Contacts of the helix formed by residues 386 - 406 (chain A) in PDB entry 2H3W
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 THR 386 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASN* 4.7 1.2 + - - -
269A ASP* 6.6 0.2 - - + -
384A ASN* 4.1 6.5 - - + +
385A ILE* 1.3 82.1 - - - +
387A PRO* 1.3 71.9 - - - +
388A GLU* 3.1 8.6 + - - +
389A ILE* 3.1 34.8 + - + +
390A LYS* 2.8 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 387 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A THR* 1.3 88.1 - - - +
388A GLU* 1.3 56.1 + - - +
390A LYS* 3.5 7.7 + - + +
391A ASN* 3.1 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 388 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LYS* 5.9 2.8 - - - -
265A ASN* 3.3 35.3 - - - +
268A LYS* 5.6 0.9 + - - -
386A THR* 3.1 8.1 + - - +
387A PRO* 1.3 79.2 - - - +
389A ILE* 1.3 65.8 + - - +
391A ASN* 3.2 10.9 + - + +
392A ASP* 3.0 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 389 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL* 5.2 0.4 - - + -
251A LEU* 4.8 6.5 - - + -
265A ASN* 3.6 19.5 - - - +
266A LEU* 4.3 23.6 - - + +
269A ASP* 6.2 0.2 - - + -
272A ASN* 3.7 14.8 - - - +
384A ASN 3.3 26.0 - - - +
385A ILE* 4.0 22.2 - - + -
386A THR* 3.1 27.5 + - + +
388A GLU* 1.3 73.4 - - - +
390A LYS* 1.3 66.0 + - - +
392A ASP* 3.0 10.8 + - - +
393A ILE* 2.9 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 390 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 2.9 43.5 + - + +
385A ILE* 4.2 7.3 - - + +
386A THR 2.8 17.3 + - - +
387A PRO* 3.6 8.5 - - + +
389A ILE* 1.3 77.1 - - - +
391A ASN* 1.3 63.8 + - - +
393A ILE* 3.1 10.6 + - + +
394A GLU* 2.9 59.6 + - + +
397A LYS* 4.4 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 391 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A PRO 3.1 14.3 + - - +
388A GLU* 3.4 13.2 + - - +
390A LYS* 1.3 77.8 - - - +
392A ASP* 1.3 64.2 + - - +
394A GLU* 3.3 8.3 + - - +
395A LYS* 3.0 51.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 3.4 23.5 - - + +
254A ASN* 4.9 1.6 + - - -
258A THR* 5.8 3.1 - - - +
262A ALA* 3.9 29.2 - - + +
265A ASN* 4.2 9.9 + - - +
388A GLU* 3.0 29.0 + - - +
389A ILE* 3.0 12.9 + - + +
391A ASN* 1.3 83.7 + - - +
393A ILE* 1.3 57.6 + - - +
395A LYS* 3.3 8.3 + - - +
396A ALA* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 3.7 37.0 - - + +
247A PRO* 3.9 18.6 - - + +
248A VAL* 4.1 15.3 - - + -
250A ILE* 3.8 16.6 - - + +
251A LEU* 3.6 24.0 - - + -
385A ILE* 4.3 1.8 - - + -
389A ILE* 2.9 33.8 + - + +
390A LYS* 3.1 8.9 + - - +
392A ASP* 1.3 76.4 - - - +
394A GLU* 1.3 58.3 + - + +
396A ALA* 3.1 5.4 + - - +
397A LYS* 2.9 36.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 4.5 0.3 - - - +
390A LYS* 2.9 53.5 + - + +
391A ASN* 3.7 10.8 - - - +
393A ILE* 1.3 72.1 - - - +
395A LYS* 1.3 67.4 + - + +
397A LYS* 3.0 34.7 + - - +
398A GLN* 3.0 41.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ASN* 4.0 9.7 + - - +
258A THR* 5.9 3.1 - - + -
391A ASN* 3.0 41.8 + - - +
392A ASP* 3.6 8.3 - - - +
394A GLU* 1.3 77.4 - - + +
396A ALA* 1.3 56.9 + - - +
398A GLN* 3.4 27.5 + - - +
399A ASN* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ILE* 3.6 31.0 - - + +
251A LEU* 4.1 11.2 - - + -
253A SER* 4.5 2.0 + - - +
254A ASN* 3.6 21.7 - - + +
392A ASP 3.0 14.7 + - - +
