Contacts of the helix formed by residues 141 - 148 (chain C) in PDB entry 2P80
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 MET 141 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LEU* 5.8 1.3 - - + -
138C PRO 2.9 8.1 + - - +
140C GLY* 1.3 82.9 - - - +
142C VAL* 1.3 63.8 + - - +
143C PRO* 3.7 3.4 - - - -
144C TRP* 3.7 16.3 + - + -
145C HIS* 2.8 29.1 + - + -
203C TYR* 4.2 11.4 - - + +
15D ALA* 2.7 40.4 - - + -
16D MET* 3.1 32.8 - - + -
81D HIS* 4.1 0.2 - - + -
84D MET* 2.3 59.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 3.3 23.1 - - + -
312A PHE* 3.3 42.0 - - + -
135C HIS* 5.8 0.9 - - + -
136C CYS 4.4 0.2 - - - +
137C ALA* 3.6 44.0 - - + +
138C PRO 3.8 7.4 - - - +
139C PRO* 4.8 2.0 - - + -
140C GLY 3.7 3.7 - - - +
141C MET* 1.3 77.1 - - - +
143C PRO* 1.3 77.3 - - + +
144C TRP 3.0 1.6 + - - -
145C HIS* 3.0 14.0 + - - +
146C VAL* 3.2 12.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 3.8 28.3 - - + +
309A ILE* 4.0 11.0 - - + +
312A PHE* 3.4 31.2 - - + -
313A GLU* 4.3 14.6 - - + +
140C GLY 5.6 0.7 - - - +
141C MET* 4.8 1.8 - - - -
142C VAL* 1.3 101.6 - - + +
144C TRP* 1.3 59.4 + - - +
146C VAL* 3.9 0.4 - - - +
147C VAL* 2.7 34.2 + - - +
210C MET* 3.7 17.0 - - + -
249C ASN* 4.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C HIS* 6.0 2.0 - - + -
62C MET* 3.9 23.6 - - + -
93C LEU* 3.9 23.6 - - + -
141C MET* 3.7 20.6 + - + +
142C VAL 3.0 0.8 + - - -
143C PRO* 1.3 82.8 - - - +
145C HIS* 1.3 68.6 + + - +
147C VAL* 2.8 22.2 - - + +
148C SER* 2.8 28.1 + - - -
199C PRO* 3.0 37.2 - - + -
200C GLY* 4.1 2.9 - - - -
202C ALA* 4.7 1.1 + - + +
203C TYR* 3.0 47.7 - + + +
206C THR* 4.3 24.7 + - + +
210C MET* 3.9 8.0 - - + +
15D ALA* 3.5 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C MET* 3.7 12.7 - - + -
93C LEU* 4.8 3.6 - - + -
94C MET 3.7 3.1 - - - -
95C HIS* 3.1 18.4 + + - -
136C CYS* 3.9 10.8 - - - +
138C PRO* 3.0 22.9 - - + +
141C MET* 2.8 26.9 - - + +
142C VAL 3.0 7.6 + - - +
144C TRP* 1.3 91.8 - + - +
146C VAL* 1.3 63.6 + - - +
148C SER* 3.4 7.3 + - - -
150C MET* 2.9 26.2 + - + +
345C CU 2.1 34.6 - - - -
84D MET* 3.0 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 3.0 30.1 - - + -
135C HIS* 4.3 13.0 - - + -
136C CYS 3.6 17.9 - - - +
142C VAL* 3.2 8.6 + - + +
143C PRO 4.0 3.4 - - - +
145C HIS* 1.3 76.0 - - - +
147C VAL* 1.3 65.3 + - - +
149C GLY 3.0 11.1 + - - -
150C MET 4.3 6.3 - - - -
151C ASN* 3.1 26.3 + - + +
181C GLN* 3.2 3.3 + - - -
248C ALA* 2.6 36.1 - - + +
249C ASN* 3.6 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ILE* 4.8 0.9 - - + -
143C PRO 2.7 27.7 + - - +
144C TRP* 2.8 29.4 - - + +
146C VAL* 1.3 68.0 - - - +
148C SER* 1.3 57.4 + - - +
149C GLY 2.8 6.7 + - - -
181C GLN* 3.3 10.4 + - - +
182C ASP 4.2 4.9 - - - +
183C PHE* 2.7 33.4 - - + -
184C TYR* 3.7 24.7 - - + +
206C THR* 5.2 3.4 - - + -
210C MET* 4.1 20.4 - - + -
249C ASN* 3.5 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C VAL* 4.7 4.5 - - - -
60C HIS 3.7 12.3 + - - -
61C ALA* 3.2 27.2 - - - +
62C MET* 3.2 37.6 + - - +
144C TRP* 2.8 32.8 + - - -
145C HIS 3.6 7.9 - - - -
146C VAL 3.1 0.8 - - - -
147C VAL* 1.3 77.3 - - - +
149C GLY* 1.3 56.9 + - - +
150C MET 3.5 0.2 - - - -
183C PHE* 3.9 8.8 - - - -
----------------------------------------------------------
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