Contacts of the helix formed by residues 425 - 442 (chain A) in PDB entry 4XZC
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 ASN 425 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TYR* 3.6 16.8 + - - -
157A LYS 3.2 22.1 + - - +
158A VAL* 4.0 0.6 - - - +
159A PRO* 4.0 14.7 - - + +
418A LYS 3.2 2.3 - - - +
419A ILE* 3.1 46.1 - - - +
420A ASP 3.0 8.5 + - - -
421A THR* 4.2 3.2 - - - +
424A GLY* 1.3 76.8 - - - +
426A PRO* 1.3 68.6 - - - +
428A ALA* 3.1 35.2 + - - +
429A LYS* 3.1 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.7 31.4 - - + +
40A LEU* 3.8 25.4 - - + -
417A TYR* 4.3 7.0 - - + -
418A LYS* 3.1 22.0 - - + +
420A ASP 4.4 0.2 - - - +
423A ALA* 3.8 22.2 - - + +
424A GLY 3.3 4.9 - - - -
425A ASN* 1.3 86.1 - - - +
427A CYS* 1.3 64.3 + - - +
429A LYS* 3.1 13.6 + - + +
430A GLU* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A LEU* 3.7 24.8 - - - +
415A LEU* 4.6 7.2 - - - -
417A TYR* 3.5 33.5 - - + +
418A LYS 3.3 6.0 + - - +
419A ILE* 3.8 6.1 - - + -
425A ASN* 3.2 6.0 - - - +
426A PRO* 1.3 82.9 - - - +
428A ALA* 1.3 56.1 + - - +
430A GLU* 3.5 2.4 + - - +
431A ILE* 3.1 49.0 + - - +
459A SER* 4.0 18.2 - - - -
463A LYS 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TYR* 4.2 8.5 - - + +
158A VAL* 4.2 20.9 - - + -
159A PRO* 5.4 0.7 - - + -
162A TYR* 5.4 1.8 - - + -
166A VAL* 5.1 4.7 - - + +
425A ASN* 3.1 33.4 + - + +
427A CYS* 1.3 77.3 - - - +
429A LYS* 1.3 66.7 + - - +
431A ILE* 3.4 11.2 + - + +
432A VAL* 3.0 28.9 + - - +
456A LEU* 5.5 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.5 30.8 - - + +
159A PRO* 4.4 8.7 - - + -
161A GLU* 5.1 3.8 + - - -
162A TYR* 3.4 49.3 - - + +
423A ALA 4.7 6.2 + - - +
424A GLY* 3.0 26.0 + - - +
425A ASN 3.1 11.9 + - - +
426A PRO* 3.1 9.4 + - + +
428A ALA* 1.3 76.3 - - - +
430A GLU* 1.3 63.2 + - - +
432A VAL* 3.2 4.5 + - - +
433A GLN* 3.0 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 3.2 21.4 - - + +
41A PRO* 2.7 33.0 - - - +
43A LEU* 3.1 29.5 - - - +
70A ALA* 3.4 9.7 - - - +
414A LEU* 3.8 18.8 - - + -
417A TYR* 3.4 26.2 - - + -
426A PRO 2.9 16.5 + - - +
427A CYS 3.9 2.0 - - - +
429A LYS* 1.3 73.5 - - - +
431A ILE* 1.3 66.0 + - - +
433A GLN* 3.3 11.6 + - - +
434A LEU* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TYR* 5.2 0.2 - - - +
169A MET* 3.6 17.0 - - + -
414A LEU* 3.5 19.7 - - + -
427A CYS* 3.1 39.4 + - - +
428A ALA* 3.8 9.2 - - - +
429A LYS 3.3 0.2 - - - -
430A GLU* 1.3 77.0 - - - +
432A VAL* 1.3 56.6 + - + +
434A LEU* 3.3 9.7 + - - +
435A PHE* 2.8 26.5 + - - +
452A SER* 3.3 29.4 - - - +
455A LEU* 4.4 6.3 - - + -
456A LEU* 3.8 33.9 - - + +
459A SER* 4.5 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A TYR* 3.5 30.1 - - + -
165A GLU* 3.9 23.6 - - + +
166A VAL* 3.8 28.5 - - + +
169A MET* 4.6 7.6 - - - -
428A ALA 3.0 17.8 + - - +
429A LYS 3.6 6.7 - - - +
431A ILE* 1.3 74.8 - - + +
433A GLN* 1.3 56.1 + - - +
435A PHE* 2.9 9.6 + - + +
436A ARG* 2.7 55.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.9 4.6 - - - +
41A PRO 3.7 6.5 + - - -
42A ASP* 3.8 8.6 - - - +
43A LEU* 2.8 44.3 + - + +
44A SER* 4.0 2.3 + - - -
47A GLU* 5.0 1.0 - - - +
162A TYR* 4.1 16.2 + - + +
429A LYS* 3.0 26.2 + - - +
