Contacts of the helix formed by residues 484 - 495 (chain A) in PDB entry 1MD9
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 484 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A ALA 5.4 2.7 - - - +
483A PRO* 1.3 78.8 - - - +
485A ALA* 1.3 58.6 + - - +
486A ALA* 4.2 6.5 - - + +
487A GLU* 2.7 46.8 + - + +
488A LEU* 3.0 12.6 + - - +
508A PHE* 4.5 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A PRO 3.9 2.2 + - - -
484A LYS* 1.3 73.2 - - - +
486A ALA* 1.3 61.5 + - - +
488A LEU* 3.4 3.8 + - - +
489A LYS* 3.1 37.1 + - - +
506A VAL* 3.5 41.4 - - + +
508A PHE* 4.1 8.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A LYS* 3.0 6.8 - - + +
485A ALA* 1.3 78.4 - - - +
487A GLU* 1.3 58.0 + - - +
489A LYS* 3.5 8.5 + - - +
490A ALA* 3.0 30.7 + - - +
493A ARG* 4.7 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A HIS* 3.5 26.8 + - - +
454A ALA* 5.6 0.3 - - - +
483A PRO* 4.3 9.9 - - + +
484A LYS* 2.7 43.0 + - + +
486A ALA* 1.3 72.2 - - - +
488A LEU* 1.3 57.4 + - - +
490A ALA* 3.5 6.8 + - - +
491A PHE* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449A LEU* 4.4 17.0 - - + -
452A HIS* 3.7 35.9 - - + +
455A VAL* 3.9 15.3 - - + -
476A ILE* 3.9 26.5 - - + -
483A PRO* 4.4 8.5 - - + -
484A LYS 3.0 11.0 + - - +
485A ALA 3.7 6.7 - - - +
487A GLU* 1.3 73.6 - - - +
489A LYS* 1.3 65.9 + - + +
491A PHE* 2.9 22.0 - - + +
492A LEU* 2.9 14.4 + - + +
506A VAL* 4.3 13.2 - - + -
508A PHE* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ALA* 3.1 23.3 + - - +
486A ALA* 3.8 6.3 - - - +
488A LEU* 1.3 76.2 - - - +
490A ALA* 1.3 58.2 + - - +
492A LEU* 3.1 7.8 + - - +
493A ARG* 2.8 48.9 + - - +
502A ILE* 4.0 23.7 - - + +
503A PRO* 3.1 24.1 + - + +
504A ASP* 3.1 22.9 + - - +
505A ARG* 4.7 1.5 - - - +
506A VAL* 4.6 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ALA 3.0 18.6 + - - +
487A GLU* 3.6 8.3 - - - +
489A LYS* 1.3 75.9 - - - +
491A PHE* 1.3 57.2 + - - +
493A ARG* 3.3 25.4 + - - +
494A GLU* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448A HIS 4.0 16.8 - - - -
449A LEU* 4.6 10.5 - - + -
451A ALA* 4.0 21.3 - - + -
452A HIS* 3.8 32.8 - + + -
453A PRO* 5.1 3.6 - - + -
487A GLU 3.1 14.4 + - - +
488A LEU* 2.9 17.0 + - - +
490A ALA* 1.3 73.0 - - - +
492A LEU* 1.3 64.7 + - - +
494A GLU* 3.2 9.0 + - + +
495A ARG* 2.9 66.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445A VAL* 4.2 13.7 - - + +
448A HIS* 3.7 27.4 - - + -
449A LEU* 3.2 37.2 - - + -
488A LEU* 2.9 12.8 + - + +
489A LYS* 3.4 8.5 - - + +
491A PHE* 1.3 78.9 - - + +
493A ARG* 1.3 62.4 + - - +
495A ARG* 3.2 14.9 + - - +
497A LEU* 3.2 34.0 + - + +
502A ILE* 4.1 11.9 - - + -
503A PRO* 3.3 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ALA* 4.7 2.6 + - - +
489A LYS* 2.8 34.5 + - - +
490A ALA* 3.4 35.1 - - - +
492A LEU* 1.3 77.2 - - - +
494A GLU* 1.3 61.1 + - - +
496A GLY* 3.1 14.6 + - - -
497A LEU 4.3 5.0 + - - +
502A ILE* 3.8 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A ALA 2.9 12.6 + - - +
491A PHE* 3.2 13.0 + - + +
493A ARG* 1.3 72.1 - - - +
495A ARG* 1.3 66.9 + - - +
496A GLY* 3.0 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A GLU* 5.0 3.2 + - - -
447A ASN* 6.1 0.4 - - - +
448A HIS* 2.6 63.5 + - + +
451A ALA* 3.9 20.1 - - - +
491A PHE* 2.9 63.4 + - + +
492A LEU* 3.2 9.8 + - - +
494A GLU* 1.3 82.3 - - - +
496A GLY* 1.3 60.5 + - - +
497A LEU 3.8 0.4 + - - +
----------------------------------------------------------
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