Contacts of the helix formed by residues 312 - 320 (chain G) in PDB entry 5JLH
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 GLY 312 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310G GLY 3.7 3.2 + - - -
311G ALA* 1.3 73.4 - - - +
313G GLU* 1.3 56.5 + - - -
314G GLN* 3.0 9.6 + - - +
315G LEU* 3.1 5.5 + - - +
316G LYS* 2.6 37.4 + - - +
342G ARG* 5.1 12.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 313 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G GLY* 1.3 72.0 - - - -
314G GLN* 1.3 66.4 + - + +
315G LEU 3.2 0.2 - - - -
316G LYS* 4.1 16.1 - - - +
317G ALA* 2.9 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 314 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G GLY* 3.0 6.4 - - - +
313G GLU* 1.3 85.8 - - + +
315G LEU* 1.3 61.1 + - + +
317G ALA* 4.7 1.3 - - - +
318G ASP* 3.4 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 315 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307G LEU* 4.5 0.2 - - + -
311G ALA* 3.9 19.5 - - + -
312G GLY 3.1 7.4 + - - +
314G GLN* 1.3 78.2 - - + +
316G LYS* 1.3 66.7 + - - +
317G ALA 3.2 1.8 - - - -
318G ASP* 3.1 6.7 + - - +
319G LEU* 2.9 70.9 + - + +
321G LEU* 4.7 0.2 - - + -
345G PHE* 4.1 14.8 - - + -
349G LEU* 4.7 12.1 - - + -
359G HIS* 5.4 11.4 - - + +
362G ILE* 5.7 3.1 - - + -
363G ILE* 5.0 12.6 - - + -
366G LEU* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 316 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308G LEU 5.0 7.8 + - - +
311G ALA* 4.3 13.6 - - + +
312G GLY 2.6 24.3 + - - +
313G GLU* 4.1 13.0 - - - +
315G LEU* 1.3 74.7 - - - +
317G ALA* 1.3 51.3 + - - +
319G LEU 4.4 0.2 - - - +
320G LEU* 2.5 37.9 + - - +
321G LEU* 3.3 48.4 + - + +
322G GLU* 5.2 2.5 - - - -
323G PRO* 5.1 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 317 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313G GLU* 2.9 24.7 + - + +
314G GLN 4.7 2.2 - - - +
316G LYS* 1.3 79.9 - - - +
318G ASP* 1.3 59.0 + - - +
320G LEU* 3.0 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 318 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G GLN 3.4 17.8 + - - +
315G LEU 3.1 7.0 + - - +
317G ALA* 1.3 79.9 - - - +
319G LEU* 1.4 61.7 + - + +
320G LEU* 2.9 17.2 - - - +
363G ILE* 3.3 30.9 - - + +
367G ARG* 4.1 21.4 + - - +
402G ARG* 5.2 1.7 + - - -
403G LEU* 5.2 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 319 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307G LEU* 4.1 2.2 - - + -
315G LEU* 2.9 46.4 + - + +
318G ASP* 1.4 82.7 - - + +
320G LEU* 1.3 71.4 + - - +
321G LEU* 3.7 31.6 - - + -
363G ILE* 4.1 12.6 - - + +
366G LEU* 3.1 34.3 - - + +
367G ARG* 3.7 32.8 - - + +
370G SER* 3.7 13.0 + - - -
374G GLN* 4.7 1.2 + - - -
399G LYS* 4.8 0.7 - - - +
403G LEU* 4.5 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 320 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316G LYS* 2.5 18.1 + - - -
317G ALA* 3.0 21.1 - - - +
318G ASP* 2.9 28.9 - - - +
319G LEU* 1.3 75.2 - - - +
321G LEU* 1.3 62.9 + - - +
322G GLU* 3.9 0.6 + - - -
374G GLN* 3.7 5.2 + - - -
399G LYS* 2.9 57.4 + - + +
402G ARG* 3.4 38.1 - - + +
----------------------------------------------------------
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