Contacts of the helix formed by residues 313 - 320 (chain D) in PDB entry 4JF7
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 THR 313 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D ASP 3.5 24.5 - - - +
283D VAL* 3.9 22.0 - - + +
309D VAL* 3.5 8.1 - - - +
310D ILE* 3.1 30.6 + - + +
311D LYS 4.6 0.2 - - - +
312D GLY* 1.3 82.6 - - - +
314D SER* 1.3 57.8 + - - +
315D LEU* 3.7 3.5 + - - +
316D TRP* 3.1 16.6 + - - +
317D ASN* 3.0 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 314 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D VAL* 6.1 0.2 - - - +
313D THR* 1.3 72.5 - - - +
315D LEU* 1.3 53.5 + - - +
317D ASN* 3.3 8.2 + - - +
318D ASN* 2.7 50.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 315 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D VAL* 4.0 12.1 - - + +
284D TRP* 3.7 26.5 - - + +
309D VAL* 3.6 33.0 - - + -
313D THR* 3.3 6.4 - - - +
314D SER* 1.3 77.3 - - - +
316D TRP* 1.3 65.7 + - - +
318D ASN* 3.4 9.3 + - + +
319D GLN* 3.1 41.6 + - - +
357D MET* 4.3 2.7 - - + -
359D GLN* 4.6 1.1 - - + +
379D PRO* 3.6 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 316 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D VAL* 3.8 9.5 - - + +
310D ILE 3.5 7.2 - - - +
311D LYS* 3.4 48.8 - - + +
312D GLY 3.8 9.2 - - - +
313D THR* 3.1 19.8 + - - +
315D LEU* 1.3 78.8 - - - +
317D ASN* 1.3 78.1 + - - +
319D GLN* 3.1 4.5 + - - +
320D ALA* 3.0 23.6 + - + +
349D TYR* 3.5 33.6 + + - -
355D ASN* 3.6 24.7 - - + -
357D MET* 3.7 36.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 317 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312D GLY* 3.7 17.7 + - - -
313D THR 3.0 23.8 + - - +
314D SER* 3.6 7.1 - - - +
316D TRP* 1.3 90.8 - - - +
318D ASN* 1.3 64.1 + - - +
320D ALA* 3.1 22.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 318 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D SER* 2.7 33.8 + - - +
315D LEU* 3.8 10.3 - - + +
317D ASN* 1.3 73.5 - - - +
319D GLN* 1.3 59.0 + - - +
320D ALA 3.3 2.0 + - - +
322D LYS* 3.2 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 319 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D LEU* 3.1 30.6 + - - +
316D TRP 3.5 5.2 - - - +
317D ASN 3.1 0.4 - - - -
318D ASN* 1.3 78.0 - - - +
320D ALA* 1.3 65.2 + - - +
321D ASN 3.4 0.3 + - - -
322D LYS* 3.2 37.8 + - - +
349D TYR* 4.4 5.3 + - - -
357D MET* 3.5 16.2 - - + -
359D GLN* 2.9 22.6 + - - +
379D PRO* 4.5 1.2 - - - +
380D PHE 3.1 19.8 + - - -
381D SER* 3.7 4.9 - - - +
382D ASN* 3.0 47.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D TRP* 3.0 15.7 + - + +
317D ASN* 3.1 20.5 + - - +
318D ASN 4.6 1.7 - - - +
319D GLN* 1.3 78.6 - - - +
321D ASN* 1.3 66.8 + - + +
322D LYS* 3.3 8.3 + - - +
349D TYR* 4.1 10.1 - - - +
----------------------------------------------------------
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