Contacts of the helix formed by residues 379 - 395 (chain A) in PDB entry 4EBC
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 VAL 379 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A LEU* 4.2 25.8 - - + -
368A VAL* 5.1 10.1 - - + +
370A GLN 4.9 12.1 - - - +
371A LYS* 4.5 29.8 - - + +
378A ASP* 1.3 80.3 - - - +
380A MET* 1.3 66.8 - - - +
381A THR 3.4 2.7 - - - -
382A PRO* 3.1 23.7 - - + +
383A MET* 3.4 21.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLU* 4.0 29.6 - - + +
325A LEU* 3.5 29.4 - - + -
326A ALA* 4.3 13.5 - - - -
329A LEU* 3.6 21.8 - - + -
378A ASP* 3.7 11.3 + - - +
379A VAL* 1.3 80.8 - - - +
381A THR* 1.3 65.6 + - + +
383A MET* 3.4 3.1 + - - +
384A VAL* 3.1 53.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ASP* 3.2 24.4 + - - +
380A MET* 1.3 75.1 - - + +
382A PRO* 1.4 81.8 - - - +
384A VAL* 3.1 23.7 - - - +
385A ASP* 3.6 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A VAL* 4.9 20.0 - - + -
378A ASP* 4.7 2.2 - - - +
379A VAL* 3.1 33.2 - - - +
381A THR* 1.4 92.3 - - - +
383A MET* 1.3 64.3 + - + +
385A ASP* 3.2 17.5 + - + +
386A ILE* 3.2 20.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A LEU* 4.0 31.2 - - + -
329A LEU* 5.9 1.1 - - + -
342A VAL* 3.8 33.0 - - + -
364A ILE* 4.1 16.4 - - + -
368A VAL* 4.0 23.8 - - + -
379A VAL* 3.4 26.5 - - + +
380A MET 3.6 8.3 - - - +
382A PRO* 1.3 80.9 - - - +
384A VAL* 1.3 61.6 + - - +
386A ILE* 3.2 22.2 + - + +
387A LEU* 3.0 26.5 + - + +
410A PHE* 4.9 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LYS* 4.4 25.8 - - + +
321A ILE* 5.4 6.1 - - + +
322A GLU* 3.8 22.9 - - + +
325A LEU* 5.3 3.8 - - + -
380A MET* 3.1 37.1 + - + +
381A THR* 3.1 22.0 - - - +
383A MET* 1.3 75.5 - - + +
385A ASP* 1.3 62.8 + - + +
387A LEU* 3.4 7.2 + - - +
388A MET* 3.0 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A THR 4.1 6.5 - - - +
382A PRO* 3.2 12.2 + - + +
384A VAL* 1.3 82.6 - - + +
386A ILE* 1.3 56.4 + - - +
388A MET* 3.3 5.9 + - - +
389A LYS* 2.9 52.7 + - - +
392A ARG* 4.2 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A VAL* 4.7 7.0 - - + -
362A CYS* 3.8 27.1 - - - -
363A PRO 5.1 2.0 - - - +
364A ILE* 5.4 1.1 - - - -
365A PRO* 4.1 29.8 - - + -
368A VAL* 5.7 2.9 - - + -
382A PRO* 3.2 18.1 + - + +
383A MET* 3.4 28.5 - - + +
385A ASP* 1.3 77.1 - - + +
387A LEU* 1.3 58.9 + - - +
389A LYS* 3.0 18.9 + - + +
390A LEU* 2.9 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ILE* 3.6 28.7 - - + -
325A LEU* 3.6 31.4 - - + -
342A VAL* 3.8 26.9 - - + -
343A ARG 4.6 2.5 - - - +
344A LEU* 3.7 40.4 - - + +
383A MET* 3.0 15.6 + - + +
384A VAL* 3.9 4.3 - - - +
386A ILE* 1.3 79.3 - - - +
