Contacts of the helix formed by residues 385 - 399 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B ASP 4.3 6.9 + - - +
384B ALA* 1.3 74.8 - - - +
386B PRO* 1.3 69.0 - - - +
387B GLU* 3.1 25.0 - - + +
388B TYR* 3.1 7.6 + - + +
389B ILE* 3.0 23.0 + - - +
428B MET 5.1 1.0 + - - -
429B GLN* 2.6 33.4 + - - +
430B VAL 4.7 1.4 + - - +
81D ARG* 4.6 13.5 - - - +
83D LYS* 4.5 20.3 - - - +
302D ALA* 5.7 6.3 - - - +
303D THR* 5.5 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 386 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B LYS* 4.8 1.3 - - - -
384B ALA 3.7 4.2 - - - +
385B ASN* 1.3 79.3 - - + +
387B GLU* 1.3 81.0 + - - +
389B ILE* 3.0 13.6 + - + +
390B ALA* 2.7 35.0 + - - +
83D LYS* 5.1 4.3 - - - +
150D VAL* 5.0 6.3 - - + -
152D VAL* 3.9 12.6 - - + -
238D SER* 3.5 27.1 - - - +
239D ALA 4.1 9.9 - - - +
240D GLU* 3.8 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 387 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ASN* 3.1 17.0 - - + +
386B PRO* 1.3 107.6 - - - +
388B TYR* 1.3 63.9 + - - +
390B ALA* 3.7 3.1 + - - +
391B GLU* 3.3 23.6 + - - +
429B GLN* 4.5 5.2 - - - +
81D ARG* 3.1 50.1 + - - +
83D LYS* 5.0 5.7 - - - -
150D VAL* 6.1 0.7 - - - +
152D VAL* 4.1 17.0 - - + +
158D ILE* 4.3 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 388 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B GLU* 3.6 29.9 - - + +
338B MET 2.9 17.5 + - - -
339B LEU* 3.6 1.9 - - - +
384B ALA* 5.2 1.1 - - + -
385B ASN* 3.1 11.9 + - + +
387B GLU* 1.3 79.5 - - - +
389B ILE* 1.3 66.6 + - - +
391B GLU* 3.1 13.8 + - + +
392B LEU* 3.0 37.8 + - + +
429B GLN* 3.1 59.8 + - + +
430B VAL 4.0 8.7 - - - -
431B ILE* 3.5 27.8 - - + -
462B PHE* 3.2 23.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B PHE* 5.7 3.8 - - + -
371B LYS* 3.8 34.8 - - + -
384B ALA* 3.9 9.4 - - + +
385B ASN 3.0 21.9 + - - +
386B PRO* 3.4 10.5 - - + +
388B TYR* 1.3 74.0 - - + +
390B ALA* 1.3 68.2 + - - +
392B LEU* 2.9 14.2 + - + +
393B ARG* 2.9 24.7 + - + +
431B ILE* 3.5 27.4 - - + -
115D GLN* 5.1 1.6 - - - +
237D VAL* 3.9 26.9 - - + +
238D SER* 3.9 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 390 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B PRO 2.7 14.9 + - - +
387B GLU 3.7 4.0 - - - +
389B ILE* 1.3 71.6 - - - +
391B GLU* 1.3 66.0 + - - +
393B ARG* 2.9 26.2 + - - +
394B ARG* 3.0 14.9 + - - +
152D VAL* 3.4 32.8 - - + -
153D LYS 3.6 11.9 - - - +
154D LYS* 4.1 7.0 - - - +
156D GLY* 5.2 2.5 - - - -
238D SER* 3.7 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 391 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B GLU* 5.6 5.2 - - - +
387B GLU 3.3 12.2 + - - +
388B TYR* 3.1 19.8 + - + +
390B ALA* 1.3 79.9 - - - +
392B LEU* 1.3 64.4 + - + +
394B ARG* 3.1 51.8 + - - +
395B ILE* 2.9 33.1 + - + +
154D LYS 4.6 3.8 - - - +
155D ASP 5.3 3.8 - - - +
