Contacts of the helix formed by residues 461 - 473 (chain C) in PDB entry 1MKD
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 461 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C ASN 4.4 4.3 + - - -
460C ALA* 1.3 74.4 + - - +
462C VAL* 1.3 66.2 + - - +
463C GLU* 3.1 7.6 - - - -
464C LYS* 2.8 51.1 + - - +
465C SER* 2.9 17.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 462 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C THR* 3.8 27.4 - - + -
431C ASP* 5.7 3.1 - - - +
434C MET* 3.9 34.8 - - + -
438C PHE* 4.9 4.9 - - + -
460C ALA* 3.6 8.8 + - + +
461C SER* 1.3 73.3 - - - +
463C GLU* 1.3 76.1 + - - +
465C SER* 3.5 7.5 + - - -
466C GLN* 3.1 23.7 + - - +
503C TYR* 4.7 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 463 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C SER* 2.9 4.8 + - - -
462C VAL* 1.3 87.1 + - - +
464C LYS* 1.3 67.1 + - + +
466C GLN* 3.2 4.5 + - - +
467C VAL* 3.1 26.0 + - - +
503C TYR* 3.6 22.8 - - + +
506C THR* 3.5 42.9 - - + +
507C ILE* 3.5 22.4 - - + -
508C PRO* 3.9 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 464 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461C SER* 2.8 36.6 + - - +
463C GLU* 1.3 74.8 - - + +
465C SER* 1.3 59.6 + - - +
467C VAL* 3.1 4.7 + - - +
468C GLY* 2.9 26.5 + - - -
507C ILE* 3.7 42.0 - - + -
508C PRO* 5.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 465 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C MET* 5.2 1.2 - - - +
454C MET* 3.5 45.1 - - - +
460C ALA* 5.9 0.2 - - - +
461C SER* 2.9 20.8 + - - -
462C VAL* 3.6 12.5 - - - -
464C LYS* 1.3 77.3 - - - +
466C GLN* 1.3 53.7 + - - +
468C GLY* 3.3 1.8 + - - -
469C PHE* 2.7 36.3 + - - +
3003C ZAR 4.1 2.6 - - - +
391F SER 5.8 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 466 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C TYR* 2.7 31.9 + - - +
430C THR* 3.4 34.1 - - + +
433C ILE* 4.6 3.4 - - - +
434C MET* 4.8 5.1 - - - -
462C VAL 3.1 16.3 + - - +
463C GLU 3.2 7.4 + - - +
465C SER* 1.3 73.6 - - - +
467C VAL* 1.3 61.7 + - - +
469C PHE* 3.2 7.9 + - - +
470C ILE* 2.9 36.6 + - - +
503C TYR* 3.9 22.4 - - + -
3003C ZAR 3.0 44.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 467 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463C GLU 3.1 15.6 + - - +
464C LYS* 3.1 6.7 + - - +
466C GLN* 1.3 75.6 - - - +
468C GLY* 1.3 58.4 + - - +
470C ILE* 3.5 6.1 + - - +
471C ASP* 2.9 38.2 + - - +
500C ARG* 3.2 45.8 - - + +
503C TYR* 4.0 5.2 - - + -
504C GLN* 3.8 33.4 - - - +
507C ILE* 3.8 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 468 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C LYS 2.9 13.5 + - - -
465C SER* 3.7 2.9 - - - -
467C VAL* 1.3 76.4 - - - +
469C PHE* 1.3 60.5 - - - +
471C ASP* 3.1 2.5 + - - -
472C TYR* 2.8 59.8 + - - -
391F SER 5.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 469 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C MET* 5.4 3.1 - - + -
416C LEU* 3.7 26.7 - - + -
419C PRO* 4.1 13.7 - - + -
465C SER 2.7 22.3 + - - +
466C GLN* 3.2 12.1 + - - +
468C GLY* 1.3 73.4 - - - +
470C ILE* 1.3 56.2 + - - +
473C ILE* 3.0 49.4 + - + +
474C VAL* 3.1 35.2 + - + -
3003C ZAR 3.6 72.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 470 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419C PRO* 4.0 22.4 - - + -
426C TYR* 3.4 26.9 - - + +
466C GLN* 2.9 21.7 + - + +
467C VAL* 3.8 4.3 - - - +
469C PHE* 1.3 76.4 - - + +
471C ASP* 1.3 66.7 + - - +
474C VAL* 3.9 6.3 - - - -
475C HIS* 2.7 43.8 + - + +
476C PRO* 3.4 1.2 - - - +
496C LEU* 3.9 21.5 - - + +
500C ARG* 3.9 45.3 - - + +
503C TYR* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 471 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C VAL* 2.9 27.7 + - - +
468C GLY* 3.7 6.0 - - - +
470C ILE* 1.3 77.3 - - - +
472C TYR* 1.3 76.9 + - + +
475C HIS* 4.7 4.1 - - - +
476C PRO* 3.2 19.8 - - - +
500C ARG* 2.7 45.2 + - - -
486F HIS* 4.1 20.4 + - + +
487F PRO* 5.4 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 472 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C HIS* 4.6 2.8 + - - -
374C MET* 4.7 8.5 - - + +
468C GLY* 2.8 45.8 + - - +
469C PHE* 5.4 0.2 - - - -
471C ASP* 1.3 87.0 + - + +
473C ILE* 1.3 75.9 + - + +
476C PRO* 3.6 13.2 - - - +
387F LYS* 4.6 13.7 - - + -
389F VAL* 4.1 37.5 - - + -
390F THR 4.9 1.6 - - - -
391F SER* 4.4 10.5 - - - -
392F SER 4.9 1.5 + - - -
393F GLY* 3.5 29.5 + - - -
486F HIS* 4.1 19.5 + - + -
487F PRO* 5.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 473 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370C MET* 3.8 26.7 - - + -
373C HIS* 3.7 34.0 + - + +
374C MET* 4.5 10.5 - - + -
416C LEU* 3.8 15.9 - - + -
469C PHE* 3.0 33.5 + - + +
472C TYR* 1.3 98.5 - - + +
474C VAL* 1.3 67.1 + - - +
476C PRO* 3.2 5.8 - - - +
477C LEU* 3.1 23.4 + - - +
----------------------------------------------------------
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