Contacts of the strand formed by residues 388 - 392 (chain G) in PDB entry 6IY6
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 PHE 388 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307G ALA* 4.0 9.0 - - - -
310G MET* 3.5 30.7 - - + -
311G VAL* 4.4 4.7 - - + -
314G PHE* 3.7 15.3 - + + -
337G PHE* 3.9 17.7 - - + -
338G LYS 3.7 0.6 + - - -
339G PHE* 4.2 10.9 - - + +
340G LEU 5.0 0.9 + - - -
343G THR* 3.3 39.9 - - + +
344G LEU 4.5 3.6 + - - -
386G THR* 2.6 22.0 + - - +
387G ASP* 1.3 78.7 - - - +
389G TYR* 1.3 60.6 + - - +
418G MET* 3.9 39.3 - - + -
419G PHE 3.2 13.0 - - - -
420G MET* 3.9 11.7 - - + -
425G ILE* 4.2 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 389 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343G THR* 4.5 2.9 - - - -
344G LEU* 3.3 32.8 - - + +
346G LEU* 4.6 9.6 - - + -
373G GLU 4.1 1.7 + - - -
376G LEU* 3.4 31.5 - - + +
377G GLY* 3.7 24.6 + - - -
380G VAL* 3.9 31.9 - - + -
386G THR 5.1 0.4 - - - -
387G ASP 4.8 3.8 - - - -
388G PHE* 1.3 76.6 - - - +
390G ILE* 1.3 72.9 + - - +
391G LEU* 4.4 7.6 - - + -
418G MET* 3.5 3.8 - - - +
419G PHE* 3.1 76.2 + + + -
422G GLY* 5.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 390 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303G MET* 3.9 34.8 - - + +
304G GLU* 5.7 2.5 - - + -
307G ALA* 3.7 28.3 - - + -
343G THR* 3.9 20.6 - - + +
344G LEU 2.8 15.9 + - - +
345G ARG* 3.3 12.1 - - + -
346G LEU* 2.8 32.1 + - - +
388G PHE* 5.2 0.2 - - + -
389G TYR* 1.3 81.9 - - - +
391G LEU* 1.3 59.3 + - - +
392G ASP 4.0 0.4 + - - -
416G TYR* 4.1 9.4 - - + -
417G ASP 3.4 11.9 - - - +
418G MET* 3.9 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 391 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346G LEU* 3.1 19.1 - - + +
347G GLU 4.0 5.8 - - - +
348G TYR* 3.8 16.6 - - + -
351G ALA* 3.5 28.0 - - + -
368G LEU* 3.1 35.7 - - + -
376G LEU* 4.2 7.0 - - + -
389G TYR* 4.3 5.8 - - + -
390G ILE* 1.3 70.8 - - - +
392G ASP* 1.3 58.3 + - - +
394G TYR* 3.4 27.7 - - + +
416G TYR* 3.1 4.6 - - - -
417G ASP 2.8 36.3 + - - -
419G PHE* 3.7 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 392 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299G TYR* 2.6 26.6 + - - -
300G HIS* 2.9 29.4 + - - -
303G MET* 3.8 13.9 - - - +
345G ARG* 3.6 25.5 + - + -
346G LEU 2.9 8.8 + - - +
347G GLU* 4.1 6.3 - - + +
348G TYR* 2.9 30.0 + - - +
391G LEU* 1.3 74.0 - - - +
393G LYS* 1.3 80.1 + - + +
394G TYR 3.4 2.1 + - - -
415G SER 3.1 10.7 - - - +
416G TYR* 4.2 1.6 - - - -
----------------------------------------------------------
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