Contacts of the helix formed by residues 77 - 95 (chain E) in PDB entry 2JG7
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 PRO 77 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E ASP 3.4 8.9 - - - +
76E ILE* 1.3 91.3 - - + +
78E ALA* 1.3 64.4 + - - +
79E PRO* 4.1 0.4 - - + -
80E LYS* 3.0 23.7 + - + +
81E ARG* 3.0 10.2 + - - +
142G SER 3.3 21.1 - - - +
143G GLU* 3.4 26.9 - - - +
144G ARG 3.8 2.0 - - - +
145G PRO* 3.6 33.7 - - + -
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Residues in contact with ALA 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E ILE 3.6 0.8 + - - -
77E PRO* 1.3 69.3 - - - +
79E PRO* 1.4 64.3 - - + +
81E ARG* 3.0 34.3 + - - +
82E GLY 2.9 24.1 + - - -
132E SER* 3.2 24.1 - - - +
135E ILE* 4.2 9.6 - - + -
181E THR 4.0 5.7 - - - +
141G PRO* 3.8 17.8 - - + +
142G SER 4.2 1.8 + - - -
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Residues in contact with PRO 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E PRO 3.5 2.7 - - - -
78E ALA* 1.4 90.1 - - + +
80E LYS* 1.3 56.3 + - - +
82E GLY* 3.2 2.6 + - - -
83E GLU* 3.1 23.4 + - - +
132E SER* 3.2 25.5 + - - +
133E ARG* 3.5 41.3 + - + +
141G PRO 3.7 15.3 - - - +
142G SER 3.5 15.3 - - - +
143G GLU* 3.8 19.1 - - + +
462H GLU* 4.8 0.2 - - - +
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Residues in contact with LYS 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E ILE* 3.7 16.6 - - + +
77E PRO* 3.0 22.3 + - + +
79E PRO* 1.3 77.2 - - - +
81E ARG* 1.3 64.9 + - - +
83E GLU* 3.4 20.4 - - + +
84E ILE* 3.5 12.3 + - - +
143G GLU* 3.1 38.0 + - + +
145G PRO* 5.3 7.4 - - + +
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Residues in contact with ARG 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E TRP* 3.6 39.0 + - + -
74E ALA 4.0 12.3 + - - -
76E ILE* 2.9 29.0 + - + +
77E PRO* 3.0 13.8 + - - +
78E ALA* 3.0 28.0 + - - +
80E LYS* 1.3 74.4 - - - +
82E GLY* 1.3 64.9 + - - +
84E ILE* 3.0 8.5 + - - +
85E VAL* 3.0 24.7 + - - +
135E ILE* 4.7 2.0 - - - +
155E PRO* 4.5 8.5 - - - +
180E LEU 3.2 20.2 - - - +
181E THR* 2.5 34.2 + - - +
182E CYS* 3.5 4.2 + - - +
183E GLY* 3.1 27.3 - - - +
488E MET* 5.6 1.8 - - - +
444F PRO* 6.3 0.2 - - - +
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Residues in contact with GLY 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ALA 2.9 12.6 + - - -
79E PRO 3.2 6.4 + - - -
81E ARG* 1.3 75.6 - - - +
83E GLU* 1.3 51.9 + - - +
85E VAL* 3.1 11.1 + - - +
86E ARG* 2.7 35.0 + - - +
129E VAL* 3.6 16.8 - - - +
132E SER* 3.8 18.1 - - - -
181E THR* 4.9 3.3 + - - +
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Residues in contact with GLU 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E PRO 3.1 11.6 + - - +
80E LYS* 3.4 16.2 - - + +
81E ARG 3.2 0.4 - - - -
82E GLY* 1.3 76.2 - - - +
84E ILE* 1.3 64.4 + - + +
86E ARG* 2.5 44.6 + - - +
87E GLN* 2.9 42.8 + - - +
129E VAL* 6.0 0.2 - - - -
212E ASN* 5.7 0.2 - - - +
93H ARG* 5.2 1.0 + - - -
123H ASP* 5.6 1.4 - - - +
126H ASP* 5.5 0.2 - - - +
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Residues in contact with ILE 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E TRP* 4.0 17.5 - - + -
76E ILE* 6.3 0.9 - - + -
80E LYS 3.7 13.9 - - - +
81E ARG 3.0 8.4 + - - +
83E GLU* 1.3 78.1 - - + +
85E VAL* 1.3 65.2 + - + +
87E GLN* 3.1 9.8 + - - +
88E ILE* 3.0 29.4 + - + +
180E LEU* 5.3 3.6 - - + -
208E VAL* 4.1 10.3 - - + +
209E LEU* 4.1 26.0 - - + -
212E ASN* 3.5 35.0 - - + +
214E LEU* 3.7 20.4 - - + -
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Residues in contact with VAL 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E TRP* 5.8 0.2 - - + -
81E ARG 3.0 12.9 + - - +
82E GLY* 3.1 9.4 + - - +
84E ILE* 1.3 75.2 - - + +
86E ARG* 1.3 62.6 + - - +
88E ILE* 3.3 10.4 + - + +
89E GLY 3.0 17.8 + - - -
125E CYS* 3.5 43.1 - - - +
128E ALA* 3.9 11.2 - - + -
129E VAL* 4.9 0.2 - - + -
176E ASN* 6.3 0.4 - - - +
177E ALA* 3.9 9.4 - - + +
180E LEU* 3.9 31.4 - - + -
181E THR* 3.7 18.6 - - - +
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Residues in contact with ARG 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E GLY 2.7 16.1 + - - +
