Contacts of the helix formed by residues 142 - 150 (chain C) in PDB entry 2R2N
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 TYR 142 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLN* 2.7 36.5 + - - -
141C ALA* 1.3 73.1 - - - +
143C SER* 1.3 71.0 + - - +
144C GLY* 3.5 22.7 - - - -
145C THR* 2.5 52.4 + - + +
146C LEU* 3.2 5.9 + - - +
195C TYR* 4.1 6.6 + - - +
197C VAL* 5.0 1.6 - - + -
201C ASN* 4.7 2.2 - - - +
202C ASN* 3.1 39.6 + - - +
387C PHE* 4.3 1.6 - + - -
426C PMP 3.4 62.3 + + + -
428C KYN 4.0 17.9 + - + +
293D LEU* 4.9 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C ALA 3.2 3.2 + - - -
142C TYR* 1.3 80.1 - - - +
144C GLY* 1.3 58.4 + - - +
146C LEU* 3.2 6.0 + - - +
147C GLN* 2.9 36.5 + - - +
386C ALA* 3.1 31.9 - - - -
387C PHE* 3.8 9.6 - - - -
428C KYN 4.9 0.9 + - - -
18D PRO* 4.1 17.4 - - - +
19D ILE* 3.4 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLN* 4.0 8.8 - - - +
142C TYR* 3.3 28.3 - - - -
143C SER* 1.3 80.7 + - - +
145C THR* 1.3 57.4 + - - +
147C GLN* 4.0 6.4 - - - +
148C SER* 3.1 26.9 + - - -
289D GLN 6.0 1.1 - - - -
290D VAL* 4.1 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLN* 4.5 5.8 - - - +
121C LEU* 4.8 2.9 - - + -
125C PHE* 4.4 13.9 - - + -
137C LEU* 5.5 0.3 - - - +
141C ALA* 4.6 2.1 - - - +
142C TYR* 2.5 38.3 + - + +
144C GLY* 1.3 74.9 - - - +
146C LEU* 1.3 60.6 + - - +
148C SER* 3.1 7.7 + - - -
149C LEU* 2.9 38.7 + - - +
195C TYR* 2.8 51.6 + - + +
230C ASP* 4.2 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LEU* 4.3 18.2 - - + -
139C GLU* 5.3 0.7 - - + -
141C ALA* 3.9 23.3 - - + +
142C TYR 3.2 8.7 + - - +
143C SER* 3.2 6.8 + - - +
145C THR* 1.3 80.8 + - - +
147C GLN* 1.3 63.8 - - + +
149C LEU* 3.3 3.5 + - - +
150C HIS* 3.0 30.0 + - - +
156C ILE* 4.3 8.0 - - + +
386C ALA 3.9 8.7 - - - +
387C PHE 3.5 34.8 - - - +
388C TYR 3.6 18.4 - - - +
389C VAL* 4.0 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C SER* 2.9 23.6 + - - +
144C GLY* 4.0 3.1 - - - +
146C LEU* 1.3 77.5 - - - +
148C SER* 1.3 61.8 + - - +
150C HIS* 4.2 5.3 - - - +
151C PRO* 2.9 27.5 - - - +
386C ALA 5.6 3.4 + - - -
391C SER* 6.2 1.8 - - - -
14D ARG* 5.0 1.0 + - - -
15D ASN* 3.0 46.6 + - - +
17D SER* 3.6 24.2 + - - +
18D PRO* 4.9 8.7 - - + +
290D VAL* 3.8 21.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
118C GLN* 5.2 2.0 - - - -
122C CYS* 4.0 22.0 - - - +
125C PHE* 3.7 22.3 - - - +
144C GLY 3.1 20.2 + - - -
145C THR* 3.1 8.3 + - - -
147C GLN* 1.3 78.9 - - - +
149C LEU* 1.3 60.2 + - - +
151C PRO* 3.4 10.4 - - - +
152C LEU* 3.6 19.2 - - - +
14D ARG* 5.0 2.1 + - - -
290D VAL* 3.9 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C PHE* 3.7 33.0 - - + -
129C ILE* 3.4 32.3 - - + -
135C VAL* 4.7 4.0 - - + -
137C LEU* 3.7 30.1 - - + -
145C THR* 2.9 24.3 + - - +
146C LEU* 3.9 4.0 - - - +
148C SER* 1.3 76.6 - - - +
150C HIS* 1.3 65.5 + - - +
152C LEU* 3.3 18.7 + - - +
153C GLY 3.8 1.0 + - - -
154C CYS* 3.6 21.7 + - - +
156C ILE* 4.0 18.8 - - + -
193C PHE* 4.0 8.7 - - + -
195C TYR* 5.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C LEU 3.0 17.0 + - - +
147C GLN* 4.2 6.3 - - - +
149C LEU* 1.3 76.4 - - - +
151C PRO* 1.4 71.3 - - + +
152C LEU 3.2 1.0 + - - -
153C GLY* 3.3 12.3 + - - -
154C CYS 5.6 0.4 - - - +
156C ILE* 5.3 2.4 - - - +
13D ALA* 3.0 43.2 + - + +
14D ARG* 5.1 0.4 - - - -
15D ASN* 3.8 20.7 + - - -
----------------------------------------------------------
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