Contacts of the strand formed by residues 465 - 470 (chain G) in PDB entry 1G9N
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 465 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357G LYS* 4.1 1.8 - - - +
358G THR* 3.4 13.4 - - - -
360G ILE* 3.9 20.3 - - - +
462G THR* 4.6 9.4 - - - +
463G ASN* 2.6 39.2 + - - +
464G GLY* 1.3 76.1 - - - -
466G GLU* 1.3 69.0 + - - +
467G ILE* 3.3 14.3 + - + +
963G NAG 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 466 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353G PHE* 4.4 13.5 - - + -
357G LYS* 3.6 40.6 + - + -
358G THR 3.2 9.0 + - - +
359G ILE* 4.0 3.8 - - + -
360G ILE* 3.2 26.0 + - - +
456G ARG* 2.8 40.1 + - - +
457G ASP 3.5 11.3 - - - +
458G GLY 4.4 4.5 - - - +
462G THR 5.6 0.9 - - - +
463G ASN 6.0 0.4 - - - -
465G THR* 1.3 75.8 - - - +
467G ILE* 1.3 59.4 + - - +
468G PHE* 3.2 25.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 467 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360G ILE* 3.7 22.0 - - + +
362G ASN* 3.8 43.1 - - + +
456G ARG* 3.1 1.6 - - - -
457G ASP* 3.0 50.6 + - + +
465G THR* 3.3 15.4 + - + +
466G GLU* 1.3 75.7 + - - +
468G PHE* 1.3 63.4 + - - +
469G ARG* 4.0 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 468 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284G ILE* 3.4 27.6 - - + -
349G LEU* 3.4 36.6 - - + -
353G PHE* 3.5 19.1 - + - -
359G ILE* 4.8 6.1 - - + -
360G ILE 2.9 10.9 + - - -
361G PHE* 3.2 30.9 - - + +
362G ASN 3.0 20.6 + - - +
391G PHE* 5.4 0.2 - - - +
454G LEU* 4.5 11.0 - - + -
456G ARG* 3.3 41.3 - - + +
466G GLU* 3.2 31.9 - - + -
467G ILE* 1.3 76.6 - - - +
469G ARG* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 469 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C PRO* 3.9 12.1 - - - +
362G ASN* 3.1 35.2 + - + +
363G PRO* 2.7 35.0 + - - +
364G SER* 4.2 2.4 + - - -
365G SER* 2.9 35.1 + - - +
391G PHE* 5.3 0.4 - - - -
454G LEU* 3.4 8.0 - - - -
455G THR* 2.9 30.7 + - + +
457G ASP* 2.7 37.9 + - - +
467G ILE* 4.0 13.1 - - + +
468G PHE* 1.3 77.4 - - - +
470G PRO* 1.3 80.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 470 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258G GLN* 3.2 38.8 - - + +
362G ASN 3.1 15.9 - - - +
363G PRO* 3.7 0.7 - - + -
364G SER* 3.7 19.2 + - - +
371G ILE* 5.0 2.8 - - - +
387G SER* 4.4 1.6 - - - +
391G PHE* 3.1 45.3 - - + -
453G LEU 3.8 5.6 - - - +
454G LEU* 4.7 0.4 - - + -
455G THR* 3.0 9.4 - - - +
469G ARG* 1.3 94.3 - - + +
471G GLY* 1.3 58.2 + - - +
----------------------------------------------------------
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