Contacts of the strand formed by residues 269 - 274 (chain D) in PDB entry 6FF7
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 GLN 269 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D CYS* 3.7 3.0 - - - +
265D GLY 3.7 24.5 + - - +
267D ASP* 3.2 15.5 - - + +
268D LYS* 1.3 78.5 - - - +
270D VAL* 1.3 62.1 + - - +
271D LYS* 4.0 4.1 + - + +
283D HIS* 6.4 0.9 - - - -
284D TYR 3.9 7.4 - - - +
285D HIS* 6.1 0.9 - - + -
291D VAL* 5.2 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 270 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D SER 3.4 9.9 - - - +
264D CYS* 4.3 10.3 - - + -
269D GLN* 1.3 73.7 - - - +
271D LYS* 1.3 61.2 + - - +
272D CYS* 4.0 0.5 + - - +
283D HIS* 3.7 1.1 - - - -
284D TYR* 2.9 53.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 271 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D PHE* 3.5 4.2 - - - +
263D SER* 2.9 42.6 + - - +
269D GLN* 4.0 5.2 - - + +
270D VAL* 1.3 72.6 - - - +
272D CYS* 1.3 61.3 + - - +
273D TRP* 3.7 5.3 + - + +
280D VAL* 4.9 13.7 - - + -
283D HIS* 4.8 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 272 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D TYR* 5.7 1.8 - - + -
261D LEU 3.6 8.3 - - - +
262D PHE* 4.6 3.4 - - + +
270D VAL 4.0 1.8 + - - +
271D LYS* 1.3 70.4 - - - +
273D TRP* 1.3 62.9 + - - +
274D ASP 3.3 4.2 + - - -
280D VAL* 3.6 4.6 - - - +
281D ILE* 3.3 23.2 + - + +
282D ARG* 3.7 29.6 - - + +
283D HIS 4.5 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 273 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D TYR* 3.3 2.0 - - - +
261D LEU* 2.9 46.4 + - + +
262D PHE* 5.6 0.7 - - - -
263D SER* 5.8 6.1 - - - +
271D LYS* 3.7 7.5 + - + +
272D CYS* 1.3 70.2 - - - +
274D ASP* 1.3 67.4 + - - +
275D LEU* 5.0 0.3 - - - +
278D ASN 5.9 1.1 - - - -
279D LYS 3.6 9.0 - - - +
280D VAL* 4.8 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 274 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260D TYR* 3.7 10.3 - - + -
272D CYS 3.3 4.8 + - - +
273D TRP* 1.3 76.4 - - - +
275D LEU* 1.3 59.5 + - - +
276D GLU* 4.5 7.0 - - + +
277D TYR* 4.6 9.2 - - + +
278D ASN* 3.3 21.8 - - - -
279D LYS* 2.8 22.0 + - + +
281D ILE* 5.0 11.7 - - + -
----------------------------------------------------------
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