Contacts of the strand formed by residues 348 - 353 (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 VAL 348 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A HIS* 2.9 37.7 + - + +
256A ILE* 3.9 23.3 - - + -
261A VAL* 4.0 25.8 - - + -
346A ASP 3.3 12.1 + - - +
347A VAL* 1.3 77.0 - - - +
349A MET* 1.3 66.6 + - - +
367A PRO* 4.1 8.5 - - + -
368A THR 3.5 19.5 - - - +
369A SER* 4.2 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 3.7 22.4 - - + -
251A VAL 3.3 14.8 - - - +
252A VAL* 4.0 6.7 - - + -
253A HIS* 3.7 7.4 - - - -
347A VAL* 4.6 2.0 - - + +
348A VAL* 1.3 78.6 - - - +
350A SER* 1.3 73.0 + - - +
351A LEU* 3.9 9.0 - - + -
364A PHE* 3.9 32.1 - - + -
366A CYS* 4.1 3.0 - - - -
367A PRO* 3.3 2.1 - - - +
368A THR* 2.9 56.9 + - + +
369A SER 4.8 1.3 - - - +
370A TYR* 3.7 44.0 - - + +
373A ALA* 5.2 0.2 - - + -
448A CYS* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A GLU 3.6 1.4 - - - +
250A LEU* 3.7 3.3 - - - +
251A VAL* 2.9 31.7 + - - +
253A HIS* 2.8 28.9 - - - -
349A MET* 1.3 77.5 - - - +
351A LEU* 1.3 59.8 + - - +
352A ASN* 3.5 22.0 - - - -
362A HIS* 4.6 2.0 + - - -
366A CYS* 3.5 13.3 - - - +
367A PRO* 3.3 18.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ARG* 3.7 24.2 - - - +
248A TYR* 3.9 13.9 - - + -
249A GLU 3.4 11.2 - - - +
250A LEU* 4.0 17.7 - - + -
349A MET* 3.9 12.8 - - - -
350A SER* 1.3 74.6 - - - +
352A ASN* 1.3 58.7 - - - +
362A HIS* 2.9 20.1 - - - -
363A PRO* 3.4 39.6 - - + +
364A PHE* 4.0 15.9 - - + -
366A CYS* 3.7 7.0 - - - -
445A ASP* 3.7 20.2 - - + +
448A CYS* 4.1 8.1 - - + -
449A GLU* 4.5 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TYR* 3.2 3.1 - - - -
249A GLU* 2.8 47.2 + - + +
251A VAL* 3.2 34.1 - - - +
350A SER* 3.5 12.2 - - - -
351A LEU* 1.3 74.1 - - - +
353A ASN* 1.3 67.4 + - - +
354A LEU 3.3 0.2 + - - -
361A LYS 3.4 3.8 - - - +
362A HIS* 3.0 28.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLN* 2.7 43.9 + - - +
248A TYR* 3.3 11.5 + - + -
249A GLU* 5.7 0.7 - - - +
352A ASN* 1.3 74.0 - - - +
354A LEU* 1.3 65.0 + - - +
355A ASP* 2.8 42.8 + - - +
356A GLU* 3.9 8.3 + - - +
358A SER* 3.3 14.3 + - - -
360A LYS* 2.9 30.9 - - - +
361A LYS* 2.9 14.4 + - - +
----------------------------------------------------------
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