Contacts of the strand formed by residues 348 - 356 (chain A) in PDB entry 1YQZ
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 348 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A LEU* 3.3 52.3 - - + +
344A LYS* 4.3 4.0 - - - -
346A PHE* 3.5 8.3 - - + -
347A ASP* 1.3 75.4 - - - +
349A LYS* 1.3 72.9 - - - +
350A MET* 5.3 2.0 - - + -
373A TYR* 3.7 34.7 - + + -
374A TYR 3.2 14.8 - - - +
376A THR* 3.9 5.3 - - - +
382A LEU* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A TYR* 1.3 83.1 - - - +
350A MET* 1.3 61.9 + - - +
351A VAL* 5.6 0.2 - - + -
373A TYR* 3.3 5.9 - - - +
374A TYR* 2.9 68.4 + - + +
376A THR* 3.8 16.1 - - + +
379A ARG* 5.6 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A TYR* 4.8 2.7 - - + -
349A LYS* 1.3 76.3 - - - +
351A VAL* 1.3 81.0 + - - +
352A GLU* 3.6 34.8 - - - +
371A ARG* 3.6 36.8 - - + +
372A VAL 3.5 4.0 - - - +
373A TYR* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LYS* 5.6 0.2 - - + -
350A MET* 1.3 81.9 - - - +
352A GLU* 1.3 66.9 + - - +
371A ARG* 3.5 0.3 - - - -
372A VAL 2.8 34.4 + - - +
374A TYR* 3.7 31.2 - - + -
409A VAL* 4.9 1.8 - - + -
433A ILE* 3.6 39.2 - - + +
436A LYS* 3.8 26.7 - - + +
437A ALA* 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A MET* 3.6 25.2 - - - +
351A VAL* 1.3 79.7 - - - +
353A VAL* 1.3 67.7 + - - +
369A HIS* 2.8 27.3 + - + +
370A LEU 3.2 13.7 - - - +
371A ARG* 2.9 25.2 + - - -
433A ILE* 3.7 1.6 - - - -
436A LYS* 2.8 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLU* 1.3 82.2 - - - +
354A THR* 1.3 73.7 + - - +
355A GLN* 3.9 25.1 - - + +
368A LEU 3.6 1.3 - - - +
369A HIS* 3.5 1.9 - - - -
370A LEU* 2.9 33.3 + - + +
429A LEU* 4.5 12.0 - - + +
432A MET* 3.9 21.3 - - + -
433A ILE* 4.0 14.3 - - + +
436A LYS* 3.3 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A VAL* 1.3 73.8 - - - +
355A GLN* 1.3 63.7 + - - +
367A PRO* 4.0 23.3 - - + -
368A LEU 3.3 11.4 - - - +
369A HIS* 3.4 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A VAL* 3.9 12.6 - - + +
354A THR* 1.3 76.2 - - - +
356A GLY* 1.3 74.3 + - - +
360A ASN* 5.3 5.3 - - - +
367A PRO* 4.4 3.8 - - - -
368A LEU* 2.8 31.9 + - - +
425A HIS* 3.6 41.1 + - + +
427A LYS 4.5 4.2 + - - -
429A LEU* 4.0 18.9 - - + +
432A MET* 3.9 22.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A GLN* 1.3 82.1 - - - +
357A ALA* 1.3 61.4 + - - -
358A HIS 3.1 2.7 - - - -
360A ASN* 4.0 8.9 + - - -
365A ASN* 3.5 19.5 - - - -
366A SER 3.5 10.5 - - - -
367A PRO* 4.5 1.1 - - - +
425A HIS* 2.6 26.3 + - - -
429A LEU* 3.6 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