Contacts of the helix formed by residues 84 - 100 (chain A) in PDB entry 2JPO
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 GLU 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A LYS* 4.6 10.8 - - + -
78A MET* 3.4 25.9 - - + +
83A ASP* 1.3 72.2 - - + +
85A THR* 1.3 57.1 + - - +
87A ALA* 4.2 3.6 - - - -
88A GLN* 3.0 27.3 + - - +
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Residues in contact with THR 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ASP* 2.9 8.0 + - - +
84A GLU* 1.3 71.5 - - - +
86A MET* 1.3 60.0 + - + +
88A GLN* 3.0 6.7 + - - +
89A GLN* 2.8 49.0 + - + +
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Residues in contact with MET 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A GLY 3.2 26.9 - - - +
82A ALA* 3.7 10.5 - - + -
83A ASP* 3.0 28.9 + - - +
85A THR* 1.3 77.0 - - + +
87A ALA* 1.3 62.5 + - - +
89A GLN* 3.1 18.9 + - - +
90A LEU* 3.3 19.3 + - - +
127A TRP* 3.4 51.5 - - + +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ALA 5.4 0.2 - - - -
74A LYS* 3.6 36.4 - - + +
77A ALA* 4.0 23.5 - - + +
78A MET* 4.5 2.9 - - + -
82A ALA* 3.9 6.2 - - + +
83A ASP 2.8 27.1 + - - +
84A GLU* 4.2 3.6 - - - -
86A MET* 1.3 72.2 - - - +
88A GLN* 1.3 58.6 + - - +
90A LEU* 4.4 3.8 - - - +
91A VAL* 3.9 15.2 + - - +
137A GLU* 4.2 6.2 - - - +
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Residues in contact with GLN 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LYS* 2.8 34.9 + - - +
84A GLU 3.0 20.0 + - - +
85A THR* 3.0 5.5 + - - +
87A ALA* 1.3 77.2 - - - +
89A GLN* 1.3 65.7 + - + +
90A LEU 3.2 0.2 - - - -
91A VAL* 3.2 20.0 + - - +
92A ASP* 2.9 41.4 + - + +
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Residues in contact with GLN 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A THR* 2.8 35.9 + - + +
86A MET* 3.1 11.6 + - - +
88A GLN* 1.3 73.0 - - + +
90A LEU* 1.3 59.1 + - + +
92A ASP* 3.1 10.1 + - - +
93A ILE* 3.0 30.3 + - - +
124A LYS* 4.9 10.6 + - - +
125A LEU* 3.6 27.7 + - + +
127A TRP* 3.5 25.8 - - + +
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ALA* 5.2 4.0 - - + -
82A ALA* 5.8 0.2 - - + -
86A MET 3.3 15.7 + - - +
87A ALA* 4.5 5.8 - - - +
88A GLN 3.2 0.2 - - - -
89A GLN* 1.3 72.1 - - - +
91A VAL* 1.3 66.1 + - - +
93A ILE* 3.0 12.0 + - + +
94A ILE 3.1 10.2 + - - -
118A PHE* 3.4 23.0 - - + -
125A LEU* 3.8 29.6 - - + -
127A TRP* 3.8 17.9 - - + -
129A PRO* 4.0 9.4 - - + -
133A LEU* 3.4 48.9 - - + +
137A GLU* 3.3 21.3 - - + +
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLY* 5.1 11.7 - - - +
73A ALA* 4.9 6.3 - - + +
74A LYS* 4.8 11.9 - - + +
87A ALA 3.9 10.5 + - - +
88A GLN* 3.2 32.8 + - - +
90A LEU* 1.3 77.0 - - - +
92A ASP* 1.3 59.2 + - - +
94A ILE* 3.3 2.3 + - + +
95A HIS* 2.8 64.5 + - + +
137A GLU* 3.3 27.4 + - - +
141A GLU* 5.4 0.7 - - - +
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Residues in contact with ASP 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A GLN* 2.9 28.5 + - + +