393A ILE 3.1 9.4 + - - +
395A LYS* 1.3 74.6 - - - +
397A LYS* 1.3 58.0 + - - +
399A ASN* 3.3 2.1 + - - +
400A LEU* 2.8 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 4.6 1.8 + - - -
247A PRO* 3.9 27.5 - - - +
250A ILE* 4.0 15.2 - - + +
314A SER* 3.6 34.4 + - - +
390A LYS* 4.4 6.1 - - - +
393A ILE* 2.9 20.9 + - + +
394A GLU* 3.0 43.3 + - - +
396A ALA* 1.3 75.2 - - - +
398A GLN* 1.3 59.2 + - + +
400A LEU* 3.3 1.8 + - - +
401A SER* 2.8 31.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A GLU* 3.0 38.9 + - - +
395A LYS* 3.5 31.5 + - - +
397A LYS* 1.3 77.9 - - + +
399A ASN* 1.3 62.6 + - - +
401A SER* 3.3 7.7 + - - -
402A ILE* 3.2 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 399 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PRO* 4.2 6.3 - - - +
253A SER 3.6 13.3 + - - -
254A ASN* 3.4 29.5 + - - +
255A HIS* 4.8 1.8 + - - +
395A LYS 3.0 16.7 + - - +
396A ALA 3.6 4.0 + - - +
398A GLN* 1.3 77.7 - - - +
400A LEU* 1.3 63.5 + - - +
402A ILE* 3.2 14.1 + - - +
403A MET* 3.1 51.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 4.3 14.4 - - + -
116A ILE* 5.3 0.2 - - + -
250A ILE* 3.8 21.1 - - + -
253A SER* 3.8 16.8 - - - +
310A HIS* 4.4 4.3 - - + +
313A GLY* 5.1 0.9 - - - -
314A SER 4.8 3.1 - - - +
318A SER* 3.3 35.9 - - - +
323A PHE* 5.6 0.4 - - + -
396A ALA 2.8 17.5 + - - +
397A LYS* 3.8 4.5 - - - +
399A ASN* 1.3 74.9 - - - +
401A SER* 1.3 63.4 + - - +
403A MET* 3.3 27.4 + - + -
404A ILE* 3.0 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 401 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A LYS 2.8 18.3 + - - -
398A GLN* 3.5 8.3 - - - -
399A ASN 3.2 0.2 - - - -
400A LEU* 1.3 78.1 - - - +
402A ILE* 1.3 63.2 + - - +
404A ILE* 3.5 6.5 + - - +
405A GLN* 2.8 55.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 402 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A GLN* 3.2 17.7 + - + +
399A ASN* 3.2 12.7 + - - +
401A SER* 1.3 78.3 - - - +
403A MET* 1.3 65.8 + - + +
405A GLN* 3.3 11.6 + - - +
406A ASP* 3.1 25.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PRO* 3.8 15.5 - - + -
115A VAL* 3.3 45.1 - - + +
116A ILE* 4.2 11.9 - - + +
117A TYR* 3.3 33.6 + - + +
253A SER 3.8 6.3 - - - +
399A ASN* 3.1 45.4 + - - +
400A LEU* 3.5 15.0 - - + +
402A ILE* 1.3 77.2 - - + +
404A ILE* 1.3 63.6 + - - +
406A ASP* 3.2 14.4 + - - +
407A LEU* 3.2 13.7 + - - +
592A TYR* 5.8 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 4.6 2.7 - - + -
310A HIS* 3.5 47.8 - - + +
312A GLY 3.6 7.4 - - - +
313A GLY* 3.5 31.6 - - - +
318A SER* 4.2 0.4 - - - +
400A LEU* 3.0 38.9 + - + +
401A SER* 3.9 5.4 - - - +
403A MET* 1.3 74.3 - - - +
405A GLN* 1.3 67.4 + - + +
407A LEU* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A SER* 2.8 49.1 + - - +
402A ILE* 3.7 10.1 - - - +
404A ILE* 1.3 79.1 - - + +
406A ASP* 1.3 57.6 + - - +
407A LEU 4.5 0.2 - - - +
593A ASN* 3.0 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TYR* 5.5 2.5 + - - +
402A ILE* 3.1 19.0 + - + +
403A MET* 3.7 6.1 - - - +
404A ILE 3.1 1.4 - - - -
405A GLN* 1.3 78.3 - - - +
407A LEU* 1.3 57.0 + - - +
592A TYR* 3.2 28.1 - - + +
593A ASN* 2.8 34.3 + - - +
594A SER* 2.7 42.4 + - - -
----------------------------------------------------------
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