Contacts of the helix formed by residues 385 - 399 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F ARG* 4.5 13.5 - - - +
83F LYS* 4.4 21.7 - - - +
302F ALA* 5.9 5.1 - - - +
303F THR* 5.6 1.7 + - - +
383G ASP 4.4 6.3 + - - +
384G ALA* 1.3 73.3 - - - +
386G PRO* 1.3 69.0 - - - +
387G GLU* 3.1 25.4 - - + +
388G TYR* 3.1 8.5 + - + +
389G ILE* 3.0 22.0 + - - +
428G MET 5.2 0.6 + - - -
429G GLN* 2.6 34.5 + - - +
430G VAL 4.7 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 386 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F LYS* 5.2 4.0 - - - +
150F VAL* 4.9 7.4 - - + +
152F VAL* 3.8 13.2 - - + -
238F SER* 3.4 28.5 - - - +
239F ALA 4.0 9.4 - - - +
240F GLU* 3.9 28.9 - - + +
371G LYS* 4.8 1.3 - - - -
384G ALA 3.7 4.0 - - - +
385G ASN* 1.3 78.4 - - + +
387G GLU* 1.3 80.6 + - - +
389G ILE* 2.9 12.9 + - + +
390G ALA* 2.7 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 387 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F ARG* 3.1 48.1 + - - +
83F LYS* 5.0 6.0 - - - -
150F VAL* 6.0 1.2 - - - +
152F VAL* 4.0 16.8 - - + +
158F ILE* 4.2 15.1 - - + +
385G ASN* 3.1 16.8 - - + +
386G PRO* 1.3 107.1 - - - +
388G TYR* 1.3 62.3 + - - +
390G ALA* 3.6 2.9 + - - +
391G GLU* 3.3 24.3 + - - +
429G GLN* 4.4 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 388 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337G GLU* 3.6 30.0 - - + +
338G MET 2.9 17.7 + - - -
339G LEU* 3.6 2.1 - - - +
384G ALA* 5.2 0.9 - - + -
385G ASN* 3.1 13.1 + - + +
386G PRO 3.1 0.6 - - - -
387G GLU* 1.3 78.2 - - - +
389G ILE* 1.3 68.3 + - - +
391G GLU* 3.2 12.8 + - + +
392G LEU* 3.1 38.6 + - + +
429G GLN* 3.1 61.2 + - + +
430G VAL 4.0 8.5 - - - -
431G ILE* 3.5 27.6 - - + -
462G PHE* 3.2 23.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F GLN* 5.1 0.9 - - - +
237F VAL* 3.9 27.1 - - + +
238F SER* 3.7 15.3 - - - -
369G PHE* 5.7 3.4 - - + -
371G LYS* 3.8 34.3 - - + -
384G ALA* 4.0 12.6 - - + +
385G ASN 3.0 19.5 + - - +
386G PRO* 2.9 13.1 + - + +
388G TYR* 1.3 73.8 - - + +
390G ALA* 1.3 67.4 + - - +
392G LEU* 3.0 13.7 + - + +
393G ARG* 2.9 24.5 + - + +
431G ILE* 3.5 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 390 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F VAL* 3.4 33.2 - - + -
153F LYS 3.5 14.1 - - - +
154F LYS 4.0 6.7 - - - +
156F GLY* 5.1 2.7 - - - -
238F SER* 3.7 6.9 - - - +
386G PRO 2.7 14.2 + - - +
387G GLU 3.7 3.8 - - - +
389G ILE* 1.3 72.0 - - - +
391G GLU* 1.3 64.2 + - + +
393G ARG* 2.9 27.1 + - - +
394G ARG* 2.9 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 391 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F LYS 4.5 4.9 - - - +
155F ASP 5.2 4.3 - - - +
156F GLY* 5.6 2.8 + - - -
337G GLU* 5.6 4.5 - - - +
387G GLU 3.3 12.7 + - - +
388G TYR* 3.2 19.0 + - + +
389G ILE 3.1 0.4 - - - -
390G ALA* 1.3 78.3 - - - +
392G LEU* 1.3 64.2 + - + +
394G ARG* 3.0 51.1 + - - +
