Contacts of the helix formed by residues 309 - 318 (chain X) 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 X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86X ILE* 3.6 19.1 - - + -
101X ILE* 3.6 21.5 - - + -
288X ILE* 3.7 21.5 - - + -
290X ILE* 3.4 39.7 - - + -
306X GLN* 4.2 9.9 + - - +
307X SER 2.8 1.4 + - - -
308X LYS* 1.3 82.3 - - + +
310X PHE* 1.3 75.1 + - - +
312X ASN* 3.4 2.8 + - - +
313X THR* 2.9 36.8 + - - -
333X LEU* 3.7 26.7 - - + -
423X LEU* 3.9 26.5 - - + -
426X TYR* 4.3 9.0 - + - -
428X MET* 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 310 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310V PHE* 6.4 1.6 - + - -
328V LYS* 6.1 1.1 - - - -
330V ARG* 3.2 40.4 - - - -
310W PHE* 6.4 2.0 - + - -
306X GLN 5.1 0.9 + - - +
307X SER* 2.7 28.9 + - - +
309X PHE* 1.3 84.1 - - - +
311X GLU* 1.3 51.7 + - - +
312X ASN 2.6 13.7 + - - -
313X THR* 3.2 9.2 + - - -
314X VAL* 3.5 19.9 + - + +
328X LYS* 4.6 13.7 - - + -
330X ARG* 6.1 3.6 - - - -
333X LEU* 4.0 14.8 - - + -
426X TYR* 3.0 44.2 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 311 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330V ARG* 3.2 54.6 - - + +
331V LYS* 5.2 6.4 + - - +
333V LEU* 6.0 0.7 - - - +
334V TYR* 3.3 35.8 + - - +
426V TYR* 3.9 20.2 - - - +
307X SER* 2.7 40.7 + - - +
308X LYS* 3.9 3.9 - - - +
310X PHE* 1.3 70.0 - - - +
312X ASN* 1.3 63.5 + - - +
314X VAL* 4.8 2.7 - - - -
315X ALA* 4.4 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 312 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59X ASN* 5.5 3.9 + - - +
78X ALA* 3.4 28.7 - - - +
86X ILE* 4.6 5.2 - - - -
88X PHE* 3.4 24.9 - - + -
308X LYS* 2.7 35.7 + - - +
309X PHE* 3.4 4.3 - - - +
310X PHE 2.6 8.5 + - - -
311X GLU* 1.3 71.3 + - - +
313X THR* 1.3 60.2 + - - +
314X VAL 2.9 3.3 - - - +
315X ALA* 3.5 12.2 - - - +
316X ASP* 2.8 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 313 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88X PHE* 4.1 16.6 - - + -
99X PHE* 3.3 41.1 - - + -
288X ILE* 5.1 0.7 - - + -
309X PHE* 2.9 39.7 + - - -
310X PHE* 4.0 3.6 - - - -
312X ASN* 1.3 76.8 + - - +
314X VAL* 1.3 54.8 + - + +
316X ASP* 3.5 1.8 - - - +
317X ILE* 2.6 44.6 + - + +
332X ALA* 5.6 0.4 - - + -
333X LEU* 4.4 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 314 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328V LYS* 6.4 1.3 - - + -
330V ARG* 3.9 30.3 - - + +
310X PHE* 3.5 22.7 - - + +
311X GLU* 4.8 3.1 - - - -
312X ASN 2.9 1.7 - - - +
313X THR* 1.3 76.6 - - + +
315X ALA* 1.3 55.3 + - - +
316X ASP 2.7 7.0 + - - -
317X ILE* 2.7 32.9 + - + -
318X MET* 2.8 14.3 + - + +
326X GLU 5.1 10.8 - - - +
328X LYS* 5.8 2.0 - - + +
333X LEU* 6.4 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 315 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331V LYS* 3.7 26.5 - - - +
59X ASN* 5.7 2.2 + - - -
63X ILE* 5.6 6.1 - - - +
311X GLU 4.4 4.5 - - - +
312X ASN* 3.3 20.3 + - - +
314X VAL* 1.3 79.0 - - - +
316X ASP* 1.3 57.4 + - - +
318X MET* 3.7 20.5 - - - +
319X SER* 4.5 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 316 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59X ASN* 3.5 14.6 + - - +
70X LEU* 4.3 20.4 - - - +
76X VAL* 3.5 26.9 - - - +
88X PHE* 4.0 27.4 - - + +
90X ILE* 5.0 4.9 - - - +
95X LEU* 5.5 8.1 - - - +
312X ASN* 2.8 18.8 + - - +
313X THR* 3.5 7.6 - - - +
314X VAL 2.7 1.2 + - - -
315X ALA* 1.3 78.3 - - - +
317X ILE* 1.3 64.0 + - - +
318X MET 3.0 1.8 - - - -
319X SER* 3.1 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 317 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95X LEU* 3.9 36.1 - - + +
96X TYR 5.4 0.2 - - - +
313X THR* 2.6 34.8 + - + +
314X VAL* 2.7 17.9 + - + +
316X ASP* 1.3 72.4 - - - +
318X MET* 1.3 64.9 + - - +
319X SER 3.3 7.3 + - - +
325X ASP* 3.3 30.6 - - + +
326X GLU 4.5 9.6 - - - +
328X LYS 5.7 0.9 - - - +
329X LEU* 4.4 17.5 - - + -
332X ALA* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 318 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63X ILE* 4.6 16.8 - - + -
65X ALA* 5.2 11.2 - - + +
314X VAL* 2.8 14.6 + - + +
315X ALA* 3.7 16.2 - - - +
316X ASP 3.0 0.2 - - - -
317X ILE* 1.3 78.3 - - - +
319X SER* 1.3 73.8 + - - +
325X ASP* 2.8 28.4 - - - +
326X GLU* 5.7 4.9 - - + +
----------------------------------------------------------
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