Contacts of the helix formed by residues 149 - 156 (chain C) in PDB entry 3P9K
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 ILE 149 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C GLY* 1.3 75.3 - - - +
150C PRO* 1.3 76.5 - - + +
151C PHE 3.8 3.6 - - - +
152C ASN* 3.2 42.0 + - - +
153C LYS* 3.0 25.7 + - - +
318C LEU 4.4 1.6 - - - +
320C HIS 3.6 22.4 - - - +
321C ASN 3.8 12.6 - - - +
322C PRO* 3.4 34.5 - - + -
323C GLY 4.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C SER 3.4 24.2 - - - +
139C TYR* 3.5 21.2 - - + +
140C LEU* 3.9 22.0 - - + +
143C ALA* 3.6 21.5 - - + -
148C GLY 4.0 1.3 - - - +
149C ILE* 1.3 82.4 - - + +
151C PHE* 1.3 61.9 + - - +
153C LYS* 3.2 8.1 + - + +
154C ALA* 3.2 17.3 + - - +
318C LEU 3.4 23.6 - - - +
319C ALA* 3.2 15.9 - - + +
73D MET* 5.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C VAL* 4.3 5.2 - - + -
133C LEU* 4.3 16.2 - - + -
136C SER* 3.5 19.7 + - - +
149C ILE 3.2 0.6 - - - -
150C PRO* 1.3 75.3 - - - +
152C ASN* 1.3 59.6 + - - +
154C ALA* 2.8 21.2 + - - +
155C TYR* 3.0 46.1 + + + -
157C MET 3.3 18.8 - - - -
158C SER 3.6 3.4 - - - -
159C ALA* 3.3 36.1 - - + -
162C TYR* 3.6 29.4 - + + -
163C HIS* 6.0 0.4 - + - -
169C PHE* 5.8 1.3 - + - -
319C ALA 3.0 14.1 + - - +
320C HIS* 3.6 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ILE* 3.2 47.9 + - + +
151C PHE* 1.3 79.2 - - - +
153C LYS* 1.3 58.5 + - + +
156C GLY* 2.7 32.7 + - - -
157C MET* 3.3 26.0 + - - +
158C SER* 3.7 24.1 + - - +
320C HIS 4.2 2.8 + - - -
322C PRO* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C TYR* 3.9 32.1 + - + +
142C ASP* 3.9 15.0 + - + +
143C ALA* 3.4 31.2 - - + +
146C ASP* 4.3 10.3 + - - +
147C GLY 2.8 30.1 + - - -
148C GLY* 4.3 4.4 - - - -
149C ILE 3.0 17.9 + - - +
150C PRO* 3.4 8.3 - - + +
151C PHE 3.1 0.2 - - - -
152C ASN* 1.3 77.5 - - + +
154C ALA* 1.3 59.8 + - - +
156C GLY* 4.7 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C GLU* 4.0 18.0 - - + +
139C TYR* 3.3 38.1 + - + -
150C PRO 3.2 5.1 + - - +
151C PHE* 2.8 11.8 + - - +
153C LYS* 1.3 79.4 - - - +
155C TYR* 1.3 75.4 + - + +
156C GLY 3.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C LYS 4.0 0.5 + - - -
132C VAL* 2.6 44.6 + - + +
135C GLU* 3.1 27.9 - - + +
136C SER* 5.0 1.1 - - - -
151C PHE* 3.0 54.7 + + + +
154C ALA* 1.3 85.4 - - + +
156C GLY* 1.3 64.1 + - - +
157C MET* 3.4 16.6 + - + +
162C TYR* 3.6 37.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C ASN* 2.7 22.7 + - - -
153C LYS 4.5 0.8 + - - -
154C ALA 3.7 1.2 - - - -
155C TYR* 1.3 71.4 - - - +
157C MET* 1.3 62.7 + - - +
----------------------------------------------------------
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