Contacts of the helix formed by residues 94 - 105 (chain A) in PDB entry 2JX3
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 VAL 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A GLY* 1.3 74.6 - - - -
95A ASN* 1.3 95.8 + - - +
96A SER* 3.7 11.2 - - - +
97A GLU* 2.8 30.9 + - + +
98A LEU* 2.9 16.0 + - - +
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Residues in contact with ASN 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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76A ARG* 2.7 43.8 - - - +
94A VAL* 1.3 88.6 - - - +
96A SER* 1.3 82.4 + - - -
98A LEU* 2.8 14.6 + - - +
99A VAL* 3.1 12.9 + - - +
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Residues in contact with SER 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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94A VAL* 3.3 9.6 - - - -
95A ASN* 1.3 89.1 + - - +
97A GLU* 1.3 58.9 + - - +
99A VAL* 4.4 3.7 - - - +
100A LYS* 2.9 30.0 + - - +
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Residues in contact with GLU 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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92A SER 4.6 2.7 - - - +
93A GLY* 3.5 18.4 - - - -
94A VAL* 2.8 28.0 + - + +
96A SER* 1.3 78.3 - - - +
98A LEU* 1.3 67.6 + - - +
100A LYS* 3.9 14.4 - - + +
101A ARG* 3.2 47.0 + - - +
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Residues in contact with LEU 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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76A ARG* 3.2 44.4 - - + +
77A ASN* 5.9 0.4 - - - -
80A LEU* 3.4 22.5 - - + +
84A CYS* 5.5 7.9 - - - -
89A LEU* 6.3 2.2 - - + -
91A ARG* 6.1 0.2 - - - -
92A SER 3.4 26.5 - - - +
93A GLY 4.9 3.4 - - - +
94A VAL 2.9 18.6 + - - +
95A ASN* 2.8 4.9 + - - +
97A GLU* 1.3 76.7 - - - +
99A VAL* 1.3 67.7 + - - +
101A ARG* 2.9 23.4 + - + +
102A ILE* 3.3 8.1 - - - +
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Residues in contact with VAL 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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69A GLU* 4.4 20.4 - - + +
73A LYS* 3.7 28.7 - - + +
76A ARG* 2.9 39.7 - - + +
95A ASN 3.1 7.0 + - - +
96A SER* 4.4 3.8 - - - +
98A LEU* 1.3 77.6 - - - +
100A LYS* 1.3 57.7 + - - +
102A ILE* 2.6 45.5 + - + +
103A LEU* 3.1 16.1 - - + +
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Residues in contact with LYS 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 SER 2.9 20.9 + - - +
97A GLU* 3.9 16.3 - - + +
99A VAL* 1.3 80.1 - - - +
101A ARG* 1.3 62.7 + - - +
103A LEU* 3.4 13.6 + - + +
104A ASN* 2.7 52.2 + - - +
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Residues in contact with ARG 101 (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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80A LEU* 6.2 1.6 - - + -
89A LEU* 4.6 37.3 - - + +
97A GLU* 3.2 36.3 + - - +
98A LEU* 2.9 19.2 + - + +
99A VAL 2.7 1.2 + - - -
100A LYS* 1.3 79.1 - - - +
102A ILE* 1.3 53.7 + - + -
104A ASN* 4.4 8.7 - - - +
105A PHE* 2.5 59.0 + - + +
106A LEU* 5.2 0.2 - - - -
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Residues in contact with ILE 102 (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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69A GLU* 4.0 6.1 - - - -
72A LEU* 3.0 68.9 - - + +
76A ARG* 4.9 0.7 - - + -
80A LEU* 4.8 16.2 - - + -
98A LEU 3.3 13.2 - - - +
99A VAL* 2.6 39.1 + - + +
101A ARG* 1.3 72.8 - - + +
103A LEU* 1.3 72.1 + - + +
106A LEU* 2.9 35.8 + - + +
107A MET* 3.0 19.2 + - + +
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Residues in contact with LEU 103 (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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60A LYS* 5.3 6.8 + - - +
65A TYR* 3.4 32.4 - - + +
69A GLU* 3.5 34.1 - - + +
99A VAL* 3.1 35.9 + - + +
100A LYS* 3.5 17.3 - - + +
101A ARG 3.2 0.4 - - - -
102A ILE* 1.3 83.3 - - + +
104A ASN* 1.3 66.8 + - - +
107A MET* 2.9 50.1 - - + +
108A HIS* 4.7 1.9 - - - +
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Residues in contact with ASN 104 (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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60A LYS* 5.8 4.6 + - - +
100A LYS* 2.7 49.0 + - - +
101A ARG* 4.0 11.7 - - - +
103A LEU* 1.3 85.5 - - - +
105A PHE* 1.3 53.8 + - - +
108A HIS* 2.3 34.6 - - - +
109A PRO* 4.2 0.5 - - - +
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Residues in contact with PHE 105 (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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17A ILE* 3.3 32.1 - - + -
56A PHE* 5.2 2.7 - + - -
87A LEU* 3.6 23.8 - - + -
88A ASP* 3.5 28.5 - - + -
89A LEU* 4.7 8.3 - - + -
101A ARG* 2.5 49.1 + - + +
103A LEU 3.4 0.2 - - - -
104A ASN* 1.3 75.4 - - - +
106A LEU* 1.3 73.9 + - + +
107A MET 2.8 3.4 - - - -
108A HIS 2.7 18.8 + - - -
109A PRO* 2.8 44.8 - - + +
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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