Contacts of the helix formed by residues 385 - 399 (chain M) 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 ASN 385 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383M ASP 4.3 7.0 + - - +
384M ALA* 1.3 73.8 - - - +
386M PRO* 1.3 67.7 - - - +
387M GLU* 3.1 25.4 - - + +
388M TYR* 3.2 6.3 + - + +
389M ILE* 3.0 22.7 + - - +
428M MET 5.2 0.8 + - - -
429M GLN* 2.6 35.1 + - - +
430M VAL 4.7 1.6 + - - -
81U ARG* 4.6 12.7 - - - +
83U LYS* 4.4 20.4 - - - +
302U ALA* 5.8 6.3 - - - +
303U THR* 5.5 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 386 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371M LYS* 4.9 0.9 - - - -
384M ALA 3.7 3.1 - - - +
385M ASN* 1.3 78.4 - - + +
387M GLU* 1.3 79.8 + - - +
389M ILE* 3.0 13.3 + - + +
390M ALA* 2.7 36.6 + - - +
83U LYS* 5.1 2.9 - - - +
150U VAL* 4.9 6.5 - - + +
152U VAL* 3.9 11.7 - - + -
238U SER* 3.3 27.9 - - - +
239U ALA 3.8 9.6 - - - +
240U GLU* 3.7 33.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 387 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385M ASN* 3.1 18.0 - - + +
386M PRO* 1.3 108.6 - - - +
388M TYR* 1.3 63.1 + - - +
390M ALA* 3.6 3.3 + - - +
391M GLU* 3.3 23.7 + - - +
429M GLN* 4.4 4.9 - - - +
81U ARG* 3.3 46.7 + - - +
83U LYS* 4.9 7.3 - - - -
150U VAL* 5.9 1.9 - - - +
152U VAL* 4.0 17.8 - - + +
158U ILE* 4.3 14.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 388 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337M GLU* 3.6 30.2 - - + +
338M MET 2.9 17.5 + - - -
339M LEU* 3.7 1.6 - - - +
384M ALA* 5.2 1.1 - - + -
385M ASN* 3.2 12.2 + - + +
386M PRO 3.1 0.4 - - - -
387M GLU* 1.3 79.0 - - - +
389M ILE* 1.3 66.4 + - - +
391M GLU* 3.2 13.1 + - + +
392M LEU* 3.1 38.8 + - + +
429M GLN* 3.1 61.1 + - + +
430M VAL 4.0 9.0 - - - -
431M ILE* 3.6 26.5 - - + -
462M PHE* 3.2 23.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369M PHE* 5.7 3.6 - - + -
371M LYS* 3.8 35.0 - - + -
384M ALA* 3.9 13.0 - - + +
385M ASN 3.0 16.9 + - - +
386M PRO* 3.0 10.7 + - + +
388M TYR* 1.3 74.7 - - + +
390M ALA* 1.3 66.8 + - - +
392M LEU* 2.9 14.8 + - + +
393M ARG* 2.9 23.7 + - + +
431M ILE* 3.5 23.8 - - + -
115U GLN* 4.9 1.3 - - - +
237U VAL* 3.7 35.7 - - + +
238U SER* 3.8 7.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 390 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386M PRO 2.7 14.3 + - - +
387M GLU 3.7 3.4 - - - +
389M ILE* 1.3 72.0 - - - +
391M GLU* 1.3 64.7 + - + +
393M ARG* 2.9 20.2 + - - +
394M ARG* 2.9 14.2 + - - +
152U VAL* 3.4 33.4 - - + -
153U LYS 3.6 13.7 - - - +
154U LYS* 4.1 6.9 - - - +
156U GLY* 5.2 1.8 - - - -
238U SER* 3.5 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 391 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337M GLU* 5.6 5.2 - - - +
387M GLU 3.3 12.6 + - - +
388M TYR* 3.2 19.2 + - + +
389M ILE 3.1 0.6 - - - -
390M ALA* 1.3 79.3 - - + +
392M LEU* 1.3 62.7 + - + +
394M ARG* 3.1 50.7 + - - +
395M ILE* 2.9 34.1 + - + +
465M ASN* 4.7 3.2 + - - +
