Contacts of the helix formed by residues 431 - 445 (chain A) in PDB entry 6NRB
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 GLY 431 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A SER 3.4 0.4 - - - -
430A MET* 1.3 82.9 - - - +
432A SER* 1.3 69.1 + - - -
434A GLU* 3.4 5.7 + - - +
435A GLN* 2.6 49.4 + - - +
462O ASN 3.8 6.1 - - - -
463O LYS* 4.7 1.6 - - - -
466O ALA* 3.9 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A GLY* 1.3 75.9 - - - +
433A ARG* 1.3 61.6 + - - +
434A GLU* 4.3 5.4 + - - +
435A GLN* 3.4 2.9 - - - +
459O ASN* 2.0 54.3 + - - +
462O ASN* 3.0 30.9 - - - +
463O LYS* 3.8 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LYS* 3.2 21.8 + - - +
112A ILE* 3.2 26.9 - - - +
116A SER* 3.7 22.7 - - - -
117A VAL* 3.7 15.7 - - + -
432A SER* 1.3 80.1 + - - +
434A GLU* 1.3 59.8 + - - +
435A GLN 3.2 0.9 - - - -
436A LEU* 2.8 11.9 + - + +
437A ALA* 2.6 31.9 + - - +
471D LEU* 3.0 33.3 - - - +
456O ASP* 3.0 26.3 + - - -
458O THR* 4.0 11.3 + - - +
459O ASN* 2.8 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A SER* 2.8 47.9 - - - +
119A SER* 4.7 2.5 - - - -
120A GLY* 3.2 20.2 - - - -
123A LEU* 6.2 1.8 - - + -
430A MET* 3.4 25.6 - - + -
431A GLY 3.4 3.6 + - - +
432A SER* 3.3 5.1 - - - +
433A ARG* 1.3 81.8 - - - +
435A GLN* 1.3 63.6 + - - +
437A ALA* 3.4 4.8 - - - +
438A ILE* 3.0 31.0 + - - +
471D LEU* 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ALA* 3.0 30.5 - - + +
428A THR* 3.0 35.0 + - - +
430A MET* 4.2 1.1 - - - +
431A GLY* 2.6 38.4 + - - +
432A SER 3.4 3.4 - - - +
434A GLU* 1.3 73.1 - - - +
436A LEU* 1.3 61.8 + - - +
438A ILE 3.4 0.3 + - - -
439A ALA* 3.2 18.1 + - + +
421O ARG* 6.0 0.4 - - - +
462O ASN* 2.8 37.1 - - - +
465O ARG* 2.8 38.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 4.2 22.4 - - + -
110A GLN* 5.7 1.6 - - - +
112A ILE* 4.4 7.9 - - + -
117A VAL* 4.9 4.7 - - + -
432A SER 3.7 0.8 + - - -
433A ARG* 2.8 30.4 + - + +
435A GLN* 1.3 73.8 - - - +
437A ALA* 1.3 63.8 + - - +
439A ALA* 3.3 8.9 + - + -
440A GLU* 3.0 40.7 + - + +
447O ARG* 6.0 1.8 - - - +
458O THR* 3.5 30.7 - - + +
462O ASN* 4.0 14.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
117A VAL* 3.4 38.3 - - - +
120A GLY* 3.6 7.0 - - - -
121A TYR* 3.0 31.1 - - - -
433A ARG 2.6 12.4 + - - +
434A GLU* 3.3 31.8 + - - +
436A LEU* 1.3 74.4 - - - +
438A ILE* 1.3 62.7 + - - +
440A GLU* 4.9 0.4 - - - -
441A PHE 3.2 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLY* 4.3 13.5 - - - +
123A LEU* 5.7 0.4 - - + -
124A ALA* 4.2 9.0 - - + +
423A LEU* 3.2 47.3 - - + +
426A TYR* 3.4 39.9 - - + +
427A ALA* 3.4 12.1 - - - +
430A MET* 3.5 24.9 - - + -
434A GLU 3.0 17.6 + - - +
436A LEU 3.3 0.2 - - - -
437A ALA* 1.3 76.0 - - + +
439A ALA* 1.3 57.7 + - - +
