Contacts of the helix formed by residues 419 - 425 (chain V) 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 ILE 419 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103V GLY* 5.5 1.3 - - - -
104V ALA* 4.8 9.0 - - - +
105V HIS* 4.7 19.5 - - + +
292V VAL* 4.3 23.6 - - + -
295V GLU* 3.5 21.0 - - + +
299V SER* 3.1 30.1 - - - +
338V MET* 4.9 3.6 - - - +
340V SER* 3.9 14.6 + - - +
341V SER 6.0 1.3 - - - +
342V ASP* 6.6 0.4 - - + -
417V GLY 5.6 0.4 - - - +
418V THR* 1.3 72.4 - - - +
420V ALA* 1.3 61.4 + - - +
421V TYR* 3.4 1.8 - - - -
422V ILE* 3.5 37.0 + - + +
423V LEU* 4.2 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 420 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338V MET* 4.0 2.1 - - - +
340V SER* 3.7 22.1 + - - +
382V ASN* 4.0 12.1 - - + +
418V THR* 3.0 19.0 - - - +
419V ILE* 1.3 78.3 - - - +
421V TYR* 1.3 64.0 + - - +
422V ILE 3.4 0.3 + - - -
423V LEU 3.6 2.4 + - - -
424V ALA* 3.4 18.4 + - - +
430V VAL* 3.8 24.0 - - + +
431V ILE 5.3 0.7 - - - -
432V ASP* 3.7 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 421 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298V GLY 5.5 2.1 + - - -
305V MET* 4.0 18.8 - - + +
380V GLY 5.6 3.6 - - - -
381V CYS* 4.7 9.6 - - - -
382V ASN* 3.6 26.8 - - + +
417V GLY* 5.6 3.4 - - - -
418V THR 3.2 26.7 + - - -
419V ILE* 4.9 0.2 - - - -
420V ALA* 1.3 76.7 - - - +
422V ILE* 1.3 86.0 + - + +
423V LEU 3.2 0.2 - - - -
424V ALA* 3.2 6.4 + - - +
425V GLU* 3.2 27.3 + - - +
300X ILE* 4.1 31.4 - - + -
301X GLY* 4.2 11.1 - - - +
305X MET* 6.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 422 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299V SER* 3.9 13.9 - - - -
304V GLY 5.2 3.1 - - - +
305V MET* 3.7 49.4 - - + +
419V ILE* 3.5 41.7 - - + +
420V ALA 3.2 0.6 - - - -
421V TYR* 1.3 106.7 - - + +
423V LEU* 1.3 66.3 + - + +
425V GLU* 3.6 19.0 - - - +
426V TYR* 4.9 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 423 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101V ILE* 5.0 0.2 - - + -
290V ILE* 3.7 23.6 - - + -
309V PHE* 3.9 23.8 - - + -
338V MET* 3.2 42.6 - - + -
419V ILE 4.2 2.8 + - - +
420V ALA 3.6 2.0 + - - -
421V TYR 3.2 0.2 - - - -
422V ILE* 1.3 83.8 - - + +
424V ALA* 1.3 62.7 + - - +
425V GLU 2.9 6.9 + - - -
426V TYR* 3.1 47.6 + - + +
428V MET* 3.5 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 424 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382V ASN* 3.4 29.2 - - - +
420V ALA 3.4 10.8 + - - +
421V TYR* 3.2 6.8 + - - +
423V LEU* 1.3 73.3 - - - +
425V GLU* 1.3 54.2 + - - +
426V TYR 2.9 5.6 - - - -
427V GLY* 2.7 22.8 + - - -
428V MET 4.3 9.2 - - - +
430V VAL* 3.8 17.2 - - + +
301X GLY 4.6 0.2 - - - -
302X ALA* 3.1 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 425 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305V MET* 6.1 1.7 - - - +
421V TYR* 3.2 14.9 + - - +
422V ILE* 3.6 21.6 - - - +
423V LEU 2.9 0.2 - - - -
424V ALA* 1.3 77.2 - - - +
426V TYR* 1.3 61.2 + - + +
427V GLY 3.4 0.2 - - - -
301X GLY* 4.1 5.3 + - - -
302X ALA 4.1 8.1 - - - +
305X MET* 3.7 40.1 - - + +
306X GLN* 3.3 5.5 - - - +
307X SER* 3.0 35.0 + - - +
----------------------------------------------------------
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