Contacts of the helix formed by residues 312 - 327 (chain A) in PDB entry 5ID6
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 SER 312 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ASN 3.8 12.1 - - - -
307A THR* 2.9 36.2 + - - -
308A LEU 3.6 2.6 - - - -
309A ASN* 2.8 26.9 + - - +
311A ASN* 1.3 84.5 - - - +
313A GLU* 1.3 60.6 + - - +
315A PHE* 3.4 13.2 + - - +
316A SER* 3.0 24.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A THR* 6.6 0.2 - - - -
312A SER* 1.3 74.1 - - - +
314A ILE* 1.3 64.9 + - + +
316A SER* 3.3 9.2 - - - -
317A SER* 2.8 25.3 + - - -
496A ILE* 3.3 37.7 - - + +
499A LYS* 3.4 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A THR* 3.7 30.1 - - + +
308A LEU* 3.8 18.6 - - + -
312A SER* 3.3 1.0 + - - -
313A GLU* 1.3 83.6 - - + +
315A PHE* 1.3 60.7 + - + +
317A SER* 3.1 18.3 + - - -
318A ILE* 3.2 18.1 + - + +
463A VAL* 4.6 0.9 - - + -
496A ILE* 4.0 23.1 - - + +
497A LEU* 4.1 11.2 - - + -
499A LYS* 4.0 12.8 - - + -
500A VAL* 3.4 45.8 - - + +
503A ILE* 5.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ASN 3.6 17.9 - - - +
310A LYS* 3.1 56.5 - - + +
312A SER* 3.4 9.2 + - - +
313A GLU 3.2 0.2 - - - -
314A ILE* 1.3 76.2 - - - +
316A SER* 1.3 65.1 + - - +
318A ILE* 3.5 12.4 + - + +
319A LYS* 3.4 40.9 + - + +
425A ILE* 5.1 0.7 - - + -
426A TYR* 3.5 34.1 - + - -
429A TYR* 3.4 45.1 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A SER 3.0 15.7 + - - -
313A GLU* 3.1 14.3 + - - -
315A PHE* 1.3 76.3 - - - +
317A SER* 1.3 63.1 + - - +
319A LYS* 3.2 24.1 + - - +
320A LYS* 3.2 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A GLU 2.8 18.1 + - - -
314A ILE 3.1 9.4 + - - -
316A SER* 1.3 74.1 - - - +
318A ILE* 1.3 59.7 + - - +
320A LYS* 4.5 5.4 - - - -
321A LEU* 3.0 32.8 + - - +
493A ALA* 3.2 36.8 + - - +
496A ILE* 3.9 10.5 - - - -
497A LEU* 3.6 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ILE* 3.2 22.1 + - + +
315A PHE* 3.7 22.2 - - + +
316A SER 3.1 0.4 - - - -
317A SER* 1.3 79.4 + - - +
319A LYS* 1.3 59.8 + - - +
321A LEU* 3.4 7.4 + - - +
322A GLU* 2.9 26.2 + - - +
422A VAL* 4.8 7.8 - - + +
425A ILE* 4.5 18.2 - - + -
426A TYR* 3.8 26.5 - - + +
429A TYR* 5.1 1.8 - - - +
463A VAL* 4.1 31.0 - - + -
466A PHE* 4.5 15.5 - - + -
497A LEU* 3.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LYS 5.0 5.3 + - - -
315A PHE* 3.4 34.9 + - + +
316A SER* 3.2 14.9 + - - +
318A ILE* 1.3 80.9 - - - +
320A LYS* 1.3 56.3 + - + +
322A GLU* 3.4 9.8 + - - +
323A LYS* 3.1 29.4 + - - +
426A TYR* 3.4 22.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A SER* 3.2 28.1 + - - +
317A SER* 3.8 11.9 - - - +
319A LYS* 1.3 74.3 - - + +
321A LEU* 1.3 56.0 + - - +
323A LYS* 3.1 28.8 + - - +
324A LEU* 2.7 35.6 + - - +
489A ASP 5.8 0.7 - - - +
492A LEU* 6.3 2.0 - - + -
493A ALA* 4.3 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A SER* 3.0 24.6 + - - +
318A ILE 3.9 3.4 - - - +
320A LYS* 1.3 74.9 - - - +
322A GLU* 1.3 63.0 + - - +
324A LEU* 4.1 9.2 - - + -
325A PHE* 3.0 38.3 + - + +
418A ILE* 5.3 0.4 - - - +
466A PHE* 4.2 21.3 - - + -
470A ILE* 4.8 7.2 - - + -
489A ASP 4.8 0.2 - - - +
490A PHE* 4.1 36.6 - - + +
493A ALA* 3.5 30.5 - - + -
494A TYR* 4.5 3.8 - - - +
497A LEU* 4.1 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ILE 2.9 18.6 + - - +
319A LYS* 3.5 11.3 - - - +
320A LYS 3.2 0.2 - - - -
321A LEU* 1.3 77.2 - - - +
323A LYS* 1.3 56.5 + - - +
325A PHE* 4.0 2.1 - - - +
326A LYS* 3.0 57.4 + - - +
418A ILE* 6.1 0.7 - - - -
419A ILE* 5.0 7.2 - - + +
422A VAL* 3.7 39.4 - - + +
423A ASP* 4.3 5.9 - - - +
426A TYR* 3.2 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A LYS* 3.1 15.0 + - - +
320A LYS* 3.4 33.8 - - - +
322A GLU* 1.3 73.8 - - - +
324A LEU* 1.3 69.5 + - - +
326A LYS* 3.3 14.5 + - - +
327A ASN* 3.4 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LYS 2.7 19.3 + - - +
321A LEU* 3.7 12.1 - - + +
323A LYS* 1.3 74.2 - - - +
325A PHE* 1.3 60.9 + - + +
327A ASN* 2.8 32.0 + - - +
328A PHE* 3.5 0.5 + - - -
331A TYR* 3.2 36.8 - - + +
486A PHE* 3.9 24.9 - - + +
489A ASP* 3.9 20.0 - - + +
490A PHE* 3.6 45.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU* 3.0 35.2 + - + +
322A GLU* 4.4 2.0 - - - +
324A LEU* 1.3 77.8 - - + +
326A LYS* 1.3 63.5 + - - +
327A ASN 3.1 0.2 - - - -
328A PHE* 3.1 53.8 + + + +
415A LYS* 3.2 20.8 - - + +
418A ILE* 3.8 37.2 - - + -
419A ILE* 5.1 3.6 - - + -
466A PHE* 5.3 0.4 - + - -
470A ILE* 3.4 33.4 - - + -
473A PHE* 4.5 8.7 - + - -
486A PHE* 3.8 13.0 - + - -
490A PHE* 3.9 28.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLU* 3.0 48.9 + - - +
323A LYS* 3.6 9.6 - - - +
324A LEU 3.2 0.4 - - - -
325A PHE* 1.3 78.4 - - - +
327A ASN* 1.3 60.1 + - - +
328A PHE 3.3 0.7 - - - -
330A GLU* 5.1 0.3 - - - +
415A LYS* 3.5 23.3 + - + +
419A ILE* 3.4 35.6 - - + +
423A ASP* 5.8 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LYS* 3.4 22.0 + - - +
324A LEU* 2.8 13.9 + - - +
326A LYS* 1.3 82.2 - - - +
328A PHE* 1.3 57.7 + - - +
329A ASP 3.1 3.6 - - - -
330A GLU* 2.8 57.9 + - + +
331A TYR* 3.3 18.4 + - + +
----------------------------------------------------------
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