Contacts of the strand formed by residues 362 - 365 (chain D) in PDB entry 1M6X
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 362 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D LYS 4.6 0.3 + - - -
210D TYR* 2.5 62.9 + + + -
211D LEU* 4.0 2.7 - - + -
356D ALA* 3.8 20.3 + - + +
357D LEU* 4.0 16.5 - - - +
359D SER* 4.4 0.2 - - - -
360D ARG* 3.0 9.2 - - - +
361D TYR* 1.3 100.4 - - + +
363D ALA* 1.3 61.2 + - - +
371D MET* 3.7 27.4 - - + -
372D ILE 3.6 7.0 - - - +
373D ALA* 3.6 32.0 - - + +
374D LEU* 4.2 5.8 - - - +
379D ASN* 5.2 3.5 + - - -
380D PRO* 3.9 9.2 - - + +
381D ILE* 4.2 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 363 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D LYS* 5.3 8.1 - - - +
357D LEU* 4.3 4.3 - - - -
362D TYR* 1.3 74.2 - - - +
364D TYR* 1.3 63.7 + - - +
370D GLU 3.6 0.2 - - - +
371D MET* 3.3 12.4 - - - +
372D ILE* 2.9 41.3 + - + +
374D LEU* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 364 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ILE* 4.1 23.0 + - + -
318D LYS* 3.6 29.9 + - + +
319D GLY* 3.6 21.8 + - - -
320D LEU* 3.9 29.1 - - + +
322D GLU* 5.7 1.0 + - - -
353D HIS* 6.1 0.4 - + - -
357D LEU* 4.1 16.2 - - + +
363D ALA* 1.3 78.8 - - - +
365D ASP* 1.3 70.7 + - - +
366D PRO* 3.4 35.4 - - + +
369D LYS* 3.6 30.0 + - - +
370D GLU 3.7 7.0 - - - -
371D MET* 4.2 15.9 - - - -
372D ILE* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 365 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363D ALA 4.1 0.4 + - - -
364D TYR* 1.3 75.0 - - - +
366D PRO* 1.3 64.3 - - - +
367D ILE* 2.6 30.9 - - - +
368D SER* 2.5 41.1 + - - +
369D LYS* 2.8 32.1 + - - -
370D GLU 3.0 13.5 + - - +
372D ILE* 4.5 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