Contacts of the helix formed by residues 373 - 384 (chain U) in PDB entry 6FF7
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 SER 373 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371U PRO 3.8 0.8 + - - -
372U LEU* 1.3 76.8 - - - +
374U SER* 1.3 66.7 + - - +
375U ASN* 3.2 10.8 - - - -
376U THR* 3.3 12.2 + - - -
377U LEU* 3.1 21.9 + - - +
400U LYS* 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 374 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372U LEU 4.0 0.2 + - - -
373U SER* 1.3 73.2 - - - +
375U ASN* 1.3 57.5 + - - +
377U LEU* 3.3 6.7 + - - +
378U HIS* 2.9 30.4 + - - +
396U THR* 4.6 8.6 - - - -
398U PHE 4.6 11.9 - - - -
400U LYS* 4.4 29.5 - - - +
403U LEU* 4.9 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 375 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373U SER* 3.2 7.0 - - - -
374U SER* 1.3 80.6 - - - +
376U THR* 1.3 56.6 + - - +
378U HIS* 3.4 7.7 + - - +
379U GLN* 3.0 27.4 + - - +
390U LEU* 5.1 3.5 - - - +
394U GLU 5.0 11.9 - - - +
395U ASP* 5.5 2.5 - - - -
396U THR* 4.8 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 376 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372U LEU* 4.3 10.3 - - - -
373U SER* 3.3 22.9 + - - -
375U ASN* 1.3 75.7 - - - +
377U LEU* 1.3 60.8 + - - +
379U GLN* 3.2 8.8 + - - +
380U VAL* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 377 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369U PHE* 5.6 5.6 - - + +
372U LEU* 5.0 7.1 - - + +
373U SER 3.1 13.2 + - - +
374U SER* 3.7 8.5 - - - +
376U THR* 1.3 72.6 - - - +
378U HIS* 1.3 66.5 + - - +
380U VAL* 3.2 8.0 + - - +
381U ALA* 2.9 24.4 + - - +
403U LEU* 3.9 29.6 - - + +
404U LEU* 5.1 2.9 - - + +
407U LEU* 6.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 378 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374U SER 2.9 17.4 + - - +
375U ASN* 3.5 5.8 - - - +
377U LEU* 1.3 74.7 - - - +
379U GLN* 1.3 58.0 + - - +
381U ALA* 3.3 8.5 + - - +
382U SER* 2.9 28.9 + - - -
387U LEU* 4.7 7.1 - - + +
388U PRO 5.1 1.3 - - - +
390U LEU* 4.9 11.9 - - + -
396U THR* 4.0 22.4 - - - -
398U PHE* 6.2 1.8 - - + -
403U LEU* 4.8 6.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 379 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375U ASN 3.0 15.2 + - - +
376U THR* 3.2 11.9 + - - +
378U HIS* 1.3 75.1 - - - +
380U VAL* 1.3 65.1 + - - +
382U SER* 3.2 8.9 + - - -
383U TYR* 3.2 20.3 + - - +
390U LEU* 5.2 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 380 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340U ALA* 5.4 3.8 - - - +
376U THR 2.9 13.3 + - - +
377U LEU* 3.2 12.1 + - - +
379U GLN* 1.3 76.1 - - - +
381U ALA* 1.3 62.0 + - - +
383U TYR* 3.1 18.7 + - - +
384U LEU* 3.4 10.8 + - - +
407U LEU* 6.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 381 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377U LEU 2.9 13.8 + - - +
378U HIS* 3.3 10.5 + - - +
380U VAL* 1.3 75.7 - - - +
382U SER* 1.3 60.4 + - - +
384U LEU* 3.1 10.9 + - - +
386U LEU* 2.9 42.0 + - + +
387U LEU* 4.1 10.5 - - + -
403U LEU* 6.0 3.6 - - + +
406U LEU* 6.0 5.4 - - + -
407U LEU* 6.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 382 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181U ALA* 5.8 1.0 - - - +
378U HIS 2.9 14.0 + - - -
379U GLN* 3.5 13.0 - - - -
380U VAL 3.2 0.2 - - - -
381U ALA* 1.3 75.8 - - - +
383U TYR* 1.3 57.6 + - - +
385U CYS* 3.1 17.7 + - - -
387U LEU 3.2 23.8 - - - +
388U PRO 3.9 11.7 - - - -
389U THR* 4.0 14.1 - - - -
390U LEU 4.9 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 383 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340U ALA* 4.1 25.5 - - + +
344U HIS* 6.4 2.7 - - + -
379U GLN 3.2 10.0 + - - +
380U VAL* 3.1 13.2 + - - +
382U SER* 1.3 76.7 - - - +
384U LEU* 1.3 56.7 + - - +
385U CYS 3.3 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 384 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337U LEU* 6.5 1.1 - - - -
380U VAL 3.4 7.3 + - - +
381U ALA* 3.1 12.3 + - - +
383U TYR* 1.3 77.9 - - - +
385U CYS* 1.3 69.1 + - - +
386U LEU* 3.2 7.3 + - + +
----------------------------------------------------------
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