Contacts of the helix formed by residues 434 - 445 (chain D) in PDB entry 4KPE
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 434 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR* 5.5 7.2 - - - -
432D VAL 3.2 5.4 + - - +
433D GLU* 1.3 75.3 - - - +
435D ASP* 1.3 61.0 + - - -
436D SER 3.5 2.2 - - - -
437D ALA 4.4 0.2 - - - -
438D GLY* 3.0 23.7 + - - -
454D PRO* 4.3 6.0 - - - +
455D LEU 3.0 20.0 + - - -
456D ARG* 4.6 7.2 - - - -
457D GLY 5.1 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 435 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASN* 4.9 0.2 + - - -
118A TYR* 5.8 0.8 + - - -
434D GLY* 1.3 70.0 - - - -
436D SER* 1.3 57.6 + - - +
438D GLY* 3.0 3.2 + - - +
439D GLY* 2.6 35.3 + - - -
454D PRO* 4.0 12.9 - - - +
456D ARG* 2.9 51.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 436 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASN* 3.6 8.4 + - - +
114A ALA* 3.6 24.0 - - - +
115A ALA 4.8 0.2 - - - -
118A TYR* 3.5 50.9 - - - +
434D GLY 3.5 0.4 - - - -
435D ASP* 1.3 76.2 - - - +
437D ALA* 1.3 70.6 + - - +
439D GLY* 2.9 16.3 + - - -
440D SER* 3.0 16.2 + - - -
583D LEU 5.3 4.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 437 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D VAL* 3.7 12.7 - - + +
433D GLU 3.7 17.9 + - - +
434D GLY 3.9 1.8 + - - -
436D SER* 1.3 79.8 + - - +
438D GLY* 1.3 61.4 + - - +
440D SER* 3.7 9.4 - - - -
441D ALA* 2.8 30.1 + - - +
504D MET* 4.8 5.8 - - + +
506D ASP* 5.1 4.5 - - - +
583D LEU* 4.4 25.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 438 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D VAL* 3.6 16.2 - - - +
434D GLY 3.0 15.1 + - - -
435D ASP 3.0 8.5 + - - -
437D ALA* 1.3 76.8 - - - +
439D GLY* 1.3 56.1 + - - +
441D ALA* 3.7 3.7 - - - +
442D LYS* 3.0 25.1 + - - +
452D ILE* 3.9 7.0 - - - +
454D PRO* 4.3 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 439 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASN* 3.7 16.2 - - - -
111A ASP* 6.4 1.8 - - - -
435D ASP 2.6 16.2 + - - -
436D SER 3.4 4.7 - - - -
438D GLY* 1.3 73.0 - - - +
440D SER* 1.3 63.8 + - - +
442D LYS* 3.2 8.3 + - - +
443D GLN* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 440 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLY* 5.3 0.5 - - - -
104A ASN* 3.2 31.2 + - - +
436D SER 3.0 8.2 + - - -
437D ALA* 3.7 11.4 - - - -
439D GLY* 1.3 75.0 - - - +
441D ALA* 1.3 57.6 + - - +
443D GLN* 3.4 8.7 + - - +
444D GLY* 2.8 27.4 + - - -
583D LEU 5.8 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 441 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430D TYR* 5.6 0.9 - - + -
432D VAL* 4.3 1.6 - - + -
437D ALA 2.8 22.3 + - - +
438D GLY* 3.7 6.1 - - - +
440D SER* 1.3 70.3 - - - +
442D LYS* 1.3 66.5 + - - +
444D GLY* 4.3 1.3 - - - +
445D ARG* 3.0 28.6 + - - +
452D ILE* 3.8 26.7 - - + -
504D MET* 4.2 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 442 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASP* 4.8 13.5 - - - +
417D THR* 4.1 22.4 - - + +
438D GLY 3.0 15.9 + - - +
439D GLY* 3.2 11.4 + - - +
441D ALA* 1.3 77.0 - - - +
443D GLN* 1.3 63.4 + - + +
445D ARG* 3.2 46.5 + - - +
452D ILE* 4.0 5.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 443 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASN* 3.3 29.8 + - - +
105A ASN* 5.1 0.8 + - - +
106A GLY 3.4 21.6 + - - +
107A SER* 4.2 13.5 - - - -
111A ASP* 3.8 22.5 - - - +
292A ASP 5.3 1.2 - - - -
293A ARG* 4.1 19.0 + - - +
439D GLY* 3.0 20.4 + - - +
440D SER* 3.6 10.7 - - - +
442D LYS* 1.3 79.2 - - + +
444D GLY* 1.3 60.6 + - - +
445D ARG 3.5 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 444 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A ARG* 2.9 25.5 + - - -
440D SER 2.8 20.1 + - - -
441D ALA* 3.8 1.8 - - - -
443D GLN* 1.3 71.3 - - - +
445D ARG* 1.3 67.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 445 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASP* 5.6 2.6 - - - +
293A ARG* 3.1 15.8 + - - -
417D THR* 3.5 22.5 - - - +
418D PRO 3.1 25.5 + - - -
420D GLN* 5.0 0.8 - - - +
441D ALA 3.0 14.5 + - - +
442D LYS* 3.2 36.3 + - - +
443D GLN 3.4 3.1 - - - +
444D GLY* 1.3 82.4 - - - +
446D ASP* 1.3 63.1 + - - +
447D ARG* 3.8 53.4 + - + +
450D GLN* 3.0 39.2 + - + +
452D ILE* 3.9 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