Contacts of the strand formed by residues 307 - 311 (chain G) in PDB entry 1O04
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 ARG 307 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G LYS* 2.9 35.5 + - + +
273G SER 3.2 6.2 + - - +
274G PRO* 3.3 14.2 - - + +
275G ASN 2.8 25.5 + - - -
305G GLY 4.5 0.7 - - - -
306G SER* 1.3 82.5 - - - +
308G THR* 1.3 63.6 + - - +
309G PHE* 3.4 30.9 + - + -
391G ASP* 5.6 2.2 + - - -
396G ALA* 3.3 32.5 - - - +
406G GLN 4.0 0.2 - - - -
408G LEU* 3.8 15.7 - - + -
419G ARG 3.1 25.9 + - - -
420G ALA* 2.9 25.2 + - - +
422G ASN 4.5 6.2 + - - -
423G SER* 3.8 17.9 - - - -
425G TYR 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 308 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G ASN* 3.4 16.2 + - - +
277G ILE* 4.4 3.6 - - + -
290G ALA* 4.2 11.8 + - + +
305G GLY 3.6 15.6 + - - -
307G ARG* 1.3 70.4 - - - +
309G PHE* 1.3 58.4 + - - +
310G VAL* 3.7 6.2 + - + -
318G PHE* 4.0 33.0 - - + -
405G MET* 3.7 17.6 - - + +
406G GLN 2.9 19.0 + - - -
407G ILE* 3.4 9.6 - - + +
408G LEU* 2.8 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 309 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G PRO* 3.8 21.1 - - + -
275G ASN 2.9 9.6 + - - +
276G ILE* 4.3 7.2 - - + -
277G ILE* 2.8 28.2 + - - +
307G ARG* 3.4 48.0 + - + -
308G THR* 1.3 70.2 - - - +
310G VAL* 1.3 60.8 + - - +
391G ASP* 4.1 7.6 - - - -
408G LEU* 3.4 21.5 - - + -
410G PHE* 3.6 17.2 - + + -
416G VAL* 3.8 20.9 - - + -
419G ARG* 3.8 50.7 - - + -
420G ALA* 4.2 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 310 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G ILE* 3.8 7.4 - - + -
308G THR* 3.9 7.2 - - + +
309G PHE* 1.3 80.5 - - - +
311G GLN* 1.3 69.2 + - - +
312G GLU 3.5 0.2 + - - -
314G ILE* 3.8 16.2 - - + -
315G TYR* 3.7 31.1 - - + -
318G PHE* 3.6 45.5 - - + -
407G ILE* 3.8 17.3 - - + -
408G LEU 2.8 12.2 + - - +
409G LYS* 3.4 8.5 - - - +
410G PHE* 3.1 21.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 311 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277G ILE 3.1 15.3 + - - +
278G MET* 5.1 4.5 - - + -
279G SER* 3.6 32.0 - - - +
310G VAL* 1.3 73.9 - - - +
312G GLU* 1.3 91.2 + - - +
313G ASP* 2.8 40.7 + - - +
314G ILE* 3.0 15.3 + - + +
315G TYR 3.1 9.2 + - - -
410G PHE* 3.3 27.0 - - + +
411G LYS* 2.8 32.6 + - - +
----------------------------------------------------------
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