441A PHE* 3.2 3.8 + - - +
442A ALA* 3.0 25.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
424A GLU* 5.0 2.2 - - + +
427A ALA* 3.4 19.2 - - + +
435A GLN* 3.2 7.6 + - + +
436A LEU* 3.3 15.2 + - + +
438A ILE* 1.3 79.9 - - - +
440A GLU* 1.3 58.7 + - + +
442A ALA* 3.1 11.7 + - - -
443A ARG* 2.8 49.7 + - - +
421O ARG* 5.4 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 4.2 0.3 - - - +
103A ASN* 2.9 61.8 + - - +
107A LEU* 3.7 20.4 - - + -
121A TYR* 3.1 26.5 - - + +
436A LEU* 3.0 32.3 + - + +
437A ALA* 4.9 0.2 - - - -
439A ALA* 1.3 77.6 - - - +
441A PHE* 1.3 58.6 + - - +
443A ARG* 3.7 18.7 + - - +
444A SER* 3.9 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 6.3 1.1 - - + -
100A LEU* 3.6 26.2 - - + -
121A TYR* 3.3 32.3 - + + -
124A ALA* 3.5 22.0 - - + -
125A CYS* 3.7 28.0 - - + -
128A ALA* 4.7 4.9 - - + -
423A LEU* 3.3 22.2 - - + -
437A ALA 3.2 5.8 + - - +
438A ILE 3.6 2.9 - - - +
439A ALA 3.2 0.4 - - - -
440A GLU* 1.3 72.9 - - - +
442A ALA* 1.3 61.8 + - - +
443A ARG 3.0 6.2 + - - -
444A SER* 3.7 7.7 + - - -
445A LEU* 3.2 37.2 + - + +
514A LEU* 4.8 11.0 - - + -
517A ALA* 6.1 1.6 - - + -
518A THR* 3.0 29.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A SER* 2.9 55.5 + - - +
423A LEU* 3.8 3.6 - - + +
424A GLU* 3.8 10.1 - - + +
438A ILE 3.0 13.6 + - - +
439A ALA 3.1 10.7 + - - +
441A PHE* 1.3 76.0 - - - +
443A ARG* 1.3 73.8 + - - +
445A LEU* 3.6 15.6 - - - +
446A LEU* 3.9 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A GLU* 4.6 3.5 - - - +
103A ASN* 3.1 22.2 - - - +
420A SER* 4.2 1.4 + - - -
424A GLU* 3.1 36.6 + - - +
439A ALA* 2.8 51.1 + - - +
440A GLU* 3.7 18.6 + - - +
441A PHE 3.0 0.6 - - - -
442A ALA* 1.3 96.2 + - - +
444A SER* 1.3 67.4 + - - +
445A LEU 3.0 2.2 - - - -
446A LEU* 2.9 31.4 + - - +
447A VAL 4.5 0.9 + - - -
468A ARG* 5.1 4.4 - - - +
421O ARG* 5.1 8.1 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
96A ILE* 4.3 12.4 - - - +
99A GLU* 3.0 24.5 + - - -
100A LEU* 3.1 32.2 + - - +
103A ASN* 2.1 35.0 + - - +
440A GLU 3.9 0.8 + - - -
441A PHE* 3.7 5.2 + - - -
443A ARG* 1.3 77.2 - - - +
445A LEU* 1.3 62.5 + - - +
446A LEU 3.1 1.3 + - - -
447A VAL* 3.2 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 6.0 3.6 - - + -
128A ALA* 5.3 3.1 - - + -
416A GLU* 3.1 52.8 - - - +
419A LEU* 3.2 43.3 - - + +
420A SER 3.4 0.9 - - - +
423A LEU* 4.2 9.2 - - + -
441A PHE* 3.2 30.3 - - + +
442A ALA* 3.6 21.3 - - - +
443A ARG 2.9 0.2 + - - -
444A SER* 1.3 77.9 - - - +
446A LEU* 1.3 59.5 + - - +
447A VAL* 3.3 1.3 + - - -
448A ILE* 4.0 5.3 + - - +
449A PRO* 3.7 3.3 - - - +
514A LEU* 4.4 15.0 - - + -
----------------------------------------------------------
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