Contacts of the helix formed by residues 93 - 108 (chain Q) in PDB entry 2X86
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 ASN 93 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74Q HIS* 4.9 0.2 + - - -
77Q ALA* 3.4 13.2 - - + +
78Q CYS* 2.8 46.3 + - - +
89Q MET* 2.9 28.4 + - - +
92Q ASN* 1.3 84.3 + - - +
94Q TYR* 1.3 62.6 + - - +
97Q SER* 2.8 33.1 + - - -
140Q PHE* 4.0 8.1 - - - -
143Q SER* 3.2 29.1 + - - +
144Q LYS* 4.6 7.8 - - + +
147Q PHE* 6.0 0.4 - - - -
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Residues in contact with TYR 94 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89Q MET 3.7 0.4 + - - -
90Q MET* 3.2 37.1 + - + +
93Q ASN* 1.3 76.4 - - - +
95Q GLN* 1.3 74.1 + - - +
97Q SER* 3.2 5.7 + - - -
98Q LYS* 2.9 40.0 + - + +
143Q SER* 4.1 9.2 - - - +
146Q LEU* 3.5 44.3 - - + +
147Q PHE* 3.6 28.4 - + + -
150Q TYR* 3.7 16.7 - - + +
48R ALA 4.3 0.7 + - - -
49R ASP* 2.4 39.8 + - - -
50R TYR* 3.6 14.4 - + - -
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Residues in contact with GLN 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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90Q MET 2.8 15.0 + - - +
91Q ASP* 3.3 26.7 - - - +
94Q TYR* 1.3 77.0 - - + +
96Q TYR* 1.3 64.2 + - - +
98Q LYS* 3.0 42.6 + - - +
99Q GLU* 3.0 47.2 + - - +
50R TYR 4.0 10.2 - - - +
51R MET* 5.4 5.7 - - - +
55R ASP* 5.6 4.0 - - - +
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Residues in contact with TYR 96 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q THR* 5.4 0.7 - - + -
30Q VAL* 4.1 0.3 - - - +
53Q LYS* 2.7 40.7 + - + +
54Q GLU* 5.4 1.6 - - - -
56Q PHE* 3.5 19.0 - + - -
57Q LEU* 3.6 33.8 + - + -
74Q HIS* 3.9 17.0 - + - +
91Q ASP 2.9 12.6 + - - +
92Q ASN* 3.0 25.6 - - - +
93Q ASN 4.0 0.2 - - - +
95Q GLN* 1.3 74.0 - - - +
97Q SER* 1.3 63.9 + - - +
99Q GLU* 3.0 18.0 + - - +
100Q LEU* 3.0 32.4 + - + +
400Q NAP 3.4 36.6 + + - -
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Residues in contact with SER 97 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74Q HIS* 2.8 32.5 + - - -
76Q GLY 5.2 0.3 + - - -
93Q ASN* 2.8 21.6 + - - -
94Q TYR 3.5 2.9 - - - -
96Q TYR* 1.3 80.7 - - - +
98Q LYS* 1.3 63.0 + - - +
100Q LEU* 3.3 3.0 + - - +
101Q LEU* 2.9 25.3 + - - +
111Q PHE* 4.1 0.9 - - - -
113Q TYR* 5.9 0.2 - - - -
144Q LYS* 5.6 3.6 + - - -
147Q PHE* 3.6 34.0 - - - -
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Residues in contact with LYS 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94Q TYR* 2.9 30.3 + - + +
95Q GLN* 3.0 45.1 + - - +
97Q SER* 1.3 76.4 - - - +
99Q GLU* 1.3 65.1 + - - +
101Q LEU* 3.2 2.8 + - - +
102Q HIS* 3.0 36.7 + - + +
147Q PHE* 3.5 13.0 - - + -
150Q TYR* 3.6 45.9 + - + +
49R ASP* 3.0 30.5 + - - -
50R TYR 4.2 1.8 + - - -
51R MET* 5.2 5.1 - - - +
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Residues in contact with GLU 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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57Q LEU* 4.0 15.0 - - + -
60Q ILE* 3.9 9.0 - - + +
61Q MET* 3.4 44.0 - - + +
95Q GLN* 3.0 38.0 + - - +
96Q TYR* 3.2 9.9 - - - +
98Q LYS* 1.3 79.2 - - - +
100Q LEU* 1.3 61.1 + - - +
102Q HIS* 3.4 8.4 + - - +
103Q TYR* 3.2 21.7 + - - +
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Residues in contact with LEU 100 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Q THR* 4.1 14.1 - - + -
56Q PHE* 3.7 24.7 - - + -
57Q LEU* 5.2 2.7 - - + -
60Q ILE* 3.9 18.4 - - + -
72Q ILE* 4.5 12.8 - - + -
74Q HIS* 3.3 45.8 - - + +
96Q TYR* 3.0 23.8 + - + +
97Q SER 3.6 7.4 - - - +
