Contacts of the helix formed by residues 90 - 104 (chain Q) in PDB entry 2JA7
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 90 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89Q GLY* 1.3 69.7 - - - -
91Q LYS* 1.3 67.8 + - + +
93Q MET* 3.7 11.0 - - - +
94Q LYS* 4.1 5.4 + - - +
117Q THR* 4.2 4.4 - - + -
119Q SER* 3.4 37.7 - - - +
120Q ALA* 3.5 21.9 - - - +
123Q LEU* 3.9 13.5 - - + +
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Residues in contact with LYS 91 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89Q GLY* 3.3 1.0 - - - -
90Q VAL* 1.3 81.2 - - + +
92Q THR* 1.3 61.7 + - - +
93Q MET 2.9 9.6 + - - -
94Q LYS* 3.3 17.3 + - - +
95Q THR* 4.0 5.0 + - - -
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Residues in contact with THR 92 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81Q GLU* 5.1 5.0 - - - +
83Q CYS* 4.6 11.9 - - - -
85Q GLU* 3.0 40.6 + - - +
88Q VAL* 4.7 13.5 - - + -
89Q GLY 4.2 4.7 + - - -
91Q LYS* 1.3 76.0 - - - +
93Q MET* 1.3 60.0 + - - +
94Q LYS 3.6 0.2 - - - -
95Q THR* 3.3 27.9 - - + +
96Q PHE* 3.8 6.2 + - - +
110Q PHE* 5.6 3.0 - - + -
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Residues in contact with MET 93 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88Q VAL* 6.1 2.5 - - + -
89Q GLY 4.0 12.0 + - - +
90Q VAL 3.7 13.5 - - - +
91Q LYS 2.9 0.6 - - - -
92Q THR* 1.3 75.4 - - - +
94Q LYS* 1.3 56.8 + - - +
95Q THR 2.8 4.3 - - - -
96Q PHE* 2.7 41.6 + - + +
97Q VAL* 2.8 43.7 + - + -
110Q PHE* 4.8 20.9 - - + -
116Q ILE* 4.9 9.9 - - + -
120Q ALA* 4.3 26.7 - - + +
121Q MET* 4.6 6.7 - - - +
123Q LEU* 4.4 16.8 - - + -
124Q VAL* 4.8 12.3 - - + -
132Q ILE* 5.8 2.5 - - + -
134Q THR* 5.8 3.6 - - + -
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Residues in contact with LYS 94 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90Q VAL 4.1 4.8 + - - +
91Q LYS 3.3 11.0 + - - +
93Q MET* 1.3 79.3 - - - +
95Q THR* 1.3 61.6 + - - +
97Q VAL* 4.1 11.9 - - + -
98Q ILE* 3.1 64.1 + - + +
101Q GLN* 6.3 0.4 - - - +
123Q LEU* 5.8 8.0 - - + +
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Residues in contact with THR 95 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81Q GLU* 5.7 5.2 - - - +
91Q LYS 4.0 2.8 + - - -
92Q THR* 3.3 31.2 + - + +
93Q MET 2.8 0.2 + - - -
94Q LYS* 1.3 79.9 - - - +
96Q PHE* 1.3 58.5 + - + +
98Q ILE* 4.7 0.5 - - - +
99Q HIS* 3.1 25.1 + - - +
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Residues in contact with PHE 96 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Q TRP* 3.3 32.1 - + - -
81Q GLU* 3.2 38.4 - - + +
92Q THR 4.3 5.4 - - - +
93Q MET* 2.7 29.2 + - + +
95Q THR* 1.3 72.8 - - - +
97Q VAL* 1.3 71.5 + - + +
99Q HIS* 2.8 22.2 + + - +
100Q ILE* 3.2 29.0 + - + +
109Q ILE 3.9 24.5 - - - -
110Q PHE* 3.8 23.8 - + + -
132Q ILE* 3.7 27.1 - - + -
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Residues in contact with VAL 97 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93Q MET* 2.8 50.6 + - + +
94Q LYS* 4.4 11.4 - - + +
96Q PHE* 1.3 77.5 - - + +
98Q ILE* 1.3 66.1 + - + +
100Q ILE* 3.3 13.4 + - - +
101Q GLN* 3.3 10.5 + - - +
123Q LEU* 4.1 24.7 - - + +
126Q SER* 5.2 0.9 - - - +
127Q ILE* 3.7 33.4 - - + +
132Q ILE* 4.5 12.6 - - + -
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Residues in contact with ILE 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94Q LYS* 3.1 62.6 + - + +
95Q THR 4.7 0.7 - - - +
96Q PHE 3.2 0.6 - - - -
97Q VAL* 1.3 73.7 - - + +
99Q HIS* 1.3 55.4 + - - +
100Q ILE 2.6 16.3 + - - -
101Q GLN* 2.8 26.9 + - + +
102Q GLU* 3.1 33.0 + - + +
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Residues in contact with HIS 99 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Q TRP* 3.6 56.9 - + - -
81Q GLU* 4.7 3.1 - - - +
95Q THR* 3.1 21.3 + - + +
96Q PHE* 2.8 16.9 + + - +
98Q ILE* 1.3 74.1 - - - +
100Q ILE* 1.3 61.2 + - + +
102Q GLU* 4.5 5.1 - - - +
103Q LYS* 3.2 49.1 + - + +
105Q PHE* 4.8 4.5 - + - -
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Residues in contact with ILE 100 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Q TRP* 4.9 3.4 - - + -
96Q PHE* 3.6 50.5 - - + +
97Q VAL* 3.6 8.1 - - - +
98Q ILE 2.6 5.5 + - - -
99Q HIS* 1.3 82.9 - - + +
101Q GLN* 1.3 64.5 + - - +
102Q GLU 3.2 2.0 - - - -
103Q LYS* 5.0 0.2 - - - -
104Q ASN* 3.0 22.5 + - - -
105Q PHE* 3.8 36.2 + - + +
106Q GLN* 4.6 5.2 - - - +
107Q THR 5.2 3.8 - - - +
108Q GLY* 4.0 15.9 - - - -
127Q ILE* 5.5 2.7 - - + -
130Q ALA* 5.0 13.0 - - + -
131Q THR 5.7 0.9 - - - +
132Q ILE* 5.0 9.4 - - + -
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Residues in contact with GLN 101 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97Q VAL* 3.3 10.7 + - - +
98Q ILE* 2.8 25.0 + - + +
100Q ILE* 1.3 77.1 - - - +
102Q GLU* 1.3 65.0 + - + +
104Q ASN* 4.0 8.4 + - - +
127Q ILE* 3.4 43.0 - - + +
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Residues in contact with GLU 102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98Q ILE* 3.1 33.3 + - + +
99Q HIS* 4.8 4.6 - - - +
101Q GLN* 1.3 77.3 - - + +
103Q LYS* 1.3 59.9 + - + +
104Q ASN* 2.7 20.2 + - - +
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Residues in contact with LYS 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99Q HIS* 3.2 45.2 + - + +
100Q ILE 3.8 0.8 + - - +
102Q GLU* 1.3 80.2 - - + +
104Q ASN* 1.3 67.4 + - - +
105Q PHE* 3.5 30.7 - - + -
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Residues in contact with ASN 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Q ILE 3.0 12.3 + - - -
101Q GLN 4.3 6.6 + - - +
102Q GLU 2.7 14.6 + - - +
103Q LYS* 1.3 80.5 - - - +
105Q PHE* 1.3 73.1 + - - +
129Q PRO* 6.2 2.6 - - - +
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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