Contacts of the helix formed by residues 305 - 312 (chain F) 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 305 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301F HIS* 5.5 0.4 - - - -
304F VAL* 1.3 76.9 - - - +
306F ASN* 1.3 64.9 + - - +
307F GLN* 3.5 10.3 + - - +
308F PHE* 3.0 18.6 + - - +
309F LEU* 3.0 21.8 + - - +
326F LEU* 4.2 3.8 - - - -
440F GLN* 3.0 25.3 + - - -
452F SER* 5.4 0.5 + - - -
3006F ZAR 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 306 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305F SER* 1.3 74.2 - - - +
307F GLN* 1.3 59.3 + - - +
309F LEU* 3.1 8.9 + - - +
310F ILE* 2.8 42.2 + - + +
324F SER* 4.2 3.4 - - - +
325F VAL* 3.4 14.3 - - + +
326F LEU* 2.7 41.3 + - - +
327F GLU* 2.9 31.3 + - - -
369F ASP* 4.1 11.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 307 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305F SER* 3.1 8.8 + - - +
306F ASN* 1.3 79.9 - - - +
308F PHE* 1.3 57.1 + - - +
310F ILE* 3.2 22.3 + - - +
311F ASN* 2.8 70.4 + - - +
452F SER* 6.0 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 308 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304F VAL* 3.5 22.7 - - + -
305F SER* 3.0 26.3 + - - +
307F GLN* 1.3 76.5 - - - +
309F LEU* 1.3 61.7 + - + +
310F ILE 3.2 0.2 + - - -
311F ASN* 3.2 6.4 + - - +
312F THR* 2.8 64.6 + - + +
440F GLN* 3.8 14.1 - - + +
443F ARG* 3.3 50.5 - - + -
444F GLU* 3.6 39.7 - - + +
447F ARG* 4.0 8.7 - - - -
449F MET* 4.3 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 309 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302F PRO* 4.6 5.8 - - + -
304F VAL* 3.9 22.0 - - + -
305F SER 3.0 16.2 + - - +
306F ASN* 3.4 8.7 - - - +
308F PHE* 1.3 79.1 - - + +
310F ILE* 1.3 59.4 + - - +
312F THR* 3.7 4.0 - - - +
313F ASN 3.5 1.2 + - - -
314F SER* 2.7 55.2 + - - +
316F LEU* 4.5 11.4 - - + -
317F ALA* 3.4 7.3 - - + +
325F VAL* 4.1 16.6 - - + -
326F LEU* 3.6 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 310 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F ASN* 2.8 27.5 + - + +
307F GLN* 3.6 26.0 - - - +
309F LEU* 1.3 76.3 - - - +
311F ASN* 1.3 62.0 + - - +
313F ASN* 3.0 24.6 + - - +
317F ALA* 3.8 10.0 - - + +
322F ASP* 3.6 58.9 - - + +
325F VAL* 4.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 311 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F GLN* 2.8 57.3 + - - +
308F PHE* 3.9 1.4 - - - +
310F ILE* 1.3 75.1 - - - +
312F THR* 1.3 60.5 + - - +
313F ASN* 3.1 11.9 + - - +
444F GLU* 5.7 1.0 + - - -
449F MET* 3.8 27.7 - - + +
351G LYS* 5.8 4.9 + - - -
355G GLN* 5.5 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 312 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308F PHE* 2.8 59.6 + - + +
309F LEU* 3.5 11.4 + - - +
311F ASN* 1.3 75.7 - - - +
313F ASN* 1.3 72.2 + - - +
314F SER* 3.2 8.0 + - - -
447F ARG* 4.1 16.4 - - - +
449F MET* 3.7 24.2 - - + -
----------------------------------------------------------
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