430A GLU* 3.5 25.0 + - - +
432A VAL* 1.3 76.2 - - - +
434A LEU* 1.3 63.4 + - - +
436A ARG* 3.3 28.2 + - - +
437A ILE* 3.1 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.8 20.6 - - + +
63A TYR* 4.0 16.8 - - + +
66A ALA* 4.2 8.5 - - + +
67A MET* 3.8 47.8 - - + -
70A ALA* 4.6 2.9 - - + -
414A LEU* 3.7 26.5 - - + -
430A GLU 3.0 20.6 + - - +
431A ILE* 3.6 6.7 - - - +
433A GLN* 1.3 74.9 - - - +
435A PHE* 1.3 64.3 + - - +
437A ILE* 3.2 8.7 + - + +
438A GLN* 3.0 24.9 + - - +
452A SER* 4.5 8.3 - - - -
455A LEU* 4.6 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLU* 4.8 9.0 - - + -
168A GLU* 4.2 17.7 - - + -
169A MET* 3.5 41.5 - - + -
172A ASP* 5.9 1.6 - - + -
431A ILE 2.8 14.3 + - - +
432A VAL* 2.9 13.2 + - - +
434A LEU* 1.3 75.1 - - - +
436A ARG* 1.3 66.3 + - + +
438A GLN* 3.0 6.1 + - - +
439A LYS* 2.9 52.9 + - + +
444A LEU* 4.3 20.9 - - + -
450A VAL* 4.8 2.0 - - + -
452A SER* 3.2 26.1 - - - +
453A GLU* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A SER* 6.1 2.6 - - - -
47A GLU* 3.1 35.1 + - - +
161A GLU* 5.4 2.4 + - - +
162A TYR* 3.3 32.9 + - - -
165A GLU* 3.3 33.4 + - - +
432A VAL* 2.7 28.1 + - + +
433A GLN* 3.5 26.2 - - - +
435A PHE* 1.3 74.7 - - + +
437A ILE* 1.3 63.0 + - - +
439A LYS* 3.2 16.8 + - - +
440A ALA* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.3 31.0 - - + +
46A PHE* 3.5 25.8 - - + +
47A GLU* 3.8 25.1 - - + +
50A MET* 3.4 39.3 - - + +
62A ILE* 4.7 0.7 - - + -
63A TYR* 4.4 17.5 - - + -
66A ALA* 3.6 16.8 - - + -
433A GLN 3.1 17.7 + - - +
434A LEU* 3.2 10.3 + - + +
436A ARG* 1.3 74.9 - - - +
438A GLN* 1.3 61.0 + - - +
440A ALA* 3.6 3.0 + - - -
441A GLY 3.6 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR* 3.7 34.3 + - + -
434A LEU 3.0 6.3 + - - +
435A PHE* 3.0 9.0 + - + +
437A ILE* 1.3 75.0 - - - +
439A LYS* 1.3 65.9 + - - +
441A GLY 3.4 0.3 + - - -
442A PHE* 3.1 44.0 + - + +
444A LEU* 3.8 12.3 - - + +
447A MET* 4.5 8.9 - - + +
449A ILE 5.1 0.2 + - - -
450A VAL* 3.5 13.3 - - - +
451A ALA* 3.3 30.5 - - - +
452A SER* 2.7 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLU* 4.6 12.5 + - - +
168A GLU* 3.3 32.0 + - - +
435A PHE* 2.9 37.5 + - + +
436A ARG* 3.4 17.2 - - - +
438A GLN* 1.3 75.2 - - - +
440A ALA* 1.3 62.0 + - - +
442A PHE 2.9 23.2 + - - +
444A LEU* 4.2 19.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
47A GLU* 4.3 14.8 - - + +
50A MET* 3.8 18.3 - - + +
51A GLY* 4.4 13.2 - - - +
59A LYS* 4.7 3.8 + - - -
436A ARG 3.1 13.1 + - - +
437A ILE* 3.8 8.7 - - - +
438A GLN 3.3 0.2 - - - -
439A LYS* 1.3 79.3 - - - +
441A GLY* 1.3 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET* 3.4 27.7 - - - +
56A ASP* 4.8 2.3 - - - +
59A LYS* 3.1 33.2 + - - +
437A ILE 3.6 0.8 + - - -
438A GLN 3.4 2.8 + - - -
439A LYS 3.2 0.4 - - - -
440A ALA* 1.3 80.3 - - - +
442A PHE* 1.3 72.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A MET* 4.1 20.4 - - + -
56A ASP* 4.1 21.1 - - + -
59A LYS* 4.0 21.5 - - + -
60A ASP* 3.4 27.1 - - - -
63A TYR* 4.9 8.3 - + + -
438A GLN* 3.1 31.9 + - + +
439A LYS* 2.9 24.4 + - - +
441A GLY* 1.3 86.0 - - - +
443A ASP* 1.3 65.1 + - - +
444A LEU* 3.7 16.2 + - + +
447A MET* 4.6 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