Contacts of the helix formed by residues 417 - 428 (chain T) in PDB entry 3FKS
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 LYS 417 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412T LEU* 3.6 32.6 - - + +
413T ASP* 3.2 49.6 - - + +
414T ALA* 4.8 1.1 - - - +
415T SER 3.4 0.8 - - - +
416T THR* 1.3 79.2 + - - +
418T GLN* 1.3 62.6 + - - +
420T LEU* 3.2 35.2 - - + +
421T VAL* 3.8 16.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 418 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414T ALA 3.9 14.4 + - - +
415T SER* 3.8 11.1 + - - +
416T THR 3.3 0.4 - - - -
417T LYS* 1.3 76.7 - - - +
419T THR* 1.3 63.1 + - + +
420T LEU 3.0 5.8 + - - -
421T VAL* 3.2 19.8 + - - +
422T ARG* 3.6 29.0 + - - +
456T ASP* 5.0 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 419 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395T PHE* 4.5 23.1 - - + -
399T TYR* 4.2 5.9 - - - -
415T SER 3.8 13.9 + - - +
416T THR* 2.9 23.5 + - + +
418T GLN* 1.3 74.5 - - + +
420T LEU* 1.3 63.0 + - - +
421T VAL 3.3 0.2 - - - -
422T ARG* 3.2 15.7 - - + +
423T GLY* 3.1 19.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 420 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399T TYR* 3.3 32.2 + - + +
402T VAL* 5.1 20.0 - - + +
416T THR 3.4 9.1 + - - +
417T LYS* 3.2 32.7 + - + +
418T GLN 3.0 0.4 - - - -
419T THR* 1.3 83.2 + - - +
421T VAL* 1.3 58.3 + - + +
424T GLU* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 421 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417T LYS* 3.8 20.6 - - - +
418T GLN* 3.2 13.6 + - - +
420T LEU* 1.3 76.8 - - + +
422T ARG* 1.3 66.3 + - - +
424T GLU* 3.8 20.6 - - - +
425T ARG* 3.4 41.3 + - - +
456T ASP* 5.1 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 422 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395T PHE* 4.9 9.4 - - + -
418T GLN* 3.6 22.6 + - - +
419T THR* 3.2 27.1 - - + +
420T LEU 3.2 0.4 - - - -
421T VAL* 1.3 77.3 - - - +
423T GLY* 1.3 60.9 + - - +
424T GLU 3.0 1.2 + - - -
425T ARG* 3.4 2.1 + - - +
426T LEU* 2.9 31.3 + - + +
450T GLY 4.6 4.1 + - - +
451T VAL 4.3 6.1 + - - -
453T GLY* 3.0 42.8 + - - +
456T ASP* 3.2 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 423 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395T PHE* 4.7 4.4 - - - -
396T LEU* 4.9 0.7 - - - -
399T TYR* 3.6 30.3 - - - -
419T THR 3.1 7.2 + - - -
422T ARG* 1.3 79.5 - - - +
424T GLU* 1.3 56.5 + - - +
426T LEU* 3.5 17.2 - - - +
427T THR* 3.0 34.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 424 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399T TYR* 3.4 12.1 + - - +
420T LEU 3.1 20.2 + - - +
421T VAL* 3.8 23.6 - - - +
422T ARG 3.0 0.6 - - - -
423T GLY* 1.3 75.6 - - - +
425T ARG* 1.3 70.1 + - - +
426T LEU 2.9 7.9 + - - -
427T THR* 3.4 2.1 + - - -
428T GLN* 3.2 20.7 + - + +
460T LEU* 3.7 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 425 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421T VAL* 3.4 32.4 + - - +
422T ARG 3.4 3.6 + - - +
424T GLU* 1.3 83.0 + - - +
426T LEU* 1.3 58.4 + - - +
428T GLN* 4.0 10.3 - - - -
429T LEU* 3.5 21.3 + - - +
455T LEU 3.6 24.2 - - - +
456T ASP* 3.3 22.2 + - - +
458T ILE 2.8 26.9 + - - -
459T GLU* 3.3 3.0 - - - +
460T LEU* 3.0 39.7 - - + +
463T ILE* 3.6 22.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 426 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392T LEU* 3.9 28.7 - - + -
395T PHE* 4.1 14.8 - - + -
396T LEU* 3.6 27.8 - - + -
422T ARG* 2.9 17.3 + - + +
423T GLY* 3.3 14.8 - - - +
424T GLU 2.9 0.2 - - - -
425T ARG* 1.3 76.8 - - - +
427T THR* 1.3 65.8 + - - +
428T GLN 3.1 1.1 - - - -
429T LEU* 3.2 23.4 + - + +
430T LEU* 3.5 15.0 + - + +
447T ILE* 5.7 0.9 - - - +
450T GLY* 4.0 30.5 - - - -
451T VAL* 6.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 427 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363T ILE* 3.9 32.9 - - + +
396T LEU* 3.8 18.6 - - + +
399T TYR* 4.3 8.8 - - - -
423T GLY 3.0 16.4 + - - -
424T GLU 4.3 2.2 - - - -
426T LEU* 1.3 75.0 - - - +
428T GLN* 1.3 61.9 + - - +
429T LEU 3.5 0.3 + - - -
430T LEU* 3.6 16.0 + - + +
431T LYS* 3.3 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 428 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424T GLU* 3.2 17.7 + - + +
425T ARG* 4.1 10.1 - - - -
426T LEU 3.1 0.6 - - - -
427T THR* 1.3 76.4 - - - +
429T LEU* 1.3 61.2 + - - +
431T LYS* 3.3 48.4 + - - +
460T LEU* 4.6 18.0 - - + +
461T SER* 6.1 1.6 - - - -
463T ILE* 3.7 31.0 - - + +
464T GLY* 4.3 9.1 + - - +
----------------------------------------------------------
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