Contacts of the strand formed by residues 348 - 353 (chain B) in PDB entry 3QFR
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B HIS* 3.2 33.5 + - + +
256B ILE* 4.4 14.4 - - + -
261B VAL* 3.9 28.0 - - + -
346B ASP 4.1 9.2 - - - +
347B VAL* 1.3 80.9 - - - +
349B MET* 1.3 63.5 + - - +
367B PRO* 3.8 15.5 - - + -
368B THR 3.7 19.1 - - - +
369B SER* 3.8 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B LEU* 3.6 15.9 - - + -
251B VAL 3.3 15.5 - - - +
252B VAL* 4.2 7.4 - - + -
253B HIS* 3.6 4.9 - - - -
347B VAL* 4.4 2.0 - - + +
348B VAL* 1.3 78.1 - - - +
350B SER* 1.3 67.0 + - - +
351B LEU* 3.7 23.1 - - + -
364B PHE* 3.9 31.2 - - + -
366B CYS* 4.1 1.4 - - - +
367B PRO* 3.4 1.6 - - - +
368B THR* 2.9 54.1 + - + +
369B SER 4.9 1.6 - - - -
370B TYR* 3.6 44.6 - - + +
373B ALA* 5.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B GLU 3.5 2.1 - - - +
250B LEU* 3.8 1.0 - - - +
251B VAL* 3.1 30.6 + - - +
253B HIS* 3.6 10.4 + - - -
349B MET* 1.3 74.0 - - - +
351B LEU* 1.3 73.0 + - - +
352B ASN* 3.4 20.0 - - - -
362B HIS* 4.4 2.2 + - - -
366B CYS* 3.5 13.0 - - - +
367B PRO* 3.3 32.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ARG* 5.5 2.7 - - - +
248B TYR* 3.2 17.6 - - + +
249B GLU 3.7 6.3 - - - +
250B LEU* 4.0 26.9 - - + +
349B MET* 3.7 12.8 - - + -
350B SER* 1.3 82.7 - - - +
352B ASN* 1.3 59.7 + - - +
362B HIS* 3.3 8.2 - - - -
363B PRO* 2.9 47.7 - - + +
364B PHE* 4.1 13.7 - - + -
366B CYS* 4.0 7.4 - - - -
445B ASP* 3.7 32.1 - - + +
448B CYS* 4.3 10.8 - - + +
449B GLU* 4.6 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B TYR* 3.3 1.6 - - - -
249B GLU* 3.1 37.0 + - + +
251B VAL* 3.4 30.5 - - - +
350B SER* 3.4 13.5 - - - -
351B LEU* 1.3 70.3 - - - +
353B ASN* 1.3 68.3 + - - +
354B LEU 3.4 0.2 + - - -
361B LYS 3.3 9.4 - - - +
362B HIS* 2.9 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B GLN* 3.2 22.0 + - - +
248B TYR* 3.2 22.3 - - + -
352B ASN* 1.3 75.1 - - - +
354B LEU* 1.3 83.6 + - - +
355B ASP* 2.7 34.4 + - - +
356B GLU* 4.2 11.3 + - - +
358B SER* 3.8 13.0 + - - -
360B LYS* 2.9 32.1 - - - +
361B LYS* 3.0 18.3 + - - +
----------------------------------------------------------
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