Contacts of the strand formed by residues 2176 - 2178 (chain C) in PDB entry 1KY5
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 ALA2176 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2152C ILE* 3.2 22.4 - - + +
2163C LEU* 3.2 36.1 - - + -
2172C LEU* 4.7 1.8 - - + -
2174C VAL 4.6 1.8 - - - +
2175C PRO* 1.3 78.7 - - - +
2177C ILE* 1.3 57.2 - - - +
2178C ASN 4.1 0.2 - - - -
2371C LEU* 4.8 0.7 - - - -
2381C GLY 3.0 11.0 + - - +
2382C VAL* 3.2 4.4 - - - -
2383C HIS* 2.8 36.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2152C ILE 2.8 11.3 + - - +
2153C SER* 4.1 1.1 - - - +
2154C GLU* 3.4 21.5 + - - +
2163C LEU* 5.5 0.4 - - - -
2176C ALA* 1.3 76.8 - - - +
2178C ASN* 1.3 70.3 + - - +
2179C VAL* 2.9 11.9 + - + +
2367C ALA* 4.1 31.6 - - + -
2370C GLU* 4.2 3.8 - - + -
2371C LEU* 3.4 32.1 - - + -
2378C TYR* 3.6 36.3 - - + +
2383C HIS 3.1 9.0 - - - +
2384C PHE 4.7 2.5 - - - +
2385C LEU* 4.1 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2178 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2154C GLU* 5.2 0.2 - - - -
2160C VAL* 3.2 33.5 - - + +
2163C LEU* 5.9 0.4 - - - -
2164C TYR* 2.9 23.9 + - - +
2176C ALA 4.1 0.8 + - - -
2177C ILE* 1.3 73.1 - - - +
2179C VAL* 1.3 59.0 + - - +
2180C ASN 3.3 0.2 + - - -
2181C ASP* 2.5 58.0 + - - +
2182C SER* 4.2 6.1 + - - -
2382C VAL* 4.3 9.4 - - + +
2383C HIS 2.5 18.3 + - - +
2384C PHE* 3.3 15.8 - - + -
2385C LEU* 4.3 3.5 + - - +
----------------------------------------------------------
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