Contacts of the strand formed by residues 152 - 156 (chain P) in PDB entry 1KYO
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 TRP 152 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P LEU* 3.3 69.3 - - + +
99P ALA* 5.6 0.4 - - - -
101P ILE* 3.9 20.4 - - + -
118P ILE* 4.1 4.5 - - + -
119P ARG 3.5 18.4 - - - -
120P HIS* 3.3 46.0 - + + -
147P VAL* 3.9 9.3 - - - +
149P ASP* 2.9 40.7 + - - +
150P PRO 4.9 0.4 - - - -
151P GLN* 1.3 92.9 + - - +
153P LEU* 1.3 62.2 + - - +
154P ILE* 3.7 14.2 + - + +
205P TYR* 4.4 4.5 + - - -
207P PHE* 3.9 18.9 - + + -
53V ARG* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117P PHE 3.5 1.7 - - - +
118P ILE* 3.2 5.4 - - - -
119P ARG* 2.9 37.3 + - + +
121P ARG* 3.9 24.0 - - + +
146P ARG* 5.1 4.7 - - + +
147P VAL* 3.7 21.8 - - + -
151P GLN 3.9 1.2 + - - -
152P TRP* 1.3 69.8 - - - +
154P ILE* 1.3 63.5 + - - +
155P MET* 3.5 36.7 - - + +
176P TRP* 3.6 16.4 - - + -
187P ILE 3.5 20.0 - - - +
188P SER* 3.7 22.0 - - - +
202P ILE* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 154 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98P LEU* 5.2 0.9 - - + -
116P VAL* 3.9 14.1 - - + -
117P PHE 3.4 1.8 - - - -
118P ILE* 3.8 30.3 - - + -
146P ARG 5.0 0.9 - - - +
147P VAL* 4.9 0.4 - - - +
152P TRP* 3.7 13.5 + - + +
153P LEU* 1.3 81.3 - - - +
155P MET* 1.3 65.5 + - - +
202P ILE* 3.5 23.9 - - - +
203P PRO* 3.9 4.9 - - + +
205P TYR* 3.3 42.4 + - + -
207P PHE* 4.5 10.3 - - + -
212P VAL* 3.8 36.3 - - + -
214P VAL* 4.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 155 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116P VAL* 3.6 4.3 - - - +
117P PHE* 2.9 44.3 + - + +
146P ARG* 4.0 7.9 - - - +
153P LEU* 3.5 23.1 - - + -
154P ILE* 1.3 77.2 - - - +
156P LEU* 1.3 61.8 + - - +
176P TRP* 3.3 50.3 - - + -
189P GLY* 3.8 19.3 - - - -
200P LEU* 3.8 22.9 - - + -
201P GLU 3.4 9.6 - - - +
202P ILE* 4.1 9.4 - - + -
203P PRO* 3.4 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 156 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111P TRP* 4.1 26.2 - - + -
114P LYS* 4.6 21.3 - - + +
115P PRO 3.8 5.8 - - - +
116P VAL* 3.7 27.8 - - + -
155P MET* 1.3 71.8 - - - +
157P GLY* 1.3 57.1 + - - +
158P ILE* 2.9 27.0 + - + +
200P LEU* 3.8 22.6 - - - +
201P GLU* 2.7 45.5 + - + +
203P PRO* 3.7 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