Contacts of the helix formed by residues 116 - 133 (chain g) in PDB entry 3J7Y
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 116 (chain g).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83g PRO* 2.8 33.8 + - + +
84g TYR* 3.5 12.7 - - - +
114g GLU 3.6 1.8 + - - -
115g GLY* 1.3 69.7 - - - +
117g ILE* 1.3 64.6 + - - +
118g TRP* 3.2 20.5 + - - +
119g ALA* 3.4 25.9 + - - +
120g LEU 3.4 7.8 + - - -
142g GLU* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 117 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113g VAL* 3.7 38.1 - - + +
114g GLU* 4.5 0.9 - - - -
115g GLY 3.6 23.1 + - - +
116g ASP* 1.3 71.5 + - - +
118g TRP* 1.3 60.2 + - + +
120g LEU* 3.2 3.6 + - - +
121g GLN* 2.9 25.8 + - - +
140g VAL* 4.0 29.8 - - + -
141g ASN 4.9 5.2 - - - +
142g GLU* 3.4 36.7 + - + +
145g GLY* 4.3 9.2 - - - -
146g THR 4.1 12.3 - - - +
147g LEU* 4.6 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 118 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116g ASP* 3.2 15.7 - - - +
117g ILE* 1.3 77.1 - - - +
119g ALA* 1.3 56.0 + - - +
121g GLN* 3.2 27.0 + - - +
122g LYS* 2.9 29.4 + - - +
140g VAL* 3.7 12.6 - - + -
142g GLU* 3.6 34.4 + - + +
85o HIS* 3.5 33.7 - + - -
87o PHE* 3.9 30.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83g PRO* 3.7 30.1 - - + -
84g TYR* 3.9 4.9 - - + -
116g ASP* 3.4 20.2 + - - +
117g ILE 3.2 0.4 - - - -
118g TRP* 1.3 78.5 - - - +
120g LEU* 1.3 58.5 + - - +
122g LYS* 3.2 10.4 + - - +
123g ASP* 2.9 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84g TYR* 3.2 49.9 - - + -
86g VAL* 4.9 10.1 - - + -
110g ILE* 4.4 10.5 - - + -
113g VAL* 3.8 28.5 - - + -
116g ASP 3.4 3.5 + - - +
117g ILE 3.2 8.6 + - - +
119g ALA* 1.3 79.7 - - - +
121g GLN* 1.3 55.3 + - - +
123g ASP* 3.2 4.4 + - - +
124g VAL* 2.9 42.5 + - + +
147g LEU* 3.4 24.9 - - + -
160g TRP* 4.4 16.8 - - + -
161g LEU* 5.0 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117g ILE 2.9 12.6 + - - +
118g TRP* 3.2 27.9 + - - +
120g LEU* 1.3 77.9 - - - +
122g LYS* 1.3 70.1 + - - +
124g VAL* 3.2 6.2 + - - +
125g GLU* 2.9 38.3 + - - +
138g THR* 3.4 30.6 + - + +
140g VAL* 3.4 32.8 - - + +
147g LEU* 3.7 13.2 - - + -
85o HIS* 3.7 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118g TRP 2.9 12.4 + - - +
119g ALA* 3.3 13.0 - - - +
121g GLN* 1.3 85.5 + - - +
123g ASP* 1.3 56.4 + - - +
125g GLU* 3.2 12.4 + - + +
126g ASP* 2.9 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 123 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84g TYR* 3.0 29.6 + - - +
119g ALA* 2.9 20.6 + - - +
120g LEU* 3.2 9.2 + - - +
122g LYS* 1.3 76.8 - - - +
124g VAL* 1.3 57.4 + - - +
126g ASP* 3.2 10.4 + - - +
127g PHE* 2.9 29.5 + - - +
160g TRP* 3.6 8.0 - - + -
164g LYS* 3.6 20.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110g ILE* 4.1 11.2 - - + -
120g LEU* 2.9 33.4 + - + +
121g GLN* 3.4 10.1 - - - +
123g ASP* 1.3 75.6 - - - +
125g GLU* 1.3 58.6 + - - +