154U LYS 4.4 5.2 - - - +
155U ASP 5.2 4.0 - - - +
156U GLY* 5.5 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339M LEU* 4.0 6.3 - - + -
369M PHE* 3.6 26.7 - - + -
388M TYR* 3.4 31.2 - - + +
389M ILE* 2.9 8.8 + - + +
391M GLU* 1.3 76.0 - - + +
393M ARG* 1.3 63.6 + - - +
395M ILE* 3.4 10.3 + - + +
396M LEU* 2.8 33.8 + - + +
431M ILE* 3.5 38.6 - - + -
462M PHE* 3.6 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 393 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389M ILE* 2.9 20.1 + - + +
390M ALA* 3.0 17.7 - - - +
392M LEU* 1.3 80.8 - - + +
394M ARG* 1.3 60.4 + - - +
396M LEU* 3.1 11.4 + - - +
397M SER* 2.7 24.3 + - - -
403M TRP* 4.3 19.9 + - + +
152U VAL 3.6 3.8 + - - -
154U LYS* 4.0 28.3 - - + +
234U GLU* 2.7 44.9 + - - +
235U ASP* 2.7 40.6 + - - +
237U VAL* 4.6 6.7 - - + -
238U SER* 2.6 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 394 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390M ALA 2.9 3.7 + - - +
391M GLU* 3.1 43.2 + - - +
393M ARG* 1.3 78.3 - - - +
395M ILE* 1.3 71.3 + - - +
397M SER* 3.0 17.7 + - - -
398M LYS* 3.2 9.8 + - + +
465M ASN* 2.5 48.4 + - - +
154U LYS* 3.7 42.1 - - + +
155U ASP* 5.2 8.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 395 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100M LYS* 5.0 2.2 - - - +
391M GLU* 2.9 25.2 + - + +
392M LEU* 3.6 20.4 - - + +
394M ARG* 1.3 81.8 - - - +
396M LEU* 1.3 57.4 + - + +
397M SER 2.7 14.8 + - - -
398M LYS* 3.2 14.7 + - + +
399M GLU* 3.3 16.7 + - + +
461M ALA* 2.9 31.2 - - + +
462M PHE* 4.7 10.3 - - + -
464M ASN 4.6 8.5 - - - +
465M ASN* 3.6 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 396 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367M ILE* 4.6 7.9 - - + -
369M PHE* 3.4 39.7 - - + -
392M LEU* 2.8 28.1 + - + +
393M ARG* 3.1 5.8 + - - +
395M ILE* 1.3 72.2 - - + +
397M SER* 1.3 54.5 + - - +
400M SER 2.3 26.6 - - - +
401M VAL* 3.3 25.3 - - + +
403M TRP* 4.1 21.4 + - + -
458M GLY* 3.4 41.1 - - - +
461M ALA* 4.4 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 397 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393M ARG 2.7 16.8 + - - -
394M ARG* 3.0 12.1 - - - -
395M ILE 2.7 0.2 + - - -
396M LEU* 1.3 81.0 + - - +
398M LYS* 1.3 71.1 + - - +
400M SER* 2.9 14.2 + - - +
403M TRP* 5.0 4.5 + - - -
154U LYS* 3.2 27.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 398 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394M ARG* 3.2 7.6 + - + +
395M ILE* 3.8 8.7 - - + +
397M SER* 1.3 78.3 - - - +
399M GLU* 1.3 98.7 + - + +
400M SER* 2.8 10.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 399 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395M ILE* 3.3 10.1 + - + +
398M LYS* 1.3 108.1 + - + +
400M SER* 1.3 70.3 + - - +
401M VAL* 3.5 7.1 + - - +
461M ALA* 3.6 38.0 - - + +
463M LEU* 4.9 9.8 - - + +
----------------------------------------------------------
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