83E GLU* 2.5 53.6 + - - +
85E VAL* 1.3 73.8 - - - +
87E GLN* 1.3 70.8 + - - +
89E GLY* 3.1 5.2 + - - +
90E ASP* 3.0 47.4 + - - +
93E ARG* 5.8 0.2 + - - -
125E CYS* 5.2 0.4 - - - -
126E ASP* 4.6 14.1 - - - +
129E VAL* 3.7 23.3 - - + +
90H ASP* 5.1 1.6 + - - -
93H ARG* 3.5 43.7 - - - +
126H ASP* 3.5 26.2 - - - +
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Residues in contact with GLN 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E GLU* 2.9 41.2 + - - +
84E ILE* 3.1 10.2 + - - +
86E ARG* 1.3 83.1 - - - +
88E ILE* 1.3 56.8 + - - +
90E ASP* 3.1 8.3 + - - +
91E ALA* 2.8 35.9 + - - +
208E VAL* 3.8 13.8 - - + +
211E GLN* 5.3 1.7 - - - +
212E ASN* 2.9 38.5 + - - +
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Residues in contact with ILE 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84E ILE* 3.0 23.8 + - + +
85E VAL* 3.3 13.2 + - + +
87E GLN* 1.3 75.3 - - - +
89E GLY* 1.3 63.0 + - - +
91E ALA* 3.3 2.2 + - - +
92E LEU* 3.0 42.3 + - + +
121E TYR* 3.8 21.3 - - + +
125E CYS* 4.1 1.8 - - - -
176E ASN* 3.9 5.2 - - - +
180E LEU* 3.8 28.5 - - + -
204E ILE* 5.7 1.1 - - + -
205E VAL* 3.9 31.0 - - + -
208E VAL* 4.0 23.8 - - + -
209E LEU* 5.6 1.3 - - + -
219E CYS* 5.2 0.2 - - - -
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Residues in contact with GLY 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E VAL 3.0 10.9 + - - -
86E ARG 3.1 6.2 + - - -
88E ILE* 1.3 77.6 - - - +
90E ASP* 1.3 57.5 + - - +
92E LEU* 3.5 8.2 + - - +
93E ARG* 3.1 28.7 + - - +
122E VAL* 3.8 17.0 - - - +
125E CYS* 3.8 23.3 - - - -
126E ASP* 5.4 1.1 - - - -
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Residues in contact with ASP 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E ARG* 3.0 35.3 + - - +
87E GLN* 3.1 11.4 + - + +
89E GLY* 1.3 75.0 - - - +
91E ALA* 1.3 64.8 + - - +
92E LEU 3.2 0.2 - - - -
93E ARG* 3.1 32.0 + - - +
94E LYS* 3.1 38.1 + - - +
86H ARG* 5.1 0.9 + - - -
90H ASP* 4.9 13.9 - - - +
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Residues in contact with ALA 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E GLN 2.8 20.0 + - - +
88E ILE 3.7 2.5 - - - +
90E ASP* 1.3 72.5 - - - +
92E LEU* 1.3 60.8 + - - +
94E LYS* 3.4 20.4 + - - +
95E LYS* 3.5 17.7 + - - +
204E ILE* 3.7 18.5 - - + +
208E VAL* 3.6 24.0 - - + -
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Residues in contact with LEU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E ILE* 3.0 33.6 + - + +
89E GLY* 3.6 9.4 - - - +
91E ALA* 1.3 73.8 - - - +
93E ARG* 1.3 64.3 + - - +
95E LYS* 3.0 16.8 + - - -
96E ILE* 3.0 13.7 + - - +
99E LEU* 3.9 27.0 - - + +
118E VAL* 4.3 8.7 - - + +
121E TYR* 3.5 52.5 - - + -
122E VAL* 3.9 13.5 - - + +
169E VAL* 5.2 0.7 - - + -
201E VAL* 5.2 5.4 - - + -
204E ILE* 4.3 18.8 - - + -
205E VAL* 5.9 0.9 - - + -
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Residues in contact with ARG 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E ARG 5.8 0.2 + - - -
89E GLY 3.1 14.2 + - - +
90E ASP* 3.1 32.5 + - - +
92E LEU* 1.3 76.5 - - - +
94E LYS* 1.3 62.5 + - + +
96E ILE* 3.2 29.7 - - + +
119E GLN* 4.5 8.7 - - - +
122E VAL* 3.4 33.2 - - + +
123E ASP* 5.3 1.2 + - - -
126E ASP* 3.1 31.1 + - - -
83H GLU* 5.1 1.4 + - - -
86H ARG* 3.5 43.2 - - - +
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Residues in contact with LYS 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E ASP* 3.1 25.6 + - - +
91E ALA* 3.6 12.8 - - - +
92E LEU 3.2 0.2 - - - -
93E ARG* 1.3 76.7 - - + +
95E LYS* 1.3 66.7 + - + +
96E ILE* 3.4 1.8 + - - +
97E LYS 5.3 0.3 + - - -
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Residues in contact with LYS 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E GLU* 3.2 32.0 + - + +
16E LEU* 4.5 5.4 - - + +
91E ALA 3.5 12.3 + - - +
92E LEU 3.0 8.9 + - - +
94E LYS* 1.3 83.3 - - + +
96E ILE* 1.3 64.0 + - - +
97E LYS 3.2 3.3 + - - -
98E VAL* 3.3 21.1 - - + +
99E LEU* 3.0 23.3 + - + +
204E ILE* 4.1 32.3 - - + -
207E GLU* 6.0 2.0 - - - -
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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