Contacts of the helix formed by residues 519 - 531 (chain M) 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 GLN 519 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516M ALA 5.2 0.8 + - - -
517M THR* 3.5 0.6 - - - +
518M PRO* 1.3 78.0 - - + +
520M ILE* 1.3 52.2 + - - +
521M VAL* 3.1 3.4 - - - -
522M ILE* 2.6 20.6 + - + +
523M ASN* 2.3 49.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 520 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516M ALA 4.6 5.5 + - - +
517M THR* 3.6 31.3 - - - +
518M PRO 3.4 3.6 - - - -
519M GLN* 1.3 74.8 - - - +
521M VAL* 1.3 57.1 + - - +
523M ASN* 4.2 7.2 - - - -
524M TYR* 2.9 31.9 + - - +
543M ARG* 5.9 3.4 - - + +
544M GLY* 5.7 6.1 - - - +
553M VAL* 5.0 8.5 - - + -
556M ILE* 6.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 521 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518M PRO 5.0 1.7 + - - +
519M GLN 3.1 1.0 - - - -
520M ILE* 1.3 80.6 - - - +
522M ILE* 1.3 56.8 + - - +
524M TYR* 3.9 2.7 - - - +
525M ALA* 2.9 29.0 + - - +
556M ILE* 5.5 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 522 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494M GLU* 4.6 16.9 - - + +
519M GLN* 2.6 22.8 + - + +
521M VAL* 1.3 73.5 - - - +
523M ASN* 1.3 58.7 + - - +
525M ALA* 3.6 7.8 - - - +
526M MET* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 523 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505M ALA* 5.5 2.1 - - - +
508M ASP* 6.3 3.8 - - + -
519M GLN* 2.3 40.8 + - + +
520M ILE* 4.0 5.8 - - - +
522M ILE* 1.3 66.5 - - - +
524M TYR* 1.3 59.2 + - - +
526M MET* 3.2 6.6 + - - +
527M PHE* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 524 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520M ILE 2.9 19.7 + - - +
521M VAL* 4.1 3.4 - - - +
523M ASN* 1.3 76.2 - - - +
525M ALA* 1.3 56.7 + - - +
527M PHE* 3.8 7.7 - - - +
528M LEU* 2.9 28.6 + - - +
536M GLU* 5.4 2.3 - - - +
540M ALA* 3.8 29.6 - - + -
560M TYR* 5.8 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 525 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521M VAL 2.9 19.7 + - - +
522M ILE* 3.6 9.0 - - - +
523M ASN 3.2 0.4 - - - -
524M TYR* 1.3 76.8 - - - +
526M MET* 1.3 58.2 + - - +
528M LEU* 3.4 7.2 + - - +
529M GLU* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 526 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492M ASP* 4.8 20.0 - - + +
494M GLU* 4.8 15.2 - - + +
505M ALA* 5.4 5.2 - - + -
522M ILE 2.9 17.9 + - - +
523M ASN* 3.2 7.1 + - - +
525M ALA* 1.3 75.0 - - - +
527M PHE* 1.3 59.7 + - - +
529M GLU* 3.0 9.0 + - - +
530M GLU* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 527 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505M ALA* 4.4 21.0 - - + +
523M ASN 2.9 16.0 + - - +
524M TYR* 3.9 7.4 - - - +
526M MET* 1.3 76.7 - - - +
528M LEU* 1.3 56.0 + - - +
530M GLU* 3.9 3.4 - - - +
531M HIS* 3.0 33.1 + - - +
532M LYS 3.7 0.2 + - - -
536M GLU* 4.0 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 528 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524M TYR 2.9 19.3 + - - +
525M ALA* 3.7 7.9 - - - +
526M MET 3.2 0.2 - - - -
527M PHE* 1.3 73.9 - - - +
529M GLU* 1.3 63.9 + - - +
532M LYS* 2.9 40.5 + - + +
536M GLU* 4.6 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 529 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525M ALA 2.9 15.8 + - - +
526M MET* 3.0 11.9 + - - +
528M LEU* 1.3 78.9 - - - +
530M GLU* 1.3 60.5 + - - +
531M HIS 5.0 0.5 - - - -
532M LYS* 5.6 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 530 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500M PHE 5.7 2.7 - - - +
501M GLN 5.2 3.6 - - - +
502M SER* 4.9 23.1 - - - +
526M MET 2.9 15.4 + - - +
527M PHE* 4.2 5.2 - - - +
529M GLU* 1.3 77.0 - - - +
531M HIS* 1.3 59.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 531 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527M PHE 3.0 15.0 + - - +
528M LEU 3.7 0.4 - - - -
529M GLU 3.4 1.3 - - - -
530M GLU* 1.3 80.6 - - + +
532M LYS* 1.3 72.4 + - - +
533M TYR* 3.6 12.4 - - + +
536M GLU* 4.8 8.3 - - + -
----------------------------------------------------------
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