388A MET* 1.3 59.2 + - - +
390A LEU* 3.3 7.8 + - + +
391A PHE* 2.8 26.0 + - - +
408A VAL* 3.9 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLU* 4.4 13.2 - - + +
317A ALA* 4.4 7.9 - - + -
318A LYS* 3.8 39.3 - - + +
321A ILE* 4.0 18.4 - - + -
384A VAL* 3.0 27.6 + - + +
385A ASP* 3.7 3.4 - - - +
387A LEU* 1.3 75.1 - - + +
389A LYS* 1.3 58.6 + - - +
390A LEU 3.1 1.6 - - - -
391A PHE* 3.0 46.7 - - + +
392A ARG* 2.8 60.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ASP* 2.9 40.2 + - - +
386A ILE* 3.0 15.9 + - + +
388A MET* 1.3 75.6 - - - +
390A LEU* 1.3 62.0 - - + +
392A ARG* 3.4 23.2 - - - +
393A ASN* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A VAL* 3.7 30.5 - - + -
344A LEU* 4.0 7.2 - - + -
360A ARG* 3.9 35.5 - - + +
361A GLN* 3.9 20.2 - - - +
362A CYS* 4.0 19.7 - - + -
386A ILE* 2.9 19.6 + - + +
387A LEU* 3.4 14.6 - - + +
389A LYS* 1.3 76.3 - - + +
391A PHE* 1.3 65.8 + - - +
393A ASN* 3.5 10.1 - - + +
394A MET* 3.4 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLU* 4.7 16.2 - - - -
317A ALA* 3.6 28.5 - - + -
321A ILE* 4.2 11.9 - - + -
344A LEU* 3.7 15.7 - - + +
346A ILE* 4.6 6.5 - - + -
387A LEU 2.8 14.3 + - - +
388A MET* 3.0 32.3 - - + +
390A LEU* 1.3 74.4 - - - +
392A ARG* 1.3 60.3 - - + +
394A MET* 2.7 9.4 + - - -
395A VAL* 2.7 65.1 + - + +
397A VAL* 6.6 0.2 - - + -
401A PHE* 4.5 15.7 - + - -
403A LEU* 3.9 22.7 - - + -
406A LEU* 4.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLU* 3.4 31.6 + - - +
385A ASP* 4.2 3.6 + - - +
388A MET* 2.8 43.2 + - - +
389A LYS* 3.4 39.0 - - - +
391A PHE* 1.3 76.6 - - + +
393A ASN* 1.3 62.2 + - - +
395A VAL 2.7 24.8 - - - +
396A ASN* 4.9 1.0 + - - -
397A VAL* 5.9 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A ARG* 3.3 33.4 + - + +
389A LYS 3.2 13.3 + - - +
390A LEU* 3.5 18.2 - - + +
391A PHE 3.1 0.4 - - - -
392A ARG* 1.3 79.7 - - - +
394A MET* 1.3 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 3.4 35.4 - - + +
346A ILE* 3.6 35.0 - - + -
348A ARG* 3.5 13.8 + - - -
358A GLU* 3.2 46.3 - - - +
359A SER* 3.8 3.1 - - - -
360A ARG* 3.6 31.9 - - + +
390A LEU 3.4 7.6 + - - +
391A PHE* 2.7 11.3 + - - +
393A ASN* 1.3 76.8 - - - +
395A VAL* 1.3 62.6 + - + +
396A ASN 4.1 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE* 4.3 16.6 - - + -
348A ARG* 4.4 10.1 - - - +
391A PHE* 2.7 55.1 + - + +
392A ARG* 2.7 30.2 - - - +
394A MET* 1.3 81.0 - - + +
396A ASN* 1.3 62.5 + - - +
397A VAL* 3.7 3.0 + - - +
401A PHE* 3.6 43.5 - - + -
403A LEU* 4.5 6.3 - - + -
----------------------------------------------------------
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