Contacts of the helix formed by residues 269 - 280 (chain D) in PDB entry 5CYP
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 HIS 269 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D TYR* 2.9 37.9 + + + +
199D PRO* 4.6 0.4 - - + -
212D VAL* 4.1 15.1 + - + +
213D ASN* 3.4 23.9 + - - -
216D PHE* 3.6 39.0 - + + +
264D LEU* 2.5 32.7 + - + +
268D THR* 1.3 95.9 - - + +
270D MET* 1.3 57.1 + - - +
271D GLN 3.5 1.8 - - - -
272D ASN* 3.3 9.1 + - - +
273D ILE* 2.8 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D PHE* 5.1 15.5 - - + +
23D GLU 4.9 1.1 - - - +
24D PHE* 3.9 27.3 - - + -
265D LEU 3.2 19.2 + - - +
266D ILE* 3.2 28.3 - - + +
267D ARG 4.0 6.0 + - - +
268D THR 3.4 3.2 - - - -
269D HIS* 1.3 78.0 - - - +
271D GLN* 1.3 82.3 + - + +
273D ILE* 3.3 3.3 + - - +
274D LYS* 3.1 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 271 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D ARG 5.3 0.6 + - - -
268D THR 5.1 1.0 + - - -
269D HIS 3.5 0.2 - - - -
270D MET* 1.3 99.3 - - + +
272D ASN* 1.3 57.5 + - - +
274D LYS* 3.4 19.1 + - - +
275D ASP* 3.0 66.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198D TYR* 2.8 29.0 + - - +
199D PRO* 5.2 0.2 - - - +
203D PHE 5.7 0.7 - - - +
209D ASP* 4.7 9.6 + - - -
213D ASN* 4.5 13.9 + - - +
268D THR 5.4 2.4 + - - +
269D HIS* 3.3 13.2 + - - +
270D MET 3.2 0.4 - - - -
271D GLN* 1.3 76.7 - - - +
273D ILE* 1.3 63.0 + - - +
275D ASP* 3.5 9.1 + - - +
276D ILE* 3.2 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 273 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D PHE* 3.9 25.1 - - + -
134D HIS* 3.6 29.6 - - + +
135D CYS* 3.9 17.3 - - + -
163D ASN* 3.1 11.5 + - + +
198D TYR* 3.4 39.3 - - + -
265D LEU* 4.3 15.7 - - + -
269D HIS* 2.8 28.2 + - + +
270D MET 3.3 4.9 + - - +
272D ASN* 1.3 76.3 - - - +
274D LYS* 1.3 61.4 + - - +
276D ILE* 3.3 2.1 + - - +
277D THR* 2.8 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 274 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D PHE* 4.8 5.8 - - + +
23D GLU* 2.8 39.3 + - - +
24D PHE* 3.8 14.8 - - + -
130D ASP* 4.3 8.5 + - - +
132D ARG* 6.0 0.4 - - - +
134D HIS* 3.7 23.5 - - + +
270D MET* 3.1 30.9 + - - +
271D GLN* 3.7 23.6 + - - +
272D ASN 3.4 0.2 - - - -
273D ILE* 1.3 77.7 - - - +
275D ASP* 1.3 57.7 + - - +
277D THR* 3.2 9.0 + - - -
278D SER* 3.0 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 275 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D GLN* 3.0 52.0 + - - +
272D ASN* 3.8 11.2 - - - +
273D ILE 3.3 0.2 - - - -
274D LYS* 1.3 76.9 - - - +
276D ILE* 1.3 54.8 + - + +
278D SER* 3.5 4.7 + - - -
279D SER* 2.7 39.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D ASN* 3.6 19.3 - - - +
198D TYR* 3.6 30.7 - - + -
199D PRO* 5.7 0.4 - - + -
200D GLN* 3.9 10.8 - - - +
203D PHE* 3.7 43.1 - - + -
272D ASN* 3.2 24.5 + - - +
273D ILE 3.8 4.0 - - - +
274D LYS 3.3 0.2 - - - -
275D ASP* 1.3 76.1 - - + +
277D THR* 1.3 65.3 + - - +
279D SER* 4.0 5.2 - - - -
280D ILE* 3.1 27.4 + - + +
281D HIS* 3.3 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D TYR* 3.8 19.3 - - + +
132D ARG* 4.8 5.8 - - + +
133D VAL 3.7 21.3 - - - +
134D HIS* 3.0 31.8 + - + +
162D VAL* 5.7 0.2 - - + -
163D ASN* 2.9 13.2 + - - +
273D ILE 2.8 18.5 + - - -
274D LYS 3.4 8.7 - - - -
276D ILE* 1.3 77.8 - - - +
278D SER* 1.3 56.9 + - - +
281D HIS* 3.5 10.7 - - + +
282D PHE* 2.8 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D ARG* 3.1 27.4 + - - +
274D LYS* 3.0 17.1 + - - +
275D ASP* 3.9 4.9 - - - -
276D ILE 3.2 0.2 - - - -
277D THR* 1.3 76.1 - - - +
279D SER* 1.3 65.8 + - - +
280D ILE 3.3 0.2 - - - -
282D PHE* 3.3 29.4 - - - +
283D GLU* 3.3 9.2 + - - +
286D ARG* 5.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D ASP 2.7 23.7 + - - -
276D ILE* 4.0 0.5 - - - -
278D SER* 1.3 78.7 - - - +
280D ILE* 1.3 78.2 + - - +
283D GLU* 3.4 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 280 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D PHE* 3.8 41.1 - - + -
276D ILE* 3.1 22.4 + - + +
278D SER 3.3 0.2 - - - -
279D SER* 1.3 97.1 - - - +
281D HIS* 1.3 77.8 + - + +
282D PHE 3.4 0.7 - - - -
283D GLU* 3.6 1.6 + - - +
284D ALA* 3.1 24.8 + - + +
----------------------------------------------------------
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