Contacts of the helix formed by residues 529 - 539 (chain D) in PDB entry 7KHC
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 529 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527D LEU* 3.2 8.1 + - - +
528D THR* 1.3 81.4 - - - +
530D PRO* 1.3 76.1 - - - +
531D LYS 3.3 2.7 - - - -
532D GLU* 3.1 20.8 + - - +
533D ALA* 3.3 6.4 + - - +
550D VAL* 5.0 4.9 - - - +
551D ARG 3.9 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 530 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529D GLY* 1.3 81.7 - - - +
531D LYS* 1.3 65.7 + - + +
533D ALA* 2.8 31.1 + - + +
534D GLU* 3.0 6.4 + - - +
551D ARG 4.4 6.7 - - - +
552D ILE* 4.4 13.5 - - + -
577D ALA* 3.8 27.8 - - + +
578D ILE* 4.0 3.6 - - - +
580D TRP* 4.3 22.0 - - + -
581D MET* 4.2 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 531 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B GLU* 3.0 41.7 + - + +
182B ARG* 4.3 28.5 - - + +
206B GLU* 3.0 32.0 + - - +
529D GLY* 3.3 1.0 - - - -
530D PRO* 1.3 79.1 - - + +
532D GLU* 1.3 58.7 + - - +
534D GLU* 3.1 8.4 + - - +
535D ARG* 2.9 24.4 + - - +
581D MET* 3.9 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 532 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LYS* 4.5 7.0 + - - -
152B TYR* 4.1 19.6 + - + -
176B CYS* 6.1 0.3 - - - -
181B GLU* 4.7 2.1 + - + +
527D LEU* 2.7 22.9 - - + +
528D THR* 2.0 54.2 + - + +
529D GLY* 3.1 21.3 - - - +
531D LYS* 1.3 75.9 - - - +
533D ALA* 1.3 60.5 + - - +
535D ARG* 3.0 19.5 + - + +
536D LEU* 2.8 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 533 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527D LEU* 3.6 15.2 - - + +
529D GLY 3.3 7.8 + - - +
530D PRO* 2.8 29.0 + - + +
532D GLU* 1.3 72.6 - - - +
534D GLU* 1.3 58.9 + - - +
536D LEU* 3.0 5.4 + - - +
537D TYR* 3.0 21.7 + - - +
550D VAL* 5.5 2.9 - - + -
574D VAL* 4.4 16.4 - - + +
577D ALA* 4.1 14.4 - - + -
578D ILE* 3.4 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 534 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ARG* 2.2 45.9 + - + +
183B ILE 3.7 20.1 + - - +
184B ALA* 4.8 2.8 - - - +
530D PRO 3.0 9.0 + - - +
531D LYS* 3.4 9.4 - - - +
533D ALA* 1.3 71.9 - - - +
535D ARG* 1.3 67.5 + - - +
537D TYR* 4.5 2.7 - - + +
538D ARG* 2.9 42.3 + - + +
578D ILE* 3.0 24.6 - - + +
581D MET* 3.7 4.8 - - + +
631D TYR* 5.2 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 535 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.3 39.7 + - + +
152B TYR* 3.3 29.6 - - + +
176B CYS* 3.0 37.0 - - - +
178B SER* 4.1 15.5 + - - -
180B VAL 2.7 29.5 + - - -
181B GLU* 3.1 35.5 - - - +
531D LYS 2.9 11.5 + - - +
532D GLU* 3.0 23.2 - - + +
534D GLU* 1.3 76.7 - - - +
536D LEU* 1.3 53.0 + - + +
538D ARG* 4.5 0.3 - - - +
539D SER* 2.7 38.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 536 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TYR* 4.2 27.6 - - + +
154B PRO* 5.5 1.1 - - + -
525D MET* 4.3 20.4 - - + -
527D LEU* 3.4 23.8 - - + -
532D GLU* 2.8 30.8 + - + +
533D ALA* 3.0 8.7 + - - +
535D ARG* 1.3 79.1 - - + +
537D TYR* 1.3 65.6 + - - +
539D SER* 2.8 16.7 + - - -
541D LEU* 3.1 54.6 + - + +
542D ALA* 3.9 14.7 + - + -
574D VAL* 5.6 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 537 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1219C GLU* 5.7 0.2 - - - +
1222C GLU* 5.1 9.2 + - - -
533D ALA 3.0 14.6 + - - +
534D GLU* 4.2 4.5 - - + +
536D LEU* 1.3 77.9 - - - +
538D ARG* 1.3 73.5 + - + +
540D GLY* 3.0 14.7 + - - -
542D ALA* 4.0 12.9 - - + +
543D SER* 5.4 1.8 - - - +
544D LEU* 3.5 59.5 - - + +
574D VAL* 5.6 6.3 - - + +
578D ILE* 5.2 8.3 - - + -
631D TYR* 3.8 13.6 - + - -
634D ARG* 2.7 61.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 538 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG* 3.2 52.9 + - - +
48B LEU* 4.0 21.1 - - + +
185B TYR* 4.9 3.4 + - - -
1217C THR* 4.3 9.5 - - - +
1219C GLU* 2.7 43.6 + - - +
534D GLU* 2.9 39.5 + - + +
537D TYR* 1.3 85.5 - - + +
539D SER* 1.3 59.3 + - - +
540D GLY 3.3 0.6 + - - -
631D TYR* 5.2 5.8 - - - -
634D ARG* 2.8 35.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 539 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.5 12.3 - - - +
49B SER* 5.7 10.8 - - - -
152B TYR* 6.3 1.1 - - - -
535D ARG 2.7 23.6 + - - -
536D LEU* 2.8 14.6 + - - -
538D ARG* 1.3 75.5 - - - +
540D GLY* 1.3 60.2 + - - +
541D LEU* 3.3 30.4 + - - +
----------------------------------------------------------
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