89A GLN* 3.1 12.3 + - - +
91A VAL* 1.3 74.6 - - - +
93A ILE* 1.3 60.3 + - - +
95A HIS* 4.2 8.9 + - - +
96A GLY* 2.8 27.2 + - - -
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Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A GLN 3.0 18.0 + - - +
90A LEU* 3.0 8.2 + - + +
92A ASP* 1.3 76.4 - - + +
94A ILE* 1.3 57.1 + - - +
96A GLY* 3.3 1.1 + - - -
97A CYS* 2.8 29.7 + - - +
118A PHE* 3.4 40.4 - - + -
121A GLU* 3.4 42.0 - - + +
122A ILE* 4.2 1.8 - - - +
124A LYS* 4.5 12.1 - - + +
125A LEU* 3.6 41.1 - - + -
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Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A LEU 3.1 6.5 + - - -
91A VAL 3.3 13.0 - - - +
93A ILE* 1.3 75.2 - - - +
95A HIS* 1.3 68.4 + - + +
97A CYS* 3.8 2.2 - - - +
98A GLU* 2.9 36.1 + - - +
114A VAL* 3.7 26.5 - - + +
118A PHE* 3.8 23.5 - - + -
137A GLU* 3.7 27.4 - - + +
138A VAL* 3.9 33.7 - - + -
141A GLU* 3.8 27.8 - - + +
142A VAL* 5.6 1.6 - - + -
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Residues in contact with HIS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLY* 5.8 1.7 - - - -
91A VAL* 2.8 48.2 + - + +
92A ASP* 4.1 11.5 + - - +
94A ILE* 1.3 78.0 - - + +
96A GLY* 1.3 60.6 + - - +
98A GLU* 3.4 25.3 - - - +
99A LYS* 3.9 12.0 - - - +
141A GLU* 2.7 38.7 + - - -
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Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ASP* 2.8 20.9 + - - -
93A ILE* 3.6 1.1 - - - -
94A ILE 3.1 0.2 - - - -
95A HIS* 1.3 75.5 - - - +
97A CYS* 1.3 63.8 + - - +
99A LYS* 3.2 6.6 + - - +
100A SER* 3.0 27.3 + - - -
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Residues in contact with CYS 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ILE 2.8 21.8 + - - +
94A ILE* 4.5 0.4 - - - -
96A GLY* 1.3 72.0 - - - +
98A GLU* 1.3 55.9 - - - +
100A SER* 3.7 4.3 - - - -
101A ALA* 3.0 29.8 + - - +
114A VAL* 3.7 20.6 - - + +
117A CYS* 2.0 67.8 - - + +
118A PHE* 3.4 6.7 - - - -
121A GLU* 3.9 11.7 - - - -
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Residues in contact with GLU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ILE* 2.9 20.2 + - + +
95A HIS* 3.4 29.3 - - - +
97A CYS* 1.3 76.9 - - - +
99A LYS* 1.3 93.5 + - - +
101A ALA* 3.4 6.9 - - - +
110A LYS* 3.1 27.2 + - - +
114A VAL* 3.4 21.1 - - + +
141A GLU* 3.4 28.9 - - + +
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A HIS 3.9 8.5 - - - +
96A GLY 3.2 7.5 + - - +
97A CYS 3.2 0.4 - - - -
98A GLU* 1.3 122.6 + - + +
100A SER* 1.3 59.1 + - - +
101A ALA 3.1 12.0 + - - +
110A LYS* 6.1 0.2 - - - +
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Residues in contact with SER 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLY* 3.0 18.2 + - - -
97A CYS* 3.7 8.3 - - - -
99A LYS* 1.3 74.8 - - - +
101A ALA* 1.3 64.0 + - - +
102A PRO* 3.8 1.7 - - - +
117A CYS* 5.3 5.4 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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