156D GLY* 5.7 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 4.0 6.3 - - + -
369B PHE* 3.5 26.9 - - + -
388B TYR* 3.0 30.5 + - + +
389B ILE* 2.9 8.2 + - + +
391B GLU* 1.3 77.9 - - + +
393B ARG* 1.3 58.1 + - - +
395B ILE* 3.3 10.3 + - + +
396B LEU* 2.8 39.3 + - + +
431B ILE* 3.5 38.1 - - + -
462B PHE* 3.6 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 393 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B ILE* 2.9 20.8 + - + +
390B ALA* 3.0 17.7 - - - +
392B LEU* 1.3 80.5 - - - +
394B ARG* 1.3 60.6 + - - +
396B LEU* 3.0 11.1 + - - -
397B SER* 2.7 24.4 + - - -
403B TRP* 4.3 26.5 + - + +
152D VAL 3.6 3.8 + - - -
154D LYS* 3.8 32.0 - - + +
232D SER* 5.3 0.2 + - - -
234D GLU* 2.8 40.1 + - - +
235D ASP* 2.9 38.4 + - - +
237D VAL* 4.8 4.0 - - + -
238D SER* 2.6 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 394 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B ALA 3.0 7.6 + - - +
391B GLU* 3.1 42.9 + - - +
393B ARG* 1.3 77.9 - - - +
395B ILE* 1.3 81.6 + - - +
397B SER* 3.0 19.7 + - - -
398B LYS* 3.2 10.2 + - + +
465B ASN* 5.7 8.4 + - - +
154D LYS* 3.8 33.7 - - + +
155D ASP* 5.4 6.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LYS* 5.0 6.5 - - - +
391B GLU* 2.9 24.8 + - + +
392B LEU* 3.6 19.3 - - + +
394B ARG* 1.3 91.6 - - - +
396B LEU* 1.3 57.6 + - + +
397B SER 2.7 14.5 + - - -
398B LYS* 3.2 12.8 + - - +
399B GLU* 3.3 14.0 + - - +
461B ALA* 2.8 30.5 - - + +
462B PHE* 4.7 10.8 - - + -
464B ASN 4.8 9.2 - - - +
465B ASN* 3.2 24.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 396 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B LEU* 6.5 0.4 - - + -
367B ILE* 4.6 3.8 - - + -
369B PHE* 3.4 39.5 - - + -
392B LEU* 2.8 26.4 + - + +
393B ARG* 3.0 5.4 + - - +
395B ILE* 1.3 74.7 - - + +
397B SER* 1.3 55.8 + - - +
400B SER 2.3 26.2 - - - +
401B VAL* 3.3 25.2 - - + +
403B TRP* 4.2 25.1 + - + +
458B GLY* 3.4 39.5 - - - +
461B ALA* 4.3 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 397 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ARG 2.7 16.3 + - - -
394B ARG* 3.0 15.5 - - - -
395B ILE 2.8 0.2 - - - -
396B LEU* 1.3 81.4 + - - +
398B LYS* 1.3 67.6 + - - +
400B SER* 2.9 14.2 + - - +
403B TRP* 5.0 4.3 + - - -
154D LYS* 3.4 26.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 398 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B ARG* 3.2 7.6 + - + +
395B ILE* 3.8 7.2 - - - +
397B SER* 1.3 81.2 - - - +
399B GLU* 1.3 90.7 + - + +
400B SER* 2.9 7.1 + - - -
465B ASN* 3.2 47.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 399 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B ILE 3.3 6.1 + - - +
398B LYS* 1.3 100.3 + - + +
400B SER* 1.3 69.5 + - - +
401B VAL* 3.5 8.0 + - + +
461B ALA* 3.6 34.2 - - + +
463B LEU* 4.9 9.0 - - - +
465B ASN 3.5 22.4 - - - +
----------------------------------------------------------
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