Contacts of the helix formed by residues 432 - 444 (chain B) in PDB entry 2XT6
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 LEU 432 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B VAL* 3.9 32.3 - - + -
373B LEU* 5.5 1.3 - - + -
405B VAL* 4.5 12.3 - - + -
410B LEU* 4.7 9.9 - - + -
411B THR 5.0 2.0 - - - +
414B ASP* 3.2 32.3 - - + +
415B LEU* 3.2 12.6 + - + +
417B ARG 3.1 9.1 + - - -
419B PHE* 3.9 15.5 - - + -
430B LYS 3.6 1.6 + - - -
431B LYS* 1.4 69.3 - - - +
433B ARG* 1.4 51.6 + - - +
435B ILE* 3.2 13.4 + - + -
436B LEU* 2.8 74.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 433 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LYS* 3.9 0.8 - - - +
137B ILE* 5.6 4.2 - - - +
138B ASP* 3.3 29.5 + - - +
141B VAL* 4.9 22.2 - - - +
415B LEU* 2.9 54.5 + - + +
416B ASP* 2.8 40.3 + - - -
431B LYS* 4.2 6.7 - - + +
432B LEU* 1.4 71.8 - - - +
434B ASP* 1.4 75.9 + - - +
436B LEU* 3.9 3.6 - - - +
437B SER* 2.9 31.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 434 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B LYS* 5.2 10.3 - - + +
431B LYS* 2.9 31.7 + - + +
433B ARG* 1.4 89.1 - - - +
435B ILE* 1.4 66.5 + - - +
437B SER* 3.0 8.5 + - - -
438B VAL* 3.0 32.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B VAL* 4.3 7.6 - - + -
374B ILE* 3.9 27.4 - - + -
419B PHE* 4.2 10.8 - - + -
421B VAL* 3.7 28.7 - - + -
430B LYS* 3.6 36.3 - - + +
431B LYS 2.9 10.9 + - - +
432B LEU* 3.4 22.9 - - + +
434B ASP* 1.4 75.6 - - - +
436B LEU* 1.3 59.1 + - + +
438B VAL* 3.4 5.4 + - - +
439B LEU* 3.1 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B LEU* 3.9 27.6 - - + -
377B TYR* 4.8 9.9 + - + +
405B VAL* 4.1 24.9 - - + -
415B LEU* 4.1 14.4 - - + -
432B LEU* 2.8 48.9 + - + +
433B ARG* 4.0 4.5 - - - +
435B ILE* 1.3 70.0 - - + +
437B SER* 1.3 60.9 + - - +
439B LEU* 3.4 16.8 + - + +
440B ARG* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ASN* 4.6 17.9 - - - -
149B ARG* 6.1 1.8 - - - -
433B ARG 2.9 19.4 + - - -
434B ASP* 3.0 13.3 + - - -
436B LEU* 1.3 72.7 - - - +
438B VAL* 1.4 60.7 + - - +
440B ARG* 3.4 9.2 + - - +
441B ASP* 2.9 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ASP* 3.0 24.4 + - + +
435B ILE* 3.8 5.4 - - - +
437B SER* 1.4 78.0 - - - +
439B LEU* 1.4 59.5 + - + +
441B ASP* 3.3 8.9 + - - +
442B ALA* 3.0 34.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
373B LEU* 4.9 0.9 - - + -
374B ILE* 4.1 32.8 - - + +
377B TYR* 3.8 50.4 - - + -
378B ARG* 4.8 4.3 - - + +
435B ILE* 3.1 38.4 + - + +
436B LEU* 3.6 12.6 - - + +
438B VAL* 1.4 79.1 - - + +
440B ARG* 1.3 56.5 + - - +
442B ALA* 4.7 0.2 - - - -
443B TYR* 2.9 54.4 + - + +
444B CYS 4.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 4.1 30.9 - - - +
350B TYR* 3.4 53.5 - - + +
351B GLU 4.5 8.5 + - - +
377B TYR* 4.6 8.7 + - + +
384B MET* 6.2 1.0 - - - +
436B LEU 3.0 17.9 + - - +
437B SER* 3.7 10.3 - - - +
439B LEU* 1.3 73.5 - - - +
441B ASP* 1.3 62.5 + - - +
444B CYS* 2.9 36.2 + - + +
445B ARG* 3.2 45.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ARG* 2.8 39.0 + - - -
437B SER* 2.9 29.2 + - - +
438B VAL* 3.7 7.4 - - - +
440B ARG* 1.3 74.9 - - - +
442B ALA* 1.3 60.0 - - + +
445B ARG* 3.1 41.6 + - - +
447B VAL* 6.1 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B VAL* 3.0 23.0 + - + +
441B ASP* 1.3 79.3 - - + +
443B TYR* 1.3 88.9 + - + +
447B VAL* 3.6 14.5 - - - +
449B VAL* 3.7 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 443 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B TYR* 3.7 25.6 - - + +
378B ARG* 3.5 43.7 + - + +
381B GLY* 3.2 19.8 - - - +
382B HIS* 3.8 3.6 + - - +
385B ALA* 3.5 9.9 - - - +
439B LEU* 2.9 40.6 + - + +
442B ALA* 1.3 98.4 - - + +
444B CYS* 1.3 66.0 + - - +
447B VAL 3.6 11.0 - - - +
448B GLY* 4.3 0.3 - - - -
449B VAL* 4.1 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 444 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B TYR* 2.5 39.6 + - + -
377B TYR* 3.5 35.2 - - - -
381B GLY* 3.5 22.4 - - - -
384B MET* 4.0 20.6 - - + +
385B ALA* 3.5 8.3 - - - +
386B ASP 3.5 8.0 + - - -
403B LEU* 5.2 0.7 - - - -
439B LEU 4.7 0.4 - - - -
440B ARG* 2.9 18.2 + - + +
443B TYR* 1.3 76.2 - - - +
445B ARG* 1.3 59.8 + - - +
----------------------------------------------------------
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