Contacts of the helix formed by residues 434 - 442 (chain B) in PDB entry 3KCZ
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 434 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B GLN 5.7 0.4 + - - -
335B GLU* 5.1 2.6 + - - +
336B ALA* 3.3 27.2 - - - +
339B ASP* 3.4 25.2 + - - +
430B SER* 2.9 26.6 + - - +
431B ARG* 3.0 26.3 + - - +
433B SER* 1.3 101.3 + - - +
435B TRP* 1.3 59.9 + - - +
436B VAL 3.4 2.2 - - - -
437B GLY* 3.2 6.1 + - - -
438B ILE* 3.0 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 435 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 3.9 21.8 - - + -
428B HIS* 4.0 21.1 - + - -
429B GLY 4.5 0.2 - - - -
430B SER* 3.6 30.7 + - - -
431B ARG 3.5 12.4 + - - -
432B MET* 3.6 28.8 + - + +
433B SER 3.5 2.2 - - - -
434B ASN* 1.3 73.5 - - - +
436B VAL* 1.3 67.6 + - - +
438B ILE* 3.9 30.1 - - + -
439B LEU* 2.9 38.3 + - + +
484B LEU* 3.2 53.0 - - + +
486B LEU* 4.1 22.2 - - + -
572B LEU* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 436 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B ILE* 3.5 42.3 + - + +
246B CYS* 4.0 14.1 - - - -
251B MET* 4.8 1.3 - - + -
339B ASP 5.2 0.2 - - - +
342B ILE* 4.6 0.9 - - + -
343B ALA* 3.6 38.4 - - + +
346B LEU* 4.0 26.9 - - + -
347B VAL* 5.4 0.7 - - + -
365B LEU* 3.9 10.3 - - + +
433B SER 4.8 1.9 + - - +
434B ASN 3.4 0.6 - - - -
435B TRP* 1.3 74.8 - - - +
437B GLY* 1.3 52.9 + - - +
440B SER* 2.5 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 437 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ASP* 3.7 20.5 + - - -
342B ILE* 4.0 16.6 - - - -
433B SER 5.3 0.2 + - - -
434B ASN 3.2 8.9 + - - -
436B VAL* 1.3 78.5 - - - +
438B ILE* 1.3 53.5 + - - +
440B SER* 3.6 4.9 - - - -
441B HIS* 2.7 39.7 + - - +
444B ARG* 3.5 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 438 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ASP* 4.4 3.1 - - - +
428B HIS* 4.5 2.0 - - - +
430B SER* 3.7 33.7 - - - +
434B ASN* 3.0 21.7 + - + +
435B TRP* 3.4 30.7 + - + +
437B GLY* 1.3 75.9 - - - +
439B LEU* 1.3 60.3 + - + +
442B GLY* 2.7 31.2 + - - -
443B LEU* 3.5 38.4 - - + +
444B ARG* 3.6 16.6 - - - +
486B LEU* 4.2 2.2 - - + -
569B MET* 3.7 13.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
245B ILE* 3.9 24.0 - - + -
365B LEU* 4.3 13.2 - - + -
367B CYS* 3.7 24.1 - - - +
369B LEU* 4.2 24.2 - - + -
407B VAL* 4.4 13.2 - - + -
409B LYS* 3.2 24.6 + - - +
435B TRP* 2.9 28.6 + - + +
436B VAL 4.2 1.6 - - - +
438B ILE* 1.3 82.1 - - + +
440B SER* 1.3 63.7 + - - +
486B LEU* 5.0 6.3 - - + -
569B MET* 4.1 12.1 - - - +
572B LEU* 4.4 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 440 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LYS* 4.9 5.7 + - - -
342B ILE* 3.7 7.4 - - - +
346B LEU* 3.9 22.2 - - - +
364B ASN 4.5 1.8 - - - -
365B LEU* 3.4 19.9 - - - +
409B LYS* 2.6 21.8 + - - -
436B VAL 2.5 27.1 + - - -
437B GLY* 3.4 3.1 + - - -
439B LEU* 1.3 79.1 - - - +
441B HIS* 1.3 75.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LYS* 3.5 27.5 + - - +
449A GLU* 5.2 6.7 - - - -
342B ILE* 3.7 40.9 - - + +
346B LEU* 6.4 0.2 - - + -
409B LYS* 4.9 3.8 - - - +
437B GLY 2.7 18.8 + - - +
440B SER* 1.3 88.5 + - - +
442B GLY* 1.3 60.7 + - - +
443B LEU 4.8 0.5 - - - +
444B ARG* 3.7 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 442 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B LYS* 4.7 3.2 - - - +
412B GLU* 4.5 7.9 - - - -
438B ILE* 2.7 26.3 + - - +
439B LEU 4.0 2.4 + - - -
440B SER 3.7 1.2 - - - -
441B HIS* 1.3 72.2 - - - +
443B LEU* 1.3 65.0 + - - -
444B ARG* 2.8 29.8 + - - -
569B MET* 4.0 14.1 - - - +
----------------------------------------------------------
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