Contacts of the strand formed by residues 267 - 272 (chain A) in PDB entry 5D3O
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 267 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A TYR* 4.3 1.3 - - - -
266A TRP* 1.3 77.6 - - - +
268A VAL* 1.3 64.5 + - - +
280A THR 3.6 8.3 - - - -
282A ASP 3.8 15.8 + - - -
283A THR* 4.0 4.5 - - - -
429A CYS* 3.5 9.0 - - - -
505A CYS* 3.3 4.3 - - - -
506A TRP 2.9 34.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ILE* 4.2 15.0 - - + -
240A TYR* 4.5 3.1 - - + -
266A TRP* 3.6 30.3 - - + -
267A GLY* 1.3 79.7 - - - +
269A SER* 1.3 68.6 + - - +
270A VAL* 4.7 0.4 - - + -
278A HIS* 4.1 0.6 - - + +
279A SER* 3.2 4.2 - - - -
280A THR* 3.0 42.3 + - + +
283A THR* 3.3 2.3 - - - +
429A CYS* 4.7 0.2 - - - -
503A MET* 3.8 24.7 - - + -
504A MET 3.6 3.4 - - - +
505A CYS* 3.9 13.5 - - - -
522A PHE* 3.9 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A VAL* 1.3 72.2 - - - +
270A VAL* 1.3 64.3 + - - +
278A HIS 3.3 6.7 - - - -
279A SER* 3.6 5.3 + - - -
283A THR* 3.3 14.0 - - - +
429A CYS* 3.1 42.5 - - - +
430A GLU* 3.2 10.2 + - - -
433A SER* 3.5 9.9 - - - -
503A MET* 3.3 10.4 - - - +
504A MET 3.2 27.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A PHE* 4.8 4.7 - - + -
232A PHE* 4.5 8.1 - - + -
236A ILE* 4.4 28.5 - - + -
268A VAL* 4.7 1.6 - - + -
269A SER* 1.3 79.6 - - - +
271A CYS* 1.3 71.9 + - - +
272A THR* 4.2 12.3 - - + -
276A GLN 4.6 1.1 - - - +
277A ARG* 3.4 8.7 + - - -
278A HIS* 2.6 42.6 + - + +
433A SER* 4.1 2.9 + - - -
501A MET* 4.1 20.9 - - + -
502A GLY 3.7 3.8 - - - +
503A MET* 3.8 22.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A VAL* 1.3 76.3 - - - +
272A THR* 1.3 69.2 + - - +
275A GLY* 4.5 1.6 - - - -
276A GLN 3.3 3.8 - - - -
277A ARG* 3.7 26.2 - - - +
433A SER* 3.8 22.3 + - - +
434A VAL* 4.1 9.0 - - - -
437A ALA* 3.2 18.9 - - - +
446A PRO* 3.8 11.4 - - - -
447A ILE* 4.1 13.5 - - - -
502A GLY 3.0 30.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A VAL* 3.9 8.0 - - - +
226A ILE* 4.6 10.3 - - + -
229A PHE* 3.9 16.8 - - + -
270A VAL* 4.2 8.7 - - + -
271A CYS* 1.3 77.8 - - - +
273A ALA* 1.3 59.0 + - - +
274A ASP* 2.8 17.9 + - - +
275A GLY 3.0 9.9 + - - -
276A GLN* 2.9 53.2 + - + +
437A ALA* 4.6 0.9 - - - -
446A PRO* 3.6 10.2 - - - +
500A VAL 3.4 11.2 - - - -
501A MET* 3.6 7.6 - - + -
----------------------------------------------------------
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