Contacts of the helix formed by residues 313 - 323 (chain K) in PDB entry 5ANC
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 LYS 313 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311K LYS* 4.8 9.8 - - - +
312K ASP* 1.3 73.0 - - - +
314K ASP* 1.3 64.6 + - + +
316K ILE* 3.3 14.2 - - - +
317K ASP* 2.9 21.3 - - - +
331K GLU 3.2 26.9 - - - +
332K ALA* 3.9 18.5 + - - +
334K HIS 4.0 16.8 + - - -
335K SER* 4.7 9.3 - - - +
336K ASP* 4.2 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 314 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312K ASP* 5.4 1.4 - - - +
313K LYS* 1.3 79.4 + - + +
315K LYS* 1.3 67.3 + - - +
316K ILE 3.2 2.0 - - - -
317K ASP* 3.2 9.8 + - + +
318K LYS* 2.7 61.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 315 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303K SER* 4.6 8.7 + - - +
306K ASP* 6.0 1.2 - - - +
307K ALA* 4.2 10.3 - - + +
310K LYS* 6.5 0.4 - - - -
312K ASP* 3.4 36.8 - - + +
313K LYS 3.6 0.6 - - - -
314K ASP* 1.3 86.6 - - - +
316K ILE* 1.3 57.1 + - - +
318K LYS* 3.2 13.4 + - + +
319K ILE* 2.9 54.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 316 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304K LEU* 3.7 21.2 - - + +
307K ALA* 3.5 24.0 - - + -
308K VAL* 4.2 15.5 - - + +
312K ASP 3.4 20.4 + - - +
313K LYS* 3.3 19.5 - - - +
315K LYS* 1.3 77.3 - - - +
317K ASP* 1.3 69.2 + - - +
319K ILE* 3.2 7.0 + - - +
320K VAL* 2.9 34.2 + - - +
336K ASP* 3.3 28.7 - - - +
337K PRO* 4.5 5.4 - - + +
340K GLN* 4.1 22.2 - - + +
341K ILE* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 317 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313K LYS 2.9 21.5 - - - +
314K ASP* 3.2 12.1 + - + +
316K ILE* 1.3 82.1 - - - +
318K LYS* 1.3 54.4 + - + +
320K VAL* 3.2 9.7 + - - +
321K THR* 2.7 37.0 + - - -
327K ILE* 3.6 21.1 - - + +
331K GLU* 3.4 44.2 - - - +
340K GLN* 3.4 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 318 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314K ASP* 2.7 47.8 + - - +
315K LYS* 3.2 13.7 + - + +
317K ASP* 1.3 77.0 - - + +
319K ILE* 1.3 57.1 + - + +
321K THR* 3.2 9.7 + - - -
322K SER* 2.9 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 319 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300K ASN* 3.2 34.8 + - + +
303K SER* 3.7 32.1 - - - +
304K LEU* 3.7 16.8 - - + +
307K ALA* 3.8 13.9 - - + -
315K LYS* 2.9 42.4 + - + +
316K ILE* 3.2 7.2 + - - +
318K LYS* 1.3 75.6 - - + +
320K VAL* 1.3 58.2 + - - +
322K SER* 3.2 9.8 + - - -
323K LEU* 2.9 28.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 320 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304K LEU* 4.1 16.2 - - + -
316K ILE 2.9 20.1 + - - +
317K ASP* 3.5 9.9 - - - +
319K ILE* 1.3 76.7 - - - +
321K THR* 1.3 62.9 + - - +
323K LEU* 3.2 23.1 + - - +
324K GLY 3.6 3.3 + - - -
325K LEU* 3.6 6.3 + - - +
326K LYS 3.4 26.2 - - - +
327K ILE* 3.8 15.0 - - + +
340K GLN* 5.3 7.2 - - + +
344K ILE* 4.0 26.7 - - + -
348K TRP* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 321 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317K ASP 2.7 23.5 + - - -
318K LYS* 3.3 10.2 - - - -
320K VAL* 1.3 78.1 - - - +
322K SER* 1.3 62.1 + - - +
324K GLY* 3.2 13.9 + - - -
325K LEU 4.1 10.7 + - - +
327K ILE* 3.2 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 322 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255K LYS* 4.3 11.8 + - - -
300K ASN* 3.6 15.0 + - - -
318K LYS* 2.9 16.5 + - - +
319K ILE* 3.4 10.6 - - - -
321K THR* 1.3 76.5 - - - +
323K LEU* 1.3 59.2 + - - +
324K GLY* 2.9 9.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247K HIS* 5.9 1.1 - - + -
251K ILE* 3.2 50.9 - - + +
297K ILE* 3.6 22.9 - - - +
300K ASN* 3.3 23.3 - - + +
301K ILE* 3.4 31.4 - - + +
304K LEU* 5.5 4.5 - - + -
319K ILE* 2.9 14.1 + - + +
320K VAL* 3.2 14.5 + - - +
322K SER* 1.3 74.0 - - - +
324K GLY* 1.3 58.5 + - - +
325K LEU* 3.6 4.6 + - + +
348K TRP* 3.6 26.9 - - + -
----------------------------------------------------------
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