395G ILE* 2.9 33.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339G LEU* 4.0 6.5 - - + -
369G PHE* 3.5 26.9 - - + -
388G TYR* 3.1 32.1 + - + +
389G ILE* 3.0 9.2 + - - +
391G GLU* 1.3 76.8 - - + +
393G ARG* 1.3 58.0 + - + +
395G ILE* 3.3 10.2 + - + +
396G LEU* 2.8 40.3 + - + +
431G ILE* 3.5 37.7 - - + -
462G PHE* 3.6 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 393 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F VAL 3.6 4.9 + - - -
154F LYS* 3.8 31.3 - - + +
232F SER* 5.2 0.2 + - - -
234F GLU* 2.8 42.0 + - - +
235F ASP* 2.8 39.6 + - - +
237F VAL* 4.8 1.6 - - - -
238F SER* 2.6 40.4 + - - +
389G ILE* 2.9 20.1 + - + +
390G ALA* 3.0 18.4 - - - +
392G LEU* 1.3 78.5 - - + +
394G ARG* 1.3 60.6 + - - +
396G LEU* 3.1 11.6 + - - +
397G SER* 2.7 25.0 + - - -
403G TRP* 4.3 25.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 394 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F LYS* 3.8 40.8 - - + +
155F ASP* 5.3 7.7 + - - +
390G ALA 2.9 2.3 + - - +
391G GLU* 3.0 41.4 + - - +
393G ARG* 1.3 79.5 - - - +
395G ILE* 1.3 76.0 + - - +
397G SER* 3.0 17.2 + - - -
398G LYS* 3.1 9.6 + - + +
465G ASN* 4.1 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 395 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G LYS* 5.0 1.1 - - - +
391G GLU* 2.9 25.0 + - + +
392G LEU* 3.6 19.5 - - + +
394G ARG* 1.3 87.8 - - - +
396G LEU* 1.3 57.8 + - + +
397G SER 2.7 15.2 + - - -
398G LYS* 3.2 15.6 + - + +
399G GLU* 3.3 17.0 + - + +
461G ALA* 2.8 31.2 - - + +
462G PHE* 4.8 8.3 - - + -
464G ASN 4.6 7.6 - - - +
465G ASN* 3.3 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 396 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339G LEU* 6.5 0.2 - - + -
367G ILE* 4.6 4.0 - - + -
369G PHE* 3.4 39.3 - - + -
392G LEU* 2.8 26.9 + - + +
393G ARG* 3.4 5.4 - - - +
395G ILE* 1.3 73.1 - - + +
397G SER* 1.3 54.2 + - - +
400G SER 2.3 28.1 - - - +
401G VAL* 3.3 24.7 - - + +
403G TRP* 4.2 25.7 + - + -
458G GLY* 3.4 39.7 - - - +
461G ALA* 4.3 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 397 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F LYS* 3.3 26.8 + - - -
393G ARG 2.7 16.5 + - - -
394G ARG* 3.0 12.1 - - - -
395G ILE 2.7 3.2 + - - -
396G LEU* 1.3 79.5 + - - +
398G LYS* 1.3 66.9 + - - +
400G SER* 2.9 15.5 + - - +
403G TRP* 5.0 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 398 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394G ARG* 3.1 7.4 + - + +
395G ILE* 3.8 8.5 - - + +
397G SER* 1.3 78.0 - - - +
399G GLU* 1.3 98.0 + - + +
400G SER* 2.8 10.5 + - - -
465G ASN* 5.8 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 399 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395G ILE* 3.3 9.9 + - + +
398G LYS* 1.3 107.7 + - + +
400G SER* 1.3 72.0 + - - +
401G VAL* 3.5 7.7 + - + +
461G ALA* 3.6 37.7 - - + +
463G LEU* 4.9 10.4 - - + +
----------------------------------------------------------
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