Contacts of the helix formed by residues 457 - 473 (chain I) in PDB entry 6MZL
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 PRO 457 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444I ASN* 5.9 1.1 - - + -
456I GLY* 1.3 70.2 - - - -
458I LEU* 1.3 55.6 + - - +
459I LEU 3.2 1.6 - - - -
460I CYS* 3.3 18.2 - - + -
461I SER* 2.4 37.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 458 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428I LEU* 3.7 21.8 - - + -
429I LYS* 2.3 43.6 + - - +
454I SER 4.9 2.5 - - - +
455I LEU 2.7 9.2 + - - +
457I PRO* 1.3 75.1 - - - +
459I LEU* 1.3 59.5 + - - +
461I SER* 4.1 3.1 - - - -
462I GLN* 2.9 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 459 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428I LEU* 4.6 9.7 - - + +
432I ALA* 5.3 6.4 - - + +
447I ALA* 6.6 0.4 - - + -
451I GLU* 5.7 2.2 - - + -
455I LEU* 2.4 49.8 + - + +
456I GLY* 4.4 1.6 - - - +
458I LEU* 1.3 68.5 - - - +
460I CYS* 1.3 57.5 + - - +
462I GLN* 3.3 6.6 + - - +
463I VAL* 2.8 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 460 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444I ASN* 3.7 30.3 - - + +
456I GLY* 5.0 0.9 - - - -
457I PRO* 2.9 25.2 + - + +
459I LEU* 1.3 76.2 - - - +
461I SER* 1.3 61.7 + - - +
463I VAL* 3.2 8.5 + - - +
464I VAL* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 461 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429I LYS* 3.4 16.6 - - - -
457I PRO 2.4 29.3 + - - -
458I LEU* 4.1 2.5 - - - -
460I CYS* 1.3 68.3 - - - +
462I GLN* 1.3 58.1 + - - +
464I VAL* 3.2 8.1 + - - +
465I LYS* 2.9 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 462 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429I LYS* 3.0 23.0 - - + +
432I ALA* 3.7 28.8 - - + +
458I LEU 2.9 19.1 + - - +
459I LEU* 3.7 4.7 - - - +
461I SER* 1.3 74.2 - - - +
463I VAL* 1.3 58.6 + - - +
465I LYS* 3.3 9.9 + - - +
466I ALA* 2.8 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 463 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432I ALA* 5.6 0.2 - - - +
436I ALA* 5.3 9.4 - - + -
441I PRO* 4.4 24.9 - - + +
459I LEU 2.8 17.2 + - - +
460I CYS* 3.2 10.1 + - - +
462I GLN* 1.3 73.0 - - - +
464I VAL* 1.3 60.0 + - - +
466I ALA* 3.3 8.1 + - - +
467I ARG* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 464 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460I CYS 2.9 12.9 + - - +
461I SER* 3.4 11.9 - - - +
463I VAL* 1.3 77.4 - - - +
465I LYS* 1.3 56.3 + - - +
467I ARG* 3.3 7.9 + - - +
468I ALA* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 465 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461I SER 2.9 13.8 + - - +
462I GLN* 3.5 12.3 - - - +
464I VAL* 1.3 78.4 - - - +
466I ALA* 1.3 55.5 + - - +
468I ALA* 3.3 7.9 + - - +
469I GLN* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 466 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433I PRO* 5.8 3.4 - - + -
436I ALA* 4.1 25.6 - - + -
462I GLN 2.8 16.6 + - - +
463I VAL* 3.6 5.6 - - - +
464I VAL 3.2 0.2 - - - -
465I LYS* 1.3 75.8 - - - +
467I ARG* 1.3 60.4 + - - +
469I GLN* 3.2 8.0 + - - +
470I ALA* 2.9 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 467 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441I PRO* 5.6 7.2 - - + -
463I VAL 2.9 16.5 + - - +
464I VAL* 3.3 8.0 + - - +
466I ALA* 1.3 76.1 - - - +
468I ALA* 1.3 57.4 + - - +
470I ALA* 3.3 8.2 + - - +
471I ALA* 2.9 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 468 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464I VAL 2.9 14.3 + - - +
465I LYS* 3.5 12.1 - - - +
466I ALA 3.2 0.2 - - - -
467I ARG* 1.3 74.5 - - - +
469I GLN* 1.3 60.1 + - - +
471I ALA* 3.2 9.1 + - - +
472I LEU* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 469 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465I LYS 2.9 16.0 + - - +
466I ALA* 3.2 9.4 + - - +
468I ALA* 1.3 75.8 - - - +
470I ALA* 1.3 60.4 + - - +
472I LEU* 3.3 21.0 + - - +
473I GLN* 3.5 6.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 470 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466I ALA 2.9 17.2 + - - +
467I ARG* 3.6 8.1 - - - +
469I GLN* 1.3 76.0 - - - +
471I ALA* 1.3 58.1 + - - +
473I GLN* 3.1 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 471 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467I ARG 2.9 17.7 + - - +
468I ALA* 3.2 9.4 + - - +
470I ALA* 1.3 73.0 - - - +
472I LEU* 1.3 62.5 + - - +
473I GLN 3.2 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 472 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468I ALA 2.9 12.3 + - - +
469I GLN* 3.3 16.2 - - - +
470I ALA 3.2 0.4 - - - -
471I ALA* 1.3 77.6 - - - +
473I GLN* 1.3 58.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 473 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469I GLN 3.5 5.5 + - - +
470I ALA* 3.1 20.2 + - - +
471I ALA* 3.2 11.1 - - - +
472I LEU* 1.3 81.6 - - - +
----------------------------------------------------------
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