Contacts of the strand formed by residues 303 - 309 (chain A) in PDB entry 3QFS
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 LEU 303 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LYS* 3.5 5.5 - - - +
295A LEU* 2.8 25.5 + - + -
296A ASN* 3.0 35.5 + - + +
301A ARG* 4.1 37.0 - - + +
302A HIS* 1.3 78.0 - - - +
304A MET* 1.3 61.1 + - - +
475A CYS* 6.1 0.7 - - - -
476A ALA 3.4 4.7 - - - +
477A VAL* 4.0 21.8 - - + -
537A GLY* 5.8 0.7 - - - -
538A THR* 4.1 8.5 - - + -
575A ASP* 4.4 7.0 - - + -
577A LEU* 3.6 43.3 - - + -
753A NAP 4.7 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ASN* 4.2 7.2 - - - +
293A ARG 3.3 10.8 - - - +
295A LEU* 3.7 6.6 - - - +
302A HIS* 3.9 13.7 - - + +
303A LEU* 1.3 75.8 - - - +
305A HIS* 1.3 60.2 - - - +
306A LEU* 3.5 21.3 - - + +
474A ILE 3.6 0.5 - - - +
475A CYS* 3.4 6.1 - - - -
476A ALA* 2.8 54.5 + - + +
478A VAL* 3.8 15.7 - - + -
494A THR* 3.3 33.7 - - - +
497A LEU* 3.8 17.5 - - + -
498A ARG* 3.7 27.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A THR* 3.8 3.0 - - - +
292A ASN* 3.5 2.6 + - - -
293A ARG* 2.8 60.2 + - + +
295A LEU* 3.7 22.0 - - + -
304A MET* 1.3 74.0 - - - +
306A LEU* 1.3 62.1 + - - +
307A GLU* 2.9 43.4 + - + +
462A ALA* 5.3 2.1 + - + -
473A HIS* 3.6 22.3 + + + +
474A ILE 3.3 9.6 - - - -
544A ILE* 6.1 0.6 - - - +
548A GLN* 6.0 0.6 + - - -
578A TYR* 2.8 36.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A VAL* 4.1 20.6 - - + -
291A THR 3.1 5.8 - - - +
292A ASN* 3.8 17.7 - - - +
304A MET* 3.5 41.7 - - + +
305A HIS* 1.3 76.2 - - - +
307A GLU* 1.3 63.7 + - - +
308A LEU* 4.1 8.5 - - + -
472A VAL 4.6 0.2 - - - -
473A HIS* 3.1 7.4 - - - +
474A ILE* 2.9 50.8 + - + +
497A LEU* 3.9 42.0 - - + +
500A LYS* 4.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A VAL* 3.6 4.3 - - - -
290A THR* 2.9 40.1 + - - +
291A THR* 3.0 31.3 + - - +
293A ARG* 5.2 1.6 + - - -
305A HIS* 2.9 35.1 + - + -
306A LEU* 1.3 71.6 - - - +
308A LEU* 1.3 61.9 + - - +
468A HIS* 5.6 2.0 + - - -
471A SER* 3.8 5.0 + - - +
472A VAL 3.7 3.1 - - - -
473A HIS* 3.4 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ALA* 3.8 12.3 - - + +
288A ALA 3.6 2.7 - - - +
289A VAL* 3.7 31.9 - - + -
306A LEU* 4.8 10.3 - - + -
307A GLU* 1.3 75.5 - - - +
309A ASP* 1.3 63.0 + - - +
310A ILE* 3.3 3.5 + - + +
323A VAL* 4.8 9.0 - - + -
325A VAL* 4.9 0.2 - - + -
471A SER* 3.2 7.7 + - - -
472A VAL* 2.8 50.1 + - + +
474A ILE* 3.8 27.8 - - + -
497A LEU* 5.6 0.9 - - + -
512A VAL* 4.1 28.3 - - + -
514A MET* 4.4 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A PHE* 3.5 5.5 - - - -
287A ALA* 3.4 19.9 - - - +
288A ALA* 2.8 28.4 + - + +
290A THR* 3.8 22.0 + - + +
307A GLU 4.0 1.0 + - - -
308A LEU* 1.3 68.6 - - - +
310A ILE* 1.3 60.0 + - - +
311A SER* 2.7 36.3 + - - -
470A ASN 3.5 7.0 - - - +
471A SER* 4.7 2.0 - - - +
----------------------------------------------------------
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