Contacts of the strand formed by residues 162 - 166 (chain C) in PDB entry 2X1L
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 GLN 162 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LEU* 3.9 33.8 - - + +
120C ASP* 3.3 21.6 - - - +
121C ALA* 3.7 7.8 + - - +
161C GLU* 1.3 70.8 - - - +
163C THR* 1.3 62.7 + - - +
211C THR* 3.9 9.5 + - + +
225C HIS* 3.2 21.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C LEU* 3.8 6.3 - - - -
120C ASP 2.9 30.4 + - - +
122C TYR* 3.4 18.1 - - + +
161C GLU* 3.5 33.1 + - + +
162C GLN* 1.3 79.1 - - - +
164C TYR* 1.3 61.4 + - - +
165C PHE* 3.4 8.1 - - - -
207C SER* 2.8 25.1 + - - +
209C SER* 3.3 27.4 - - - +
210C ARG* 4.6 1.8 - - - +
211C THR* 4.9 0.7 - - - +
225C HIS* 4.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 164 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C TRP* 4.1 14.6 - + + -
117C ILE* 3.8 22.9 - - + -
118C TYR* 3.4 18.2 - - - -
119C LEU* 3.8 27.4 - - + +
163C THR* 1.3 74.0 - - - +
165C PHE* 1.3 60.6 + - - +
207C SER* 3.5 5.0 + - - -
208C ILE* 2.8 27.5 + - + -
209C SER* 2.7 28.5 + - - +
219C VAL* 4.5 3.1 - - + -
222C HIS* 2.9 48.4 + + + -
225C HIS* 3.7 33.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 165 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ASP 3.3 1.2 - - - +
117C ILE* 3.3 7.8 - - - +
118C TYR* 2.7 57.4 + - + +
120C ASP* 3.8 22.2 - - + -
121C ALA 3.5 25.8 - - - -
122C TYR* 3.8 23.6 - + + -
163C THR* 3.4 33.2 - - - -
164C TYR* 1.3 74.9 - - - +
166C PHE* 1.3 59.9 + - - +
205C ASP* 4.1 14.4 - - + -
206C LEU 3.3 12.6 - - - -
207C SER* 3.5 26.5 - - - -
208C ILE* 3.9 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 166 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C MET* 3.7 23.6 - - - -
116C ASP* 3.3 18.8 - - + -
117C ILE* 4.7 4.9 - - + -
165C PHE* 1.3 72.8 - - - +
167C ARG* 1.3 62.4 + - - +
168C LEU* 2.8 30.7 + - + -
171C TYR* 4.0 10.1 - + - -
205C ASP* 3.4 6.1 - - - +
206C LEU* 2.7 33.5 + - + +
208C ILE* 3.8 27.0 - - + +
276C ALA* 3.4 42.6 - - + -
277C PHE* 3.6 20.0 - + + -
280C SER* 3.6 23.6 - - - -
----------------------------------------------------------
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