Contacts of the helix formed by residues 146 - 156 (chain C) in PDB entry 1NPP
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 ASN 146 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 5.6 0.2 - - - +
42C LEU* 3.7 23.0 - - - +
144C HIS* 3.6 15.6 + - + +
145C MET* 1.3 75.1 - - - +
147C ASP* 1.3 67.3 + - - +
148C LYS* 3.1 11.8 + - - +
149C LEU* 2.8 36.8 + - - +
150C LEU* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C ASN* 1.3 75.5 - - - +
148C LYS* 1.3 57.6 + - - +
150C LEU* 3.3 19.5 - - - +
151C MET* 2.9 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C GLU* 3.4 44.1 + - - +
39C LEU* 3.7 23.9 - - + +
146C ASN* 3.1 13.1 + - - +
147C ASP* 1.3 74.7 - - - +
149C LEU* 1.3 66.3 + - - +
151C MET* 3.1 8.8 + - + +
152C ALA* 2.9 22.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
30C LEU* 5.3 0.9 - - + -
34C LEU* 4.1 26.5 - - + -
39C LEU* 4.3 8.0 - - + +
42C LEU* 4.8 8.1 - - + -
43C VAL* 4.5 9.9 - - + -
141C ILE* 4.1 4.5 - - + -
143C ALA* 3.9 24.7 - - + -
144C HIS 3.9 10.1 - - - +
145C MET* 3.8 30.1 - - + -
146C ASN* 2.8 26.6 + - - +
148C LYS* 1.3 72.0 - - - +
150C LEU* 1.3 64.7 + - - +
152C ALA* 3.2 3.8 + - + -
153C ILE* 2.9 41.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C MET* 3.2 29.6 - - + -
146C ASN 3.0 15.9 + - - +
147C ASP* 3.3 26.2 - - - +
149C LEU* 1.3 78.4 - - - +
151C MET* 1.3 65.5 + - + +
153C ILE* 3.4 5.4 + - + +
154C GLU* 3.0 28.4 + - - +
162C PRO* 3.9 20.6 - - + +
164C MET* 5.9 3.4 - - - -
169C PRO* 3.9 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C GLU* 5.5 1.3 - - - +
147C ASP* 2.9 22.5 + - + +
148C LYS* 3.1 11.6 + - + +
150C LEU* 1.3 81.8 - - + +
152C ALA* 1.3 65.5 + - - +
154C GLU* 3.5 20.3 + - + +
155C LYS* 3.0 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 4.7 1.1 - - + -
33C VAL* 3.7 20.9 - - + +
34C LEU* 4.7 5.4 - - + -
37C GLU* 4.4 4.7 + - - +
39C LEU* 3.7 21.8 - - + -
148C LYS 2.9 16.5 + - - +
149C LEU* 3.2 13.0 + - + +
151C MET* 1.3 72.4 - - - +
153C ILE* 1.3 61.3 + - - +
155C LYS* 3.3 13.9 + - - +
156C THR* 2.9 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 4.0 21.5 - - + -
30C LEU* 4.2 12.3 - - + -
141C ILE* 4.0 16.2 - - + -
145C MET* 4.4 3.8 - - + -
149C LEU* 2.9 49.7 + - + +
150C LEU* 3.5 6.7 - - - +
152C ALA* 1.3 76.2 - - - +
154C GLU* 1.3 63.6 + - - +
156C THR* 3.1 14.7 + - - -
159C VAL* 3.4 36.7 - - + +
161C ARG* 4.2 19.1 - - - -
162C PRO* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C LEU 3.0 16.3 + - - +
151C MET* 3.9 20.4 - - + +
152C ALA 3.4 0.2 - - - -
153C ILE* 1.3 78.8 - - + +
155C LYS* 1.3 63.3 + - - +
156C THR 4.3 0.9 - - - +
159C VAL 4.1 7.1 - - - +
160C PHE 4.4 18.0 - - - +
161C ARG* 6.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C VAL* 4.6 13.9 - - + -
37C GLU* 3.2 37.5 + - - +
151C MET* 3.0 29.4 + - - +
152C ALA* 3.5 5.1 - - - +
153C ILE 3.1 0.2 - - - -
154C GLU* 1.3 82.4 + - - +
156C THR* 1.3 62.2 + - - +
157C PRO* 3.4 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ASN* 3.4 30.7 - - + +
30C LEU* 3.4 20.9 - - - +
33C VAL* 3.5 18.3 - - + +
152C ALA 2.9 15.5 + - - -
153C ILE 3.1 9.9 + - - -
154C GLU 4.3 1.0 - - - +
155C LYS* 1.3 76.6 - - - +
157C PRO* 1.3 75.5 - - + +
158C HIS 3.3 0.5 + - - -
159C VAL* 3.0 37.0 + - + +
----------------------------------------------------------
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