Contacts of the strand formed by residues 328 - 331 (chain B) in PDB entry 4MVX
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 TYR 328 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B PHE* 3.5 23.6 - + + -
282B ALA 3.2 3.4 + - - -
283B LEU* 3.5 19.2 - - + +
284B THR 3.2 24.4 + - - +
326B ILE* 3.5 8.1 - - - +
327B ASP* 1.3 80.9 - - - +
329B PHE* 1.3 83.4 + - - +
330B ILE* 3.5 15.0 - - + +
331B ARG 5.3 1.2 + - - -
334B ASN* 4.8 6.8 + - - +
484B GLY* 5.3 0.2 - - - -
487B LEU* 3.5 27.4 - - + +
489B VAL* 3.8 16.2 - - + -
493B GLY* 3.3 27.4 - - - -
494B LYS* 4.6 0.4 - - - -
495B GLU* 3.1 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B THR* 3.4 20.4 - - + -
285B GLY* 3.9 12.6 - - - -
286B THR* 3.8 30.3 - - + -
312B ALA* 4.0 9.9 - - + -
315B PHE* 3.8 20.0 - + + -
316B LYS* 3.8 50.1 + - + -
319B PHE* 3.9 29.6 - + - -
326B ILE* 5.9 0.2 - - + -
328B TYR* 1.3 91.9 + - - +
330B ILE* 1.3 61.3 + - - +
331B ARG* 4.0 10.6 + - + +
493B GLY 5.2 0.6 + - - -
808B DMS 5.7 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ILE* 4.0 11.2 - - + -
283B LEU* 3.9 6.5 - - + -
284B THR 3.0 19.9 + - - +
285B GLY* 3.1 2.8 - - - -
286B THR 2.9 25.9 + - - +
328B TYR* 3.5 17.6 - - + +
329B PHE* 1.3 74.5 - - - +
331B ARG* 1.3 75.9 + - - +
332B THR* 4.9 0.7 - - + +
334B ASN* 5.3 3.1 - - + +
337B HIS* 4.5 6.1 - - + +
480B ASN* 3.6 44.0 - - + +
483B THR* 3.6 32.8 - - + -
484B GLY* 4.0 8.5 - - - +
487B LEU* 4.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B THR* 3.6 15.7 - - + -
288B GLU* 2.7 36.3 + - - +
305B TYR* 5.5 3.8 - - - -
308B THR* 3.7 3.0 + - - -
309B THR* 3.2 50.2 + - - +
312B ALA* 3.7 12.1 - - - +
316B LYS* 4.5 16.1 - - - +
328B TYR* 5.3 1.0 + - - -
329B PHE* 4.0 12.3 + - + +
330B ILE* 1.3 85.3 - - - +
332B THR* 1.3 58.5 + - - +
333B THR* 3.1 17.6 + - - +
334B ASN* 2.9 33.8 + - + +
337B HIS* 4.3 0.9 - - - +
----------------------------------------------------------
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