Contacts of the strand formed by residues 386 - 392 (chain A) in PDB entry 3QTC
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 ASP 386 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ARG* 3.0 50.5 + - - +
378A GLY 5.7 0.2 - - - +
385A GLY* 1.3 71.0 - - - -
387A THR* 1.3 67.0 + - - +
388A LEU* 4.5 2.6 - - - +
401A LEU* 3.4 5.4 - - - +
402A VAL* 2.8 50.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A VAL 4.4 0.2 - - - +
378A GLY* 4.1 15.1 - - - +
385A GLY* 3.6 13.7 + - - +
386A ASP* 1.3 82.2 + - - +
388A LEU* 1.3 69.2 + - - +
389A ASP* 6.5 0.2 - - - -
399A SER* 6.0 0.9 - - - -
400A ALA 3.6 4.3 - - - -
401A LEU* 3.5 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ARG* 3.1 48.9 - - + +
359A LEU* 4.2 24.5 - - + -
360A GLU* 3.8 28.7 - - + +
363A ILE* 4.8 4.0 - - + -
376A ILE* 3.9 15.0 - - + -
377A VAL 3.5 6.7 - - - +
378A GLY* 4.7 0.7 - - - -
386A ASP* 4.3 5.4 - - - +
387A THR* 1.3 83.1 - - - +
389A ASP* 1.3 68.3 + - - +
390A VAL* 4.3 1.3 + - + -
399A SER* 4.1 0.9 + - - -
400A ALA* 2.8 44.6 + - + +
402A VAL* 5.6 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A LYS 3.6 1.4 - - - +
376A ILE* 3.5 1.7 - - - -
377A VAL* 2.7 47.3 + - + +
387A THR* 5.9 0.4 - - - -
388A LEU* 1.3 82.1 - - - +
390A VAL* 1.3 61.4 + - - +
391A MET* 3.8 19.4 + - + -
396A GLU* 3.7 18.8 - - - +
398A SER 3.6 3.1 - - - +
399A SER* 3.8 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ILE* 3.9 31.0 - - + -
367A LEU* 3.7 31.2 - - + -
374A PHE* 4.0 19.1 - - + -
375A LYS 3.6 2.7 - - - -
376A ILE* 4.4 9.2 - - + -
388A LEU* 5.1 0.9 - - + +
389A ASP* 1.3 74.5 - - - +
391A MET* 1.3 57.5 + - - +
396A GLU* 3.7 1.9 - - - -
397A LEU* 2.8 37.9 + - + +
398A SER* 2.9 35.8 + - - +
400A ALA* 5.0 4.7 - - + -
422A PHE* 4.6 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A PHE* 3.2 7.8 - - - +
375A LYS* 2.8 41.5 + - + +
377A VAL* 4.0 25.6 - - + -
389A ASP* 4.2 17.5 - - - +
390A VAL* 1.3 76.6 - - - +
392A HIS* 1.3 60.3 + - - +
393A GLY 3.6 13.8 + - - +
394A ASP* 3.6 29.4 - - - +
395A LEU 3.3 12.1 - - - -
396A GLU* 3.7 22.2 - - + +
397A LEU* 4.5 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A ASP* 2.8 45.7 + - + +
374A PHE* 4.8 0.4 - - - +
391A MET* 1.3 72.5 - - - +
393A GLY* 1.3 67.1 + - - +
394A ASP 3.1 0.7 + - - -
395A LEU* 2.8 30.2 + - + +
397A LEU* 4.0 17.6 - - + +
430A VAL* 3.3 45.1 - - + +
813A EDO 4.6 15.1 - - - -
----------------------------------------------------------
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