Contacts of the helix formed by residues 341 - 351 (chain I) in PDB entry 5FUR
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 341 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337I ASP 5.1 1.1 - - - +
338I GLU* 5.2 3.1 - - - -
339I THR 3.7 3.2 - - - +
340I PRO* 1.3 91.1 - - + +
342I THR* 1.3 65.5 + - + +
344I ARG* 3.2 30.8 + - - +
345I CYS* 3.1 17.7 + - - -
693I ARG* 5.8 5.8 - - - +
793I TYR* 3.4 35.7 - - + +
848I HIS* 6.3 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 342 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331I HIS* 5.4 6.5 - - + +
333I ALA* 5.1 8.1 - - + +
336I ILE* 4.8 20.4 - - + -
338I GLU* 1.9 56.7 + - + +
341I LEU* 1.3 79.3 - - + +
343I ARG* 1.3 59.3 + - - +
344I ARG 3.4 0.4 - - - -
345I CYS* 3.4 18.4 - - + -
346I LEU* 2.8 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 343 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283I TYR* 3.6 37.4 - - - +
286I GLU* 5.4 2.8 + - - -
287I VAL* 3.7 20.9 - - - +
338I GLU* 2.7 40.1 + - - +
339I THR* 3.1 34.8 - - - +
340I PRO 3.3 3.0 + - - +
342I THR* 1.3 75.7 + - - +
344I ARG* 1.3 64.9 + - - +
346I LEU* 3.4 29.4 - - - +
347I ALA* 3.2 26.9 + - - +
378I TYR* 4.3 3.4 - - - -
382I MET* 4.4 12.3 - - - -
386I PHE* 3.8 35.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 344 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319I TYR* 5.7 0.2 - - - -
340I PRO 2.8 13.6 + - - +
341I LEU* 3.2 36.2 + - - +
343I ARG* 1.3 73.7 - - - +
345I CYS* 1.3 79.8 + - - +
347I ALA* 3.2 0.9 + - - +
348I GLN* 2.9 53.5 + - - +
378I TYR* 2.6 52.4 + - + +
382I MET* 4.7 0.2 - - - -
398I GLU* 5.4 5.1 + - - -
450I GLN* 5.8 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 345 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319I TYR* 4.4 12.2 + - - +
320I ALA* 4.4 20.6 - - + +
331I HIS* 6.0 2.0 - - + -
341I LEU* 3.1 12.0 + - - -
342I THR* 3.2 23.0 + - + +
344I ARG* 1.3 113.5 - - - +
346I LEU* 1.3 54.2 + - + +
348I GLN* 3.7 4.4 + - - +
349I SER* 2.7 35.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 346 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280I THR* 5.9 7.6 - - + -
283I TYR* 5.4 4.3 - - + -
284I LEU* 5.1 15.0 - - + -
287I VAL* 4.8 10.1 - - + +
291I TYR* 4.1 5.4 + - - -
320I ALA* 4.9 8.5 - - + +
321I SER* 4.1 19.5 - - - +
328I ASN* 4.8 3.8 - - - +
330I LEU* 4.5 21.3 - - + -
331I HIS* 6.5 0.4 - - + -
338I GLU* 4.8 3.1 - - - +
342I THR* 2.8 21.3 + - - +
343I ARG* 3.4 30.1 - - - +
345I CYS* 1.3 76.1 - - + +
347I ALA* 1.3 58.6 + - - +
349I SER* 3.8 6.7 - - - +
350I LEU* 3.5 31.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 347 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291I TYR* 3.3 23.1 - - - +
343I ARG 3.2 18.7 + - - +
346I LEU* 1.3 75.5 - - - +
348I GLN* 1.3 63.9 + - - +
349I SER 3.4 0.4 - - - -
350I LEU 4.2 0.4 - - - -
351I ALA* 3.4 21.8 + - - +
378I TYR* 4.1 21.6 - - + -
381I TRP* 3.6 23.6 - - + -
382I MET 5.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 348 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319I TYR* 4.2 12.7 + - - +
344I ARG* 2.9 45.1 + - - +
345I CYS 4.0 2.9 - - - +
347I ALA* 1.3 74.7 - - - +
349I SER* 1.3 63.6 + - - +
351I ALA* 3.2 19.2 + - - +
352I GLN* 3.3 25.9 + - - +
371I LYS* 5.3 6.7 + - - +
374I SER* 4.8 7.4 - - - +
375I GLY* 5.0 6.2 - - - -
378I TYR* 3.6 33.7 - - + +
398I GLU* 5.1 2.4 + - - -
450I GLN* 3.6 29.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 349 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319I TYR* 4.5 8.2 + - - -
320I ALA* 4.5 1.0 - - - +
321I SER* 2.9 40.5 + - - -
345I CYS 2.7 24.0 + - - -
346I LEU* 3.8 12.6 - - - +
347I ALA 3.4 0.2 - - - -
348I GLN* 1.3 78.1 - - - +
350I LEU* 1.3 65.3 + - - +
351I ALA 3.1 0.2 - - - -
352I GLN* 2.9 27.6 + - - +
353I GLN* 3.8 8.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 350 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284I LEU* 5.1 4.7 - - + -
287I VAL* 3.4 32.3 - - + -
288I PHE* 3.8 22.9 - - + +
291I TYR* 3.4 26.9 - - + -
304I PHE* 4.1 24.0 - - + -
328I ASN* 4.6 8.5 - - - +
346I LEU* 3.5 15.5 + - + +
347I ALA 4.0 0.4 + - - -
348I GLN 3.6 0.2 - - - -
349I SER* 1.3 84.7 - - - +
351I ALA* 1.3 59.4 + - - +
352I GLN 3.7 0.2 + - - -
353I GLN* 4.0 25.9 + - - +
354I PHE* 3.0 26.8 - - - -
381I TRP* 4.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 351 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347I ALA 3.4 11.4 + - - +
348I GLN 3.2 12.3 + - - +
349I SER 3.1 0.2 - - - -
350I LEU* 1.3 75.8 - - - +
352I GLN* 1.3 57.1 + - - +
353I GLN 3.1 5.2 - - - -
354I PHE* 3.1 30.5 + - - +
355I PHE* 4.0 5.7 + - - +
374I SER* 4.3 16.9 + - - +
377I ILE* 3.3 34.3 - - + -
381I TRP* 4.3 3.6 - - - -
----------------------------------------------------------
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