Contacts of the helix formed by residues 144 - 157 (chain C) in PDB entry 2JG1
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 ASP 144 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C ASN* 3.6 15.9 + - - +
143C GLN* 1.3 75.3 + - - +
145C TYR* 1.3 52.1 + - - +
146C TYR 3.4 1.6 - - - -
147C ALA* 3.1 18.4 + - + -
148C GLN* 2.6 65.3 + - + +
171C THR* 4.6 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 3.6 32.3 - - + -
58C PHE* 4.0 2.1 - + - -
114C ALA* 2.6 36.6 + - + -
117C PHE* 3.6 20.9 - + - +
118C ILE* 3.5 21.5 - - + +
137C LEU* 4.9 7.9 - - + -
141C LEU* 3.7 39.9 - - + -
142C ASN* 3.3 17.8 + - + +
143C GLN 3.2 4.4 + - - -
144C ASP* 1.3 77.9 + - - +
146C TYR* 1.3 62.8 + - - +
148C GLN* 3.4 19.4 + - - +
149C ILE* 3.1 39.0 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
5C LEU* 5.4 0.6 + - + -
7C LEU* 3.6 27.4 + - + +
133C ILE* 3.4 34.9 - - + +
134C SER 4.2 4.7 + - - -
135C GLY 2.7 29.0 + - - -
136C SER 3.6 6.2 + - - -
137C LEU* 3.2 32.7 - - + +
143C GLN 4.8 2.5 + - - +
145C TYR* 1.3 75.1 - - - +
147C ALA* 1.3 60.3 + - - +
149C ILE* 3.2 10.6 + - + +
150C ILE* 2.9 41.1 + - + +
162C LEU* 4.1 11.2 - - + -
164C CYS* 4.1 9.6 - - + -
168C THR* 3.8 24.9 - - + +
172C VAL* 3.8 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C GLN 5.3 0.2 + - - -
144C ASP* 3.1 24.2 + - + +
146C TYR* 1.3 77.9 - - - +
148C GLN* 1.3 55.0 + - - +
150C ILE* 3.4 5.6 + - - +
151C GLU* 2.9 31.5 + - - +
171C THR* 5.2 4.7 - - + +
172C VAL* 4.5 8.6 - - + +
175C ASN* 3.8 41.0 - - + +
177C TYR* 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ILE* 4.4 16.2 - - + +
142C ASN* 4.9 8.3 - - - +
144C ASP* 2.6 54.9 + - + +
145C TYR* 3.4 21.3 - - - +
147C ALA* 1.3 72.6 - - - +
149C ILE* 1.3 61.9 + - - +
151C GLU* 3.5 15.3 - - - +
152C ARG* 3.2 54.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LEU* 4.0 16.6 - - + -
7C LEU* 4.2 9.9 - - + -
117C PHE* 4.3 7.2 - - + -
118C ILE* 4.0 17.0 - - + -
121C PHE* 3.4 36.4 - - + -
133C ILE* 3.8 22.9 - - + -
145C TYR* 3.1 38.6 + - + +
146C TYR* 3.2 13.9 + - + +
148C GLN* 1.3 76.7 - - - +
150C ILE* 1.3 66.4 + - - +
152C ARG* 3.2 8.6 + - - +
153C CYS* 3.1 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C ILE* 4.2 7.9 - - + -
146C TYR* 2.9 24.1 + - + +
147C ALA* 3.9 3.6 - - - +
149C ILE* 1.3 75.8 - - - +
151C GLU* 1.3 56.5 + - - +
153C CYS* 3.2 7.9 + - - +
154C GLN* 2.8 31.3 + - + +
160C VAL* 4.1 26.2 - - + -
162C LEU* 4.3 18.8 - - + -
172C VAL* 3.8 29.8 - - + -
177C TYR* 3.4 22.0 - - - +
178C LYS 3.7 19.5 - - - +
179C PRO* 4.0 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C ALA 2.9 17.2 + - - +
148C GLN* 3.5 16.4 - - - +
149C ILE 3.3 0.2 - - - -
150C ILE* 1.3 77.2 - - - +
152C ARG* 1.3 68.5 + - + +
154C GLN* 3.4 2.4 + - - +
155C ASN* 3.1 37.5 + - - +
177C TYR* 3.5 56.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ILE* 3.5 22.5 - - - +
119C LYS* 5.2 2.6 - - - +
121C PHE* 4.4 5.8 - - + -
122C GLU* 2.3 47.4 + - + +
125C MSE 3.7 16.2 - - + -
148C GLN* 3.2 41.7 + - - +
149C ILE* 3.2 12.4 + - - +
151C GLU* 1.3 83.3 + - + +
153C CYS* 1.3 64.6 + - - +
155C ASN* 3.5 10.6 + - - +
156C LYS* 3.4 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PHE* 3.6 24.2 - - - -
125C MSE 3.9 18.6 - - - -
131C VAL* 4.1 10.8 - - - -
149C ILE* 3.1 21.7 + - - -
150C ILE 3.2 4.5 + - - +
152C ARG* 1.3 73.5 - - - +
154C GLN* 1.3 59.4 + - - +
156C LYS 3.1 1.9 + - - -
157C GLY 2.9 24.1 + - - -
158C VAL* 3.0 27.9 + - + +
160C VAL* 3.5 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C ILE* 2.8 23.5 + - + +
151C GLU* 3.6 7.6 - - - +
152C ARG 3.4 0.2 - - - -
153C CYS* 1.3 72.2 - - - +
155C ASN* 1.3 63.9 + - - +
157C GLY* 3.2 14.0 + - - +
158C VAL 4.5 1.5 + - - -
160C VAL* 6.5 0.2 - - + -
177C TYR* 4.4 15.3 - - + -
178C LYS* 2.7 45.8 + - - +
179C PRO 5.3 0.2 - - - -
180C THR* 5.3 4.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C GLU* 3.1 32.0 + - - +
152C ARG* 3.7 10.7 - - - +
153C CYS 3.2 0.4 - - - -
154C GLN* 1.3 78.5 - - - +
156C LYS* 1.3 66.1 + - + +
177C TYR* 4.7 9.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C MSE 3.8 29.8 - - + -
126C GLU* 4.9 26.2 + - + +
152C ARG 3.4 16.1 + - - +
153C CYS 3.1 3.7 + - - +
155C ASN* 1.3 84.4 - - + +
157C GLY* 1.3 62.2 + - - +
158C VAL* 3.5 9.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C CYS 2.9 4.5 + - - -
154C GLN* 3.2 13.9 + - - -
155C ASN 3.5 0.6 - - - -
156C LYS* 1.3 78.6 - - - +
158C VAL* 1.3 61.5 + - - +
159C PRO* 3.6 8.2 - - - +
----------------------------------------------------------
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