99Q GLU* 1.3 74.7 - - - +
101Q LEU* 1.3 67.0 + - - +
103Q TYR* 3.1 7.7 + - - +
104Q CYS* 2.9 26.5 + - - -
111Q PHE* 3.7 13.7 - - + -
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Residues in contact with LEU 101 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97Q SER 2.9 16.5 + - - +
98Q LYS 3.2 4.2 + - - +
100Q LEU* 1.3 77.6 - - - +
102Q HIS* 1.3 59.6 + - + +
104Q CYS* 3.3 1.2 + - - +
105Q LEU* 2.8 41.3 + - + +
111Q PHE* 3.8 31.3 - - + -
147Q PHE* 4.0 20.4 - - + -
150Q TYR* 4.0 28.5 - - + -
151Q VAL* 4.3 9.6 - - + -
154Q ILE* 4.3 13.2 - - + -
162Q ILE* 3.8 29.6 - - + -
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Residues in contact with HIS 102 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98Q LYS* 3.0 35.3 + - + +
99Q GLU* 3.9 8.1 - - - +
101Q LEU* 1.3 76.9 - - + +
103Q TYR* 1.3 63.9 + - - +
105Q LEU* 3.5 13.7 - - + +
106Q GLU* 3.0 29.6 + - - +
150Q TYR* 2.6 38.0 + + - -
154Q ILE* 4.5 14.8 - - + -
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Residues in contact with TYR 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Q ILE* 6.0 0.4 - - + -
60Q ILE* 3.5 58.3 - - + +
63Q GLY* 4.3 0.7 - - - -
64Q GLU 2.6 27.5 + - - -
65Q GLU* 3.8 5.5 + - - -
66Q PHE* 3.3 18.1 + + - -
69Q VAL* 5.7 2.3 - - + +
72Q ILE* 4.7 7.2 - - + -
99Q GLU 3.2 12.9 + - - +
100Q LEU 3.1 9.1 + - - +
102Q HIS* 1.3 76.2 - - - +
104Q CYS* 1.3 71.8 + - - +
106Q GLU* 3.6 1.3 + - - -
107Q ARG* 3.1 77.8 + - - +
109Q ILE* 4.1 13.2 - - + +
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Residues in contact with CYS 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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72Q ILE* 3.4 36.3 - - - -
100Q LEU 2.9 15.0 + - - +
101Q LEU* 3.6 7.2 - - + +
103Q TYR* 1.3 77.8 - - - +
105Q LEU* 1.3 56.0 + - + +
107Q ARG 3.0 1.9 + - - -
108Q GLU 2.7 31.9 + - - -
109Q ILE* 2.9 42.5 + - - +
111Q PHE* 3.8 26.7 - - + -
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Residues in contact with LEU 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101Q LEU* 2.8 31.2 + - + +
102Q HIS* 3.3 15.5 + - + +
104Q CYS* 1.3 77.4 - - + +
106Q GLU* 1.3 63.4 + - - +
108Q GLU* 3.3 17.3 + - - +
111Q PHE* 6.3 0.4 - - + -
154Q ILE* 3.5 32.3 - - + -
158Q ALA* 4.3 14.1 - - + -
159Q ASN* 5.2 3.5 + - - +
160Q SER* 4.3 15.2 + - - +
161Q GLN 5.7 0.2 - - - +
162Q ILE* 3.7 29.8 - - + -
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Residues in contact with GLU 106 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102Q HIS* 3.0 19.6 + - - +
103Q TYR* 3.8 5.7 - - - +
105Q LEU* 1.3 78.7 - - - +
107Q ARG* 1.3 79.2 + - + +
108Q GLU* 3.4 3.9 + - - +
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Residues in contact with ARG 107 (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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63Q GLY* 3.5 28.5 + - - -
65Q GLU* 3.3 37.0 + - - +
103Q TYR* 3.1 63.4 + - - +
104Q CYS 3.0 2.0 + - - -
106Q GLU* 1.3 101.3 + - + +
108Q GLU* 1.3 71.0 + - - +
109Q ILE* 3.2 23.6 + - + +
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Residues in contact with GLU 108 (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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104Q CYS 2.7 4.6 + - - -
105Q LEU 3.3 10.4 + - - +
106Q GLU 4.9 2.9 - - - +
107Q ARG* 1.3 82.3 - - - +
109Q ILE* 1.3 57.6 + - - +
110Q PRO* 3.4 10.9 - - - +
159Q ASN* 3.9 30.9 + - + +
160Q SER* 3.4 28.8 - - - +
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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