Contacts of the helix formed by residues 432 - 447 (chain B) in PDB entry 4XHS
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 432 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B ILE* 2.8 16.7 + - - -
429B THR 4.3 1.8 + - - -
430B HIS 3.8 0.6 - - - -
431B PHE* 1.3 82.2 - - - +
433B PRO* 1.3 71.4 - - - +
434B GLU* 3.4 5.6 - - - -
435B GLU 4.3 0.4 - - - -
436B ALA* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE* 3.7 24.9 - - + -
336B GLN* 3.5 15.5 - - - +
372B ALA 5.3 1.6 - - - +
376B ALA* 3.7 29.0 - - + +
428B ILE* 3.9 21.6 - - + +
432B GLY* 1.3 80.2 - - - +
434B GLU* 1.3 87.0 + - + +
436B ALA* 3.5 1.6 + - - +
437B TRP* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLN* 3.5 42.3 + - + +
100B TYR* 4.2 2.9 + - - -
335B PRO* 3.6 20.5 - - + +
336B GLN* 2.6 32.7 + - - +
432B GLY* 4.2 4.0 - - - -
433B PRO* 1.3 89.9 - - + +
435B GLU* 1.3 65.6 + - - +
437B TRP* 3.4 5.4 + - - +
438B ARG* 3.1 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLN* 3.5 20.6 - - - +
101B ASN* 4.1 22.3 + - - +
431B PHE* 3.6 31.2 - - + +
432B GLY 3.7 2.0 + - - -
433B PRO 3.4 0.2 - - - -
434B GLU* 1.3 77.2 + - + +
436B ALA* 1.3 60.6 + - - +
438B ARG* 3.9 20.6 + - - +
439B LEU* 2.8 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B LEU* 4.2 6.7 - - + +
427B LEU* 3.6 37.0 - - + +
428B ILE* 3.8 12.8 - - + +
431B PHE* 3.9 8.4 - - - +
432B GLY 3.0 21.2 + - - +
433B PRO 3.7 4.0 - - - +
435B GLU* 1.3 77.2 - - - +
437B TRP* 1.3 57.8 + - - +
439B LEU* 3.7 4.9 - - - +
440B ALA* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ALA* 5.8 1.1 - - + -
379B ARG* 3.4 63.5 - - + +
380B LEU* 4.1 28.2 - - + +
383B TYR* 3.8 33.7 - + + -
433B PRO 3.1 15.0 + - - +
434B GLU* 3.6 4.9 - - - +
436B ALA* 1.3 78.0 - - - +
438B ARG* 1.3 73.1 + - + +
440B ALA* 3.2 5.1 + - + +
441B LEU* 3.0 62.2 + - + +
444B PHE* 5.3 0.4 - + - -
456B GLY* 3.5 24.7 + - - -
459B GLU* 4.1 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLN* 2.9 49.8 + - - +
74B SER* 5.1 0.2 - - - +
434B GLU* 3.1 19.3 + - - +
435B GLU* 3.3 21.0 + - - +
437B TRP* 1.3 85.0 - - + +
439B LEU* 1.3 58.5 + - - +
441B LEU* 3.4 7.7 + - + +
442B SER* 3.0 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 439 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B LEU* 4.1 23.8 - - + -
427B LEU* 4.9 4.5 - - + -
431B PHE* 3.6 45.3 - - + -
435B GLU* 2.8 17.9 + - - +
436B ALA 3.7 3.4 - - - +
438B ARG* 1.3 74.9 - - - +
440B ALA* 1.3 64.3 + - - +
442B SER* 3.4 9.9 + - - +
443B THR* 2.8 35.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
380B LEU* 3.5 28.5 - - + -
395B PHE* 4.0 22.2 - - + -
427B LEU* 5.1 1.5 - - + +
436B ALA 2.9 18.3 + - - +
437B TRP* 3.4 7.0 - - + +
439B LEU* 1.3 75.6 - - - +
441B LEU* 1.3 57.8 + - - +
443B THR* 3.1 4.3 + - - -
444B PHE* 2.9 43.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B TYR* 4.8 0.2 - - + -
437B TRP* 3.0 69.2 + - + +
438B ARG* 3.8 6.5 - - - +
440B ALA* 1.3 76.6 - - - +
442B SER* 1.3 63.1 + - - +
444B PHE* 3.2 34.8 + - + +
445B GLU 3.3 4.9 + - - -
452B LEU 4.0 4.5 - - - +
453B TRP* 3.2 28.3 - - + +
456B GLY* 3.8 24.9 - - - -
457B GLN* 4.0 22.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B ARG 3.0 18.8 + - - -
439B LEU* 3.5 12.5 - - - +
441B LEU* 1.3 77.3 - - - +
443B THR* 1.3 61.5 + - - +
445B GLU* 3.4 11.8 + - - +
446B ARG* 3.4 28.9 + - - +
453B TRP* 4.2 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 3.5 46.7 - - + +
398B TYR* 4.2 17.5 - - + -
399B LEU* 3.6 17.6 - - + +
439B LEU* 2.8 21.4 + - - +
440B ALA 3.6 4.0 - - - -
442B SER* 1.3 75.4 + - - +
444B PHE* 1.3 65.7 + - - +
446B ARG* 2.9 19.5 + - + +
447B ILE* 3.0 17.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B LEU* 5.1 0.7 - - + -
383B TYR* 3.9 35.4 - + + -
384B LEU* 3.9 18.8 - - + -
387B LEU* 4.0 18.6 - - + -
395B PHE* 3.7 26.7 - + - -
437B TRP* 5.3 0.4 - + - -
440B ALA* 2.9 26.8 + - + -
441B LEU* 3.3 34.3 - - + +
443B THR* 1.3 75.5 - - - +
445B GLU* 1.3 58.7 + - - +
446B ARG 3.3 0.7 + - - -
447B ILE* 3.3 10.4 + - + +
449B ARG* 2.8 46.9 + - + +
452B LEU* 3.6 24.0 - - + -
453B TRP 4.1 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 445 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B LEU 3.3 7.2 + - - +
442B SER* 3.4 13.8 - - - +
444B PHE* 1.3 79.5 - - - +
446B ARG* 1.3 61.7 + - - +
447B ILE 3.5 0.5 + - - -
448B ASN 3.8 5.2 + - - -
449B ARG 4.2 0.2 + - - -
450B LYS* 3.7 48.6 + - + +
453B TRP* 3.5 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 446 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B TYR* 3.3 48.2 + - + -
442B SER* 3.4 19.7 + - - +
443B THR* 2.9 17.1 + - - +
445B GLU* 1.3 80.9 - - - +
447B ILE* 1.3 56.7 + - - +
448B ASN 3.4 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 447 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B LEU* 4.2 22.2 - - + -
391B GLU* 3.6 32.8 - - + +
394B LYS* 4.1 47.0 - - + +
395B PHE* 4.0 17.9 - - + +
398B TYR* 4.2 13.9 - - + -
443B THR* 3.0 23.3 + - + +
444B PHE* 3.3 12.1 + - - +
446B ARG* 1.3 80.1 - - - +
448B ASN* 1.3 66.7 + - - +
449B ARG* 4.2 7.2 - - + +
----------------------------------------------------------
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