Contacts of the helix formed by residues 509 - 518 (chain A) in PDB entry 1MMG
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 ASP 509 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A LEU* 1.4 78.3 - - + +
510A SER* 1.3 66.9 - - - +
512A ALA* 3.4 3.1 + - - +
513A THR* 3.1 27.0 + - - -
557A LYS* 2.1 40.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A GLU* 3.9 20.1 + - - -
479A GLN* 5.0 1.6 - - - +
480A GLN* 3.5 40.9 + - - +
483A ASN* 5.2 4.7 + - - -
484A HIS* 6.4 0.2 - - - -
508A LEU* 3.8 7.3 - - - +
509A ASP* 1.3 81.9 - - - +
511A GLN* 1.4 67.0 + - - -
513A THR* 3.4 1.6 + - - -
514A ILE* 2.9 31.5 + - - +
573A TYR* 5.2 7.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A LYS* 6.0 0.4 - - - +
480A GLN* 3.1 22.9 + - - +
508A LEU 3.1 25.8 + - - +
510A SER* 1.4 81.7 - - - +
512A ALA* 1.3 57.4 + - - +
514A ILE* 3.2 23.0 + - - +
515A ASP* 2.8 58.8 + - - +
518A ASP* 5.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A LEU 3.2 14.7 + - - +
509A ASP* 3.7 7.6 - - - +
510A SER 3.2 0.2 - - - -
511A GLN* 1.3 74.2 - - - +
513A THR* 1.3 64.6 + - - +
515A ASP* 3.4 8.6 + - - +
516A LEU* 2.9 24.6 + - - +
555A ASN* 5.0 3.0 + - - +
557A LYS* 3.8 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A GLU* 3.7 31.5 + - + +
509A ASP 3.1 16.0 + - - -
510A SER 4.0 2.7 - - - -
512A ALA* 1.3 77.1 - - - +
514A ILE* 1.3 64.9 + - - +
516A LEU* 3.1 13.8 + - - +
517A ILE* 3.2 16.0 + - + +
557A LYS* 3.5 14.9 + - - +
570A VAL* 3.8 13.2 - - + -
571A THR 2.9 28.5 + - - +
572A HIS* 3.8 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A TYR* 4.3 4.7 - - + -
476A GLU* 3.9 29.8 - - + +
477A LYS* 4.1 27.6 - - + -
480A GLN* 3.2 35.7 - - + +
510A SER 2.9 27.1 + - - +
511A GLN* 3.5 20.0 - - - +
513A THR* 1.3 76.8 - - - +
515A ASP* 1.3 52.9 + - - +
517A ILE* 3.1 9.0 + - - +
518A ASP* 2.7 58.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A GLN* 2.8 52.1 + - - +
512A ALA* 3.6 8.0 - - - +
514A ILE* 1.3 73.6 - - - +
516A LEU* 1.3 65.9 + - - +
518A ASP* 3.9 8.1 - - - +
519A GLY* 2.7 33.0 + - - +
522A PRO 5.4 0.3 - - - +
524A GLY* 4.0 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A ALA 2.9 18.4 + - - +
513A THR* 3.1 6.9 + - - +
515A ASP* 1.3 75.9 - - - +
517A ILE* 1.3 58.0 + - + +
524A GLY* 3.1 6.4 - - - -
525A ILE* 2.7 37.9 + - + +
551A PHE* 3.5 43.7 - - + -
555A ASN* 3.6 22.4 - - + +
557A LYS* 3.6 38.4 - - + +
558A TYR* 4.0 7.2 - - + +
570A VAL* 4.1 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LEU* 4.2 24.2 - - + -
473A TYR* 3.9 37.2 - - + -
476A GLU* 4.8 2.9 - - + -
513A THR* 3.2 22.2 + - + +
514A ILE* 3.1 6.1 + - - +
515A ASP 3.1 0.4 - - - -
516A LEU* 1.3 79.3 - - + +
518A ASP* 1.3 62.7 + - - +
519A GLY 3.6 0.2 - - - -
524A GLY 3.8 0.3 - - - -
525A ILE* 3.4 14.3 + - + +
526A LEU* 2.9 55.1 + - + +
570A VAL* 4.9 3.8 - - + -
572A HIS* 3.9 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A TYR* 2.3 46.0 + - + +
477A LYS* 3.7 12.5 + - - -
511A GLN* 5.4 0.2 + - - -
514A ILE* 2.7 38.8 + - - +
515A ASP* 3.9 5.0 - - - +
517A ILE* 1.3 75.8 - - - +
519A GLY* 1.3 68.2 + - - +
520A ARG 3.7 0.2 + - - -
526A LEU* 4.4 6.3 - - + -
527A ALA 5.8 0.4 - - - -
635A LYS* 2.8 45.3 + - + +
----------------------------------------------------------
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