127g PHE* 3.2 5.8 + - - +
128g LEU* 2.9 51.8 + - + +
136g PRO* 5.8 0.2 - - + -
138g THR* 5.1 4.9 - - + -
147g LEU* 4.8 2.5 - - + -
149g ILE* 3.6 23.1 - - + -
157g LEU* 4.2 4.7 - - + -
160g TRP* 3.5 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121g GLN* 2.9 23.7 + - - +
122g LYS* 3.3 15.7 - - - +
124g VAL* 1.3 76.7 - - - +
126g ASP* 1.3 55.3 + - - +
128g LEU 3.3 0.2 + - - -
129g SER* 2.8 41.8 + - - -
135g THR* 3.9 25.4 - - + +
136g PRO* 3.8 28.9 - - + +
137g VAL 5.8 0.7 + - - +
138g THR* 4.9 13.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 126 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122g LYS* 2.9 33.9 + - - +
123g ASP* 3.4 13.9 - - - +
125g GLU* 1.3 80.9 - - - +
127g PHE* 1.3 60.8 + - - +
129g SER* 2.9 17.8 + - - -
130g PRO* 3.3 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 127 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123g ASP 2.9 13.4 + - - +
124g VAL 3.4 7.2 - - - +
126g ASP* 1.3 77.6 - - - +
128g LEU* 1.3 84.2 + - + +
130g PRO* 3.2 20.8 - - - +
131g LEU* 4.8 11.3 - - + +
156g GLU* 4.1 25.4 - - + -
157g LEU* 4.6 6.5 - - + -
160g TRP* 3.6 60.6 - + + +
163g GLU* 6.0 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 128 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124g VAL* 2.9 38.6 + - + +
125g GLU 3.3 0.2 + - - -
127g PHE* 1.3 100.6 - - + +
129g SER* 1.3 65.4 + - - +
130g PRO 3.4 1.3 - - - -
131g LEU* 3.3 26.7 + - + +
132g LEU* 3.4 16.0 + - + +
136g PRO* 3.6 16.6 - - + -
149g ILE* 4.2 13.7 - - + -
153g PHE* 3.8 51.8 - - + -
156g GLU* 4.4 1.1 - - - +
157g LEU* 4.6 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 129 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125g GLU* 2.8 21.4 + - - -
126g ASP* 2.9 17.2 + - - -
128g LEU* 1.3 74.2 - - - +
130g PRO* 1.4 59.1 - - - +
132g LEU* 5.2 0.2 - - - -
133g GLY* 2.8 31.5 + - - -
134g LYS 3.2 24.9 + - - +
135g THR* 5.1 2.0 - - - -
136g PRO* 4.2 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 130 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126g ASP 3.3 6.7 - - - +
127g PHE 3.2 19.7 - - - +
129g SER* 1.4 99.8 - - - +
131g LEU* 1.3 66.8 + - + +
133g GLY* 4.2 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127g PHE* 4.8 15.5 - - + +
128g LEU* 3.3 23.1 + - + +
130g PRO* 1.3 84.2 - - + +
132g LEU* 1.3 64.2 + - - +
153g PHE* 4.8 10.3 - - + -
156g GLU* 3.2 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128g LEU 3.4 8.5 + - - +
131g LEU* 1.3 80.7 - - - +
133g GLY* 1.3 61.8 + - - +
134g LYS* 3.9 30.8 - - + +
136g PRO* 3.7 39.5 - - + +
150g LYS 5.3 0.9 - - - +
153g PHE* 3.5 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 133 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129g SER 2.8 16.8 + - - -
130g PRO* 4.2 3.7 + - - -
131g LEU 3.5 1.6 - - - -
132g LEU* 1.3 74.6 - - - +
134g LYS* 1.3 67.8 + - - +
----------------------------------------------------------
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