Contacts of the helix formed by residues 2254 - 2259 (chain A) in PDB entry 4YPU
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 ASP2254 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2218A HIS* 3.6 2.4 - - - -
2219A SER 3.9 14.4 - - - +
2220A CYS 4.6 1.4 - - - +
2222A PRO* 3.8 18.5 - - + +
2224A CYS 4.6 0.4 + - - -
2253A TYR* 1.3 75.6 - - - +
2255A TYR* 1.3 59.4 + - - +
2256A ASN* 3.2 22.3 + - - +
2257A PHE* 3.8 25.3 + - + -
2258A HIS* 3.0 27.8 + - + -
2276A ARG* 2.7 33.6 + - - -
2157B LYS* 5.3 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR2255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2193A HIS 5.0 2.0 - - - -
2216A ILE 2.5 21.2 + - - -
2217A ASN* 3.6 0.9 - - - -
2218A HIS* 3.0 49.2 + - + +
2253A TYR* 3.4 42.2 - + - -
2254A ASP* 1.3 71.2 - - - +
2256A ASN* 1.3 62.5 + - - +
2258A HIS 2.8 1.9 + - - -
2259A SER* 2.5 55.6 + - - +
2266A GLN* 6.3 0.4 - - - -
2279A ILE* 3.9 19.3 - - + -
2304A SAM 3.2 48.4 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2218A HIS* 3.8 11.5 + - - -
2254A ASP* 3.2 8.8 + - - +
2255A TYR* 1.3 77.3 - - - +
2257A PHE* 1.3 69.4 + - + +
2258A HIS 3.0 0.3 + - - -
2259A SER* 3.8 11.2 + - - +
2261A ASN* 5.8 0.2 - - - +
2276A ARG* 3.0 42.5 - - - +
2278A ILE 4.7 4.0 + - - -
2279A ILE* 3.5 3.6 - - - +
2280A GLY* 2.6 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2197A ASN* 5.6 1.0 - - - +
2254A ASP* 3.8 30.7 + - + +
2255A TYR 3.3 0.8 - - - -
2256A ASN* 1.3 82.2 - - + +
2258A HIS* 1.3 83.1 + - + +
2276A ARG* 4.8 7.6 - - - -
2071B LYS* 6.1 2.9 - - - -
2142B LEU 4.9 4.7 - - - -
2143B GLU* 4.6 15.9 - - + -
2144B ARG* 4.6 34.5 - - + -
2157B LYS* 5.9 4.9 - - - -
2212B GLU* 5.0 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS2258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2196A LEU* 3.5 22.4 - - + -
2197A ASN* 2.6 49.9 + - - +
2225A GLU* 5.2 4.7 - - + -
2226A MET* 3.4 46.6 + - + +
2237A ILE* 6.6 0.2 - - + -
2253A TYR* 4.0 11.4 - + - -
2254A ASP* 3.0 27.5 + - + +
2255A TYR 2.8 12.1 + - - +
2256A ASN 4.3 0.2 - - - -
2257A PHE* 1.3 91.9 - - + +
2259A SER* 1.3 54.3 + - - +
2071B LYS* 5.6 5.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER2259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2195A CYS* 3.4 25.7 + - - -
2196A LEU* 4.8 2.4 - - - +
2197A ASN* 3.5 2.3 - - - +
2253A TYR* 5.4 0.5 + - - -
2255A TYR* 2.5 52.5 + - - +
2256A ASN* 4.2 8.6 - - - +
2258A HIS* 1.3 70.9 - - - +
2260A PHE* 1.3 69.8 + - - +
2261A ASN* 3.4 7.4 + - - +
2264A LEU* 5.5 4.9 - - - -
2279A ILE* 6.0 0.9 - - - -
----------------------------------------------------------
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