Contacts of the strand formed by residues 275 - 279 (chain D) in PDB entry 3MQ6
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 PHE 275 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D PRO* 4.0 20.4 - - + -
238D ALA* 3.3 20.6 - - + -
240D ALA* 4.1 13.2 - - + -
252D GLN* 6.1 0.2 - - - -
253D PRO* 3.9 25.4 - - + -
256D GLU* 4.4 4.3 - - + -
257D ALA* 3.3 33.2 - - + -
260D MET* 3.8 21.5 - - + -
273D VAL* 3.5 10.5 + - + +
274D GLU* 1.3 76.2 - - - +
276D GLU* 1.3 75.3 + - - +
309D ALA 3.9 14.5 + - - +
310D ILE* 3.3 22.1 - - + -
311D ARG* 2.8 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 276 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D MET* 5.8 0.2 - - - +
237D LEU* 3.8 28.1 - - + +
238D ALA 2.9 7.5 + - - +
239D VAL* 3.3 13.2 - - + +
240D ALA 3.0 23.0 + - - -
275D PHE* 1.3 78.7 - - - +
277D VAL* 1.3 65.4 + - - +
278D HIS* 2.7 31.4 + - - +
310D ILE* 4.3 0.9 - - - -
311D ARG* 2.9 36.5 + - + -
312D GLU 3.6 14.6 - - - +
314D TYR* 5.8 0.2 - - + -
325D ARG* 3.0 24.3 + - - +
329D PHE* 5.1 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 277 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D ALA* 3.3 15.3 - - + +
242D LYS* 4.8 13.9 - - + -
245D LEU* 5.0 3.1 - - + -
253D PRO* 4.0 25.6 - - + -
276D GLU* 1.3 78.2 - - - +
278D HIS* 1.3 74.1 + - - +
291D TYR* 4.1 20.9 - - + +
310D ILE* 4.0 20.0 - - + -
312D GLU 3.1 7.4 + - - +
313D LEU* 3.6 23.4 - - + +
314D TYR* 2.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D PHE* 3.6 9.7 - - + -
106D SER* 5.4 0.4 + - - -
110D MET* 4.8 7.6 - - - -
239D VAL* 3.7 21.8 - - + +
240D ALA 2.9 7.5 + - - -
241D PHE* 3.6 26.8 - + + -
242D LYS 2.9 26.9 + - - +
276D GLU* 2.7 32.4 + - + -
277D VAL* 1.3 83.9 - - - +
279D THR* 1.3 62.4 - - - +
314D TYR* 3.2 32.6 - + + +
316D PRO* 4.6 5.7 - - + +
322D LEU* 3.8 24.3 - - + +
325D ARG* 4.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D PHE* 4.3 2.9 - - - -
242D LYS 2.7 21.0 + - - -
243D ARG 3.3 4.2 + - - -
244D SER* 3.6 0.7 - - - -
245D LEU* 3.5 38.8 - - + +
278D HIS* 1.3 75.3 - - - +
280D LEU* 1.3 64.7 + - - +
281D ALA 3.3 14.1 + - - +
282D PRO* 3.9 8.5 - - + -
313D LEU* 4.0 10.1 - - + -
314D TYR 3.1 5.9 + - - -
315D VAL* 3.3 38.8 - - + +
316D PRO* 3.4 5.2 - - - +
----------------------------------------------------------
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