Contacts of the helix formed by residues 145 - 156 (chain C) in PDB entry 1XHU
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 ALA 145 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ILE 3.4 4.0 + - - -
144C SER* 1.3 71.2 - - - +
146C TYR* 1.3 56.3 + - - +
149C ALA 2.9 17.0 + - - -
200C ILE* 3.4 31.6 - - + -
202C TRP* 5.4 0.2 - - + -
206C MET* 2.7 24.3 + - + +
208C ILE* 3.5 19.3 - - + +
230C TYR* 2.6 25.0 + - - +
234C PHE* 3.0 12.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C SER* 3.5 6.5 + - - +
145C ALA* 1.3 78.3 - - - +
147C LYS* 1.3 58.0 + - - +
149C ALA* 2.7 23.0 + - + +
150C GLN* 2.9 41.3 + - + +
206C MET* 4.1 12.8 + - + +
234C PHE* 3.4 16.3 - + + -
248D LYS* 2.9 40.7 + - - +
249D PHE* 3.3 35.2 - + + -
253D PHE* 3.8 21.1 - + - -
5K G 4.6 9.2 - - - -
6K T 3.9 16.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C PHE* 3.3 21.4 + - + -
88C LEU* 3.6 24.2 - - + -
110C ASN* 4.3 5.3 + - - +
112C THR* 2.3 41.5 + - + +
143C ILE* 5.4 4.0 - - + -
144C SER* 2.9 25.5 + - - +
146C TYR* 1.3 76.8 - - - +
148C LEU* 1.3 52.8 + - - +
150C GLN* 3.6 0.6 + - - +
151C THR* 2.5 36.7 + - - +
6K T 3.8 26.5 + - - +
7K C 3.3 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C ILE* 4.0 22.4 - - + -
144C SER 2.8 16.4 + - - +
145C ALA 3.5 1.8 - - - +
147C LYS* 1.3 74.1 - - - +
149C ALA* 1.3 57.1 + - - +
151C THR* 3.1 9.9 + - + -
152C CYS* 2.8 46.9 + - - -
166C ILE* 4.2 13.9 - - + -
190C LEU* 4.1 23.3 - - + -
191C PHE* 4.9 7.2 - - + -
198C LEU* 4.5 10.3 - - + -
208C ILE* 4.5 3.1 - - + -
226C TRP* 4.7 8.3 - - + +
230C TYR* 3.4 40.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ALA 2.9 6.4 + - - +
146C TYR* 2.7 16.9 + - + +
148C LEU* 1.3 76.7 - - - +
150C GLN* 1.3 55.0 + - - +
152C CYS 3.2 1.2 + - - -
153C ALA 2.9 21.0 + - - -
230C TYR* 3.5 11.4 - - - -
231C LEU* 3.2 14.5 - - + +
234C PHE* 3.5 44.4 - - + -
253D PHE* 3.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C PHE* 3.4 39.7 - - + -
146C TYR* 2.9 47.0 + - + +
147C LYS 3.8 0.9 - - - +
149C ALA* 1.3 71.5 - - - +
151C THR* 1.3 60.3 + - - +
153C ALA* 2.7 23.9 + - - +
154C LYS* 2.8 14.5 + - - +
253D PHE* 3.7 23.1 - - + -
6K T 4.0 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C THR* 4.6 4.0 - - + +
87C PHE* 3.2 18.6 - - - -
88C LEU* 3.2 33.4 - - + +
147C LYS* 2.5 25.5 + - - +
148C LEU* 3.4 18.9 - - + -
150C GLN* 1.3 76.6 - - - +
152C CYS* 1.3 59.4 + - - +
154C LYS* 3.7 4.9 + - - +
155C MET* 2.9 31.1 + - + +
164C PHE* 3.6 21.3 - - + -
166C ILE* 5.2 3.4 - - + -
191C PHE* 5.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C LEU* 2.8 29.5 + - - +
149C ALA 3.5 1.8 - - - +
151C THR* 1.3 76.8 - - - +
153C ALA* 1.3 64.8 + - - +
154C LYS 3.3 0.2 - - - -
155C MET* 3.6 12.0 + - - +
156C ILE 3.4 15.4 + - - -
191C PHE* 5.8 0.2 - - - -
226C TRP* 3.9 23.6 - - - -
227C ALA* 3.9 8.6 - - - +
230C TYR* 3.3 30.1 - - + -
231C LEU* 3.4 33.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ALA 2.9 4.0 + - - -
150C GLN* 2.7 16.7 + - - +
152C CYS* 1.3 71.9 - - - +
154C LYS* 1.3 61.4 + - - +
156C ILE 3.5 2.3 + - - -
157C ASP* 3.3 16.6 + - - +
231C LEU* 3.7 1.5 - - - +
253D PHE* 3.3 33.0 - - + -
256D TYR* 2.6 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C PRO* 5.2 4.7 - - + -
84C THR* 3.4 28.3 - - + +
87C PHE* 5.8 5.6 - - + -
150C GLN 2.8 13.2 + - - +
151C THR* 4.0 5.2 - - - +
153C ALA* 1.3 74.7 - - - +
155C MET* 1.3 54.9 + - - +
157C ASP* 2.8 26.1 + - - -
158C ASN* 2.6 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C THR* 3.9 6.5 - - + +
151C THR* 2.9 25.5 + - - +
152C CYS* 3.7 16.2 - - - +
153C ALA 3.3 0.2 - - - -
154C LYS* 1.3 77.5 - - - +
156C ILE* 1.3 56.1 + - - +
157C ASP 3.1 4.5 + - - -
158C ASN* 3.6 14.7 - - - +
159C LYS 3.6 10.0 + - - -
160C GLU 3.9 14.5 + - - +
161C PHE* 3.6 27.3 - - + -
164C PHE* 3.2 40.4 - - + -
191C PHE* 4.6 4.5 - - + -
223C ARG* 3.4 35.4 - - + +
226C TRP* 4.7 9.9 - - - -
227C ALA* 4.5 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C CYS 3.4 8.6 + - - +
154C LYS 3.2 1.0 - - - -
155C MET* 1.3 76.4 - - - +
157C ASP* 1.3 77.8 + - - +
158C ASN 3.8 1.1 - - - -
159C LYS 5.1 1.1 - - - -
161C PHE* 4.1 15.9 - - + -
227C ALA* 4.7 9.0 - - + -
228C LYS* 5.0 13.5 - - + +
231C LEU* 4.8 0.2 - - + -
256D TYR* 3.3 52.3 - - + -
----------------------------------------------------------
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