Contacts of the helix formed by residues 309 - 318 (chain O) in PDB entry 2GLJ
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 309 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86O ILE* 3.6 18.3 - - + +
101O ILE* 3.6 21.1 - - + -
288O ILE* 3.8 21.5 - - + -
290O ILE* 3.3 40.4 - - + -
306O GLN* 4.2 10.0 + - - +
307O SER 2.8 1.0 + - - -
308O LYS* 1.3 81.6 - - + +
310O PHE* 1.3 75.0 + - - +
312O ASN* 3.3 4.1 + - - +
313O THR* 3.0 37.0 + - - -
333O LEU* 3.7 26.7 - - + -
423O LEU* 3.9 25.8 - - + -
426O TYR* 4.3 9.4 - + - -
428O MET* 5.7 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 310 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310N PHE* 6.3 3.6 - + - -
306O GLN 5.2 0.6 + - - +
307O SER* 2.7 30.6 + - - +
309O PHE* 1.3 83.8 - - - +
311O GLU* 1.3 52.2 + - - +
312O ASN 2.6 14.2 + - - -
313O THR* 3.2 8.8 + - - -
314O VAL* 3.5 18.8 - - + +
328O LYS* 4.6 13.2 - - + -
330O ARG* 6.1 3.8 - - - -
333O LEU* 4.0 15.3 - - + -
426O TYR* 3.0 43.1 - + - +
310P PHE* 6.3 3.1 - + - -
328P LYS* 6.0 1.3 - - - -
330P ARG* 3.1 40.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 311 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307O SER* 2.7 34.1 + - - +
308O LYS* 3.9 3.9 - - - +
310O PHE* 1.3 69.8 - - - +
312O ASN* 1.3 62.9 + - - +
314O VAL* 4.8 2.7 - - - -
315O ALA* 4.4 9.7 - - - +
330P ARG* 3.2 56.0 - - + +
331P LYS* 5.2 5.4 + - - +
333P LEU* 5.8 0.5 - - - +
334P TYR* 3.2 39.7 + - - +
426P TYR* 3.7 21.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 312 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59O ASN* 5.5 3.2 + - - +
78O ALA* 3.3 29.4 - - - +
86O ILE* 4.6 5.4 - - - -
88O PHE* 3.5 25.1 - - + -
308O LYS* 2.7 34.4 + - - +
309O PHE* 3.3 5.6 - - - +
310O PHE 2.6 8.5 + - - -
311O GLU* 1.3 72.1 + - - +
313O THR* 1.3 59.3 + - - +
314O VAL 2.9 3.6 - - - +
315O ALA* 3.5 12.3 - - - +
316O ASP* 2.8 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 313 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88O PHE* 4.1 17.0 - - + -
99O PHE* 3.3 41.7 - - + -
288O ILE* 5.1 0.7 - - + -
309O PHE* 3.0 38.4 + - - -
310O PHE* 3.2 4.2 + - - -
312O ASN* 1.3 76.1 - - - +
314O VAL* 1.3 55.0 + - + +
316O ASP* 3.5 3.0 - - - +
317O ILE* 2.7 41.6 + - + +
332O ALA* 5.6 0.2 - - + -
333O LEU* 4.4 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 314 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310O PHE* 3.5 21.3 - - + +
311O GLU* 4.8 1.1 - - - -
312O ASN 2.9 1.5 - - - +
313O THR* 1.3 77.7 - - - +
315O ALA* 1.3 56.7 + - - +
316O ASP 2.7 7.0 + - - -
317O ILE* 2.7 33.3 + - + -
318O MET* 2.7 14.1 + - + +
326O GLU 5.1 11.0 - - - +
328O LYS* 5.8 2.0 - - + +
333O LEU* 6.4 1.3 - - + -
328P LYS* 6.1 3.4 - - + -
330P ARG* 3.8 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 315 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59O ASN* 5.7 2.0 + - - -
63O ILE* 5.6 5.9 - - - +
311O GLU 4.4 4.0 - - - +
312O ASN* 3.3 21.4 + - - +
314O VAL* 1.3 79.1 - - - +
316O ASP* 1.3 57.3 + - - +
318O MET* 3.7 20.2 - - - +
319O SER* 4.4 6.1 + - - -
331P LYS* 3.4 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 316 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59O ASN* 3.5 13.1 + - - +
70O LEU* 4.2 21.9 - - - +
76O VAL* 3.4 27.6 - - - +
88O PHE* 4.0 27.2 - - + +
90O ILE* 5.0 4.2 - - - +
95O LEU* 5.5 7.6 - - - +
312O ASN* 2.8 19.2 + - - +
313O THR* 3.5 7.2 - - - +
314O VAL 2.7 1.4 + - - -
315O ALA* 1.3 78.2 - - - +
317O ILE* 1.3 62.8 + - - +
318O MET 3.0 1.6 - - - -
319O SER* 3.1 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 317 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95O LEU* 3.9 34.5 - - + +
313O THR* 2.7 31.7 + - + +
314O VAL* 2.7 20.5 + - + +
316O ASP* 1.3 72.3 - - - +
318O MET* 1.3 62.7 + - - +
319O SER 3.3 7.3 + - - +
325O ASP* 3.3 30.9 - - + +
326O GLU 4.6 9.4 - - - +
328O LYS 5.7 0.4 - - - +
329O LEU* 4.4 17.3 - - + -
332O ALA* 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 318 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63O ILE* 4.6 17.3 - - + -
65O ALA* 5.2 11.0 - - + -
314O VAL* 2.7 14.4 + - + +
315O ALA* 3.7 15.3 - - - +
316O ASP 3.0 0.4 - - - -
317O ILE* 1.3 79.4 - - - +
319O SER* 1.3 73.8 + - - +
325O ASP* 2.9 28.2 - - - +
326O GLU* 5.7 5.4 - - + +
----------------------------------------------------------
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