Contacts of the helix formed by residues 389 - 396 (chain C) in PDB entry 5Y9F
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 MET 389 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C LEU* 3.6 47.6 - - + +
385C THR 3.3 13.7 - - - +
386C THR* 5.6 4.0 - - - -
388C VAL* 1.3 79.8 - - - +
390C SER* 1.3 55.4 + - - +
391C TYR 3.3 2.5 - - - +
392C ILE* 3.6 19.1 - - - +
393C HIS* 2.7 29.3 + - - +
400C LEU* 3.2 29.3 - - + +
405C PHE* 4.0 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 390 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C THR* 5.9 0.4 - - - -
387C GLU* 2.8 31.4 + - - -
388C VAL 2.6 11.7 + - - -
389C MET* 1.3 77.3 - - - +
391C TYR* 1.3 54.6 + - - -
393C HIS* 3.3 8.9 + - - +
394C ASN* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 391 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LYS 3.9 15.9 - - - -
21C VAL* 3.3 14.5 - - - +
22C VAL* 2.9 52.1 + - + -
27C TYR* 3.4 41.1 + + - -
242C TYR* 3.7 20.6 + + - -
387C GLU 3.0 15.1 + - - +
388C VAL* 4.3 7.9 - - + -
390C SER* 1.3 79.8 + - - +
392C ILE* 1.3 67.2 + - + +
394C ASN* 3.4 6.1 + - + +
395C MET* 2.9 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 392 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C TYR* 4.4 13.2 - - + -
325C TRP* 4.7 8.1 - - + -
382C ILE* 4.0 27.1 - - + -
384C LEU* 4.6 7.9 - - + -
388C VAL* 4.4 4.7 - - + -
389C MET* 3.3 25.4 + - - +
390C SER 3.3 0.2 - - - -
391C TYR* 1.3 88.0 - - + +
393C HIS* 1.3 57.8 + - - +
395C MET* 4.1 7.6 - - + -
396C ASN 2.7 34.8 + - - +
399C ILE* 3.6 36.8 - - + -
400C LEU* 3.9 11.7 - - + -
403C TRP* 4.6 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 393 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C MET 2.7 21.0 + - - +
390C SER* 3.5 10.2 + - - +
391C TYR 3.2 0.2 - - - -
392C ILE* 1.3 73.4 - - - +
394C ASN* 1.3 65.5 + - - +
396C ASN 3.6 4.9 + - - -
397C THR* 3.2 62.4 + - + +
400C LEU* 4.1 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 394 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C TYR* 4.1 11.4 + - - +
390C SER 2.9 16.4 + - - +
391C TYR* 3.9 6.7 - - + +
392C ILE 3.4 0.2 - - - -
393C HIS* 1.3 81.5 + - - +
395C MET* 1.3 62.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 395 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C THR* 5.9 1.3 - - + -
27C TYR* 4.1 17.3 - - - +
242C TYR* 3.4 51.6 + - + +
244C ASP* 3.3 29.6 - - - +
320C ASN* 4.8 0.9 - - + +
325C TRP* 3.5 32.3 - - + +
391C TYR* 2.9 23.0 + - + +
392C ILE* 3.4 9.4 - - + +
393C HIS 4.1 0.2 - - - -
394C ASN* 1.3 81.5 - - - +
396C ASN* 1.3 78.7 + - + +
399C ILE* 4.8 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 396 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ASP* 5.1 6.9 + - - -
326C HIS* 4.7 3.9 - - - -
392C ILE 2.7 21.1 + - - +
393C HIS* 4.3 0.2 - - - -
395C MET* 1.3 89.7 + - - +
397C THR* 1.3 66.6 + - - +
398C THR* 3.1 22.3 - - + +
399C ILE* 3.1 38.6 + - + +
400C LEU 4.1 1.6 + - - -
----------------------------------------------------------
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