Contacts of the helix formed by residues 82 - 101 (chain Q) in PDB entry 5A0Q
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 ASP 82 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P LEU* 5.1 1.8 - - - +
118P GLN* 2.4 43.3 + - - +
122P GLN* 4.3 3.6 - - - -
79Q ILE* 4.5 15.5 - - + +
80Q THR 3.2 0.2 - - - -
81Q SER* 1.3 75.0 - - - +
83Q ALA* 1.3 65.7 + - - +
84Q ASN 3.2 0.7 - - - -
85Q VAL* 3.0 17.3 + - - +
86Q LEU* 3.1 15.3 + - - +
128Q ARG* 2.9 34.0 + - - -
130Q PHE* 4.1 12.5 - - + -
131Q GLY 4.1 8.1 + - - -
132Q VAL* 3.7 19.2 - - + +
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Residues in contact with ALA 83 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Q TYR* 5.2 5.2 - - + +
76Q VAL* 2.8 40.6 - - + +
79Q ILE 3.1 18.7 + - - +
80Q THR* 3.4 9.8 - - - +
82Q ASP* 1.3 77.4 - - - +
84Q ASN* 1.3 59.3 + - - +
86Q LEU* 3.2 9.8 + - - +
87Q THR* 2.9 32.9 + - - -
132Q VAL* 4.4 0.8 - - + +
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Residues in contact with ASN 84 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111P GLN* 5.8 1.9 - - - +
114P ALA* 5.9 2.1 - - - +
115P SER* 5.1 9.2 - - - +
152P GLY 4.6 7.9 + - - -
153P ALA* 5.7 0.6 - - - +
154P TYR* 4.7 20.3 + - - -
66Q TYR* 3.2 25.7 + - - -
80Q THR* 2.7 30.5 + - - -
81Q SER* 4.0 11.4 + - - +
82Q ASP 3.2 0.6 - - - -
83Q ALA* 1.3 78.8 - - - +
85Q VAL* 1.4 58.4 + - + +
87Q THR* 3.3 7.6 + - - -
88Q ASN* 2.9 27.9 + - - +
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Residues in contact with VAL 85 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115P SER* 5.1 15.3 - - - +
118P GLN* 3.7 31.2 - - + +
122P GLN* 5.8 0.2 - - - +
81Q SER 4.1 2.7 - - - +
82Q ASP* 3.0 7.7 + - - +
84Q ASN* 1.4 73.5 - - + +
86Q LEU* 1.3 64.3 + - - +
88Q ASN* 3.4 8.6 + - + +
89Q GLU* 3.0 34.2 + - + +
130Q PHE* 4.2 21.5 - - + -
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Residues in contact with LEU 86 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82Q ASP 3.1 14.4 + - - +
83Q ALA* 3.2 11.2 + - - +
85Q VAL* 1.3 77.0 - - - +
87Q THR* 1.3 57.8 + - - +
89Q GLU* 3.3 5.3 + - + +
90Q LEU* 2.9 32.8 + - - +
114Q LEU* 3.7 21.6 - - + +
117Q ILE* 6.2 0.7 - - + -
118Q LYS* 4.2 14.1 - - + -
130Q PHE* 3.5 40.2 - - + -
132Q VAL* 3.9 34.1 - - + -
134Q LEU* 3.9 29.2 - - + -
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Residues in contact with THR 87 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Q TYR* 3.2 41.7 - - + -
68Q LEU* 4.0 8.1 - - + -
74Q CYS* 4.2 2.3 - - - -
76Q VAL* 4.1 6.4 - - - +
83Q ALA 2.9 17.6 + - - -
84Q ASN* 3.6 6.3 - - - -
86Q LEU* 1.3 72.0 - - - +
88Q ASN* