3 80.3 - - - +
432A ASN* 1.3 64.9 + - - +
433A ASP* 3.8 9.5 + - - +
434A GLN* 3.2 36.7 + - - +
435A LEU* 3.1 20.0 + - - +
616A LEU* 3.8 30.1 - - + +
617A TYR* 3.4 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PHE* 5.5 1.0 - - - -
348A ALA 5.3 3.8 - - - +
349A ILE* 4.7 9.9 - - - +
350A TYR 5.6 2.7 - - - +
351A HIS* 3.9 32.7 - - + +
354A HIS* 2.9 31.6 + - - -
431A THR* 1.3 72.6 - - - +
433A ASP* 1.3 72.6 + - - +
435A LEU* 3.2 15.0 + - - +
436A VAL* 2.9 30.2 + - - +
617A TYR* 3.1 15.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A VAL 4.8 0.8 - - - +
351A HIS* 5.8 1.9 + - - -
431A THR* 3.2 9.2 + - - +
432A ASN* 1.3 87.9 + - - +
434A GLN* 1.3 58.5 + - + +
436A VAL* 3.5 5.0 + - - +
437A ALA* 3.1 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A VAL* 2.9 55.5 - - + +
430A ARG* 3.3 40.7 + - - +
431A THR* 3.2 26.8 + - - +
433A ASP* 1.3 74.9 - - + +
435A LEU* 1.3 66.7 + - - +
437A ALA 3.5 0.2 + - - -
438A PHE* 3.1 11.6 + - - +
595A PHE* 3.6 8.0 - - + -
616A LEU* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ILE* 3.7 22.4 - - + -
330A PHE* 4.3 9.9 - - + -
420A ILE* 4.6 1.3 - - + -
430A ARG 5.6 0.9 - - - +
431A THR 3.1 12.9 + - - +
432A ASN* 3.6 16.4 - - - +
434A GLN* 1.3 77.0 - - - +
436A VAL* 1.3 62.7 + - - +
438A PHE* 3.3 2.8 + - - +
439A LEU* 3.0 46.5 + - + +
497A LEU* 4.8 7.0 - - + -
550A LEU* 5.4 0.2 - - + -
595A PHE* 3.7 39.4 - - + -
596A PHE* 4.0 28.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
322A PRO* 4.5 5.2 - - + -
325A PRO* 3.6 31.2 - - + -
326A VAL* 4.0 15.8 - - + +
328A ILE* 4.7 5.4 - - + -
354A HIS* 3.7 21.3 - - + +
432A ASN* 2.9 39.7 + - - +
433A ASP* 3.9 5.2 - - - +
435A LEU* 1.3 75.5 - - - +
437A ALA* 1.3 56.1 + - - +
439A LEU 3.8 0.2 - - - -
440A SER* 2.7 42.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
318A VAL* 3.7 23.3 - - - +
320A TYR* 2.8 59.9 + - + +
322A PRO* 4.5 10.5 - - + +
433A ASP 3.1 18.3 + - - +
434A GLN 3.9 1.8 - - - +
435A LEU 3.3 0.2 - - - -
436A VAL* 1.3 75.9 - - - +
438A PHE* 1.3 61.8 + - - +
441A ARG* 3.3 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A VAL* 4.2 9.2 - - + -
313A TRP* 4.0 19.3 - + - -
317A SER* 5.0 7.6 - - - -
318A VAL* 4.1 9.4 - - + +
434A GLN 3.1 10.3 + - - +
435A LEU 3.7 2.0 - - - +
436A VAL 3.3 0.2 - - - -
437A ALA* 1.3 77.0 - - - +
439A LEU* 1.3 72.2 + - + +
441A ARG* 3.1 13.6 + - - +
442A TYR* 3.3 48.9 + + - -
447A PHE* 3.9 17.0 - + - -
550A LEU* 3.9 22.9 - - + -
593A PRO* 3.8 33.2 - - + -
595A PHE* 3.5 33.9 - + + -
----------------------------------------------------------
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
----------------------------------------------------------
326A VAL* 3.8 14.3 - - + +
328A ILE* 4.0 22.2 - - + -
418A PHE* 3.8 27.1 - - + -
420A ILE* 4.3 2.0 - - + -
435A LEU* 3.0 38.1 + - + +
438A PHE* 1.3 85.9 - - + +
440A SER* 1.3 64.5 + - - +
442A TYR* 3.3 2.5 + - - +
443A ARG* 3.2 28.8 + - - +
447A PHE* 4.1 26.0 - - + -
497A LEU* 4.2 23.6 - - + -
550A LEU* 4.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TYR* 3.6 14.8 - - - -
322A PRO* 4.0 14.0 - - - +
324A ASN 4.3 0.2 - - - -
325A PRO* 3.4 6.8 - - - +
326A VAL* 3.2 31.9 + - - +
436A VAL* 2.7 26.5 + - - +
439A LEU* 1.3 76.5 - - - +
441A ARG* 1.3 59.0 + - - +
443A ARG* 3.7 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A SER* 5.4 6.3 - - - +
320A TYR* 3.5 15.0 + - + +
437A ALA 3.3 9.5 + - - +
438A PHE* 3.1 12.0 + - - +
440A SER* 1.3 80.4 - - - +
442A TYR* 1.3 85.4 + - + +
443A ARG 3.7 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ASN 4.8 3.6 - - - -
311A VAL* 4.0 37.6 - - + -
313A TRP* 5.4 3.3 - + - -
317A SER* 5.2 7.2 + - - -
418A PHE* 3.7 8.0 - - - -
438A PHE* 3.3 56.4 + + - +
439A LEU* 3.3 7.1 + - - +
441A ARG* 1.3 98.7 - - + +
443A ARG* 1.3 62.6 + - - +
444A ASP 3.1 4.6 + - - -
445A MET* 3.1 33.8 + - + +
447A PHE* 4.2 10.5 - - + -
----------------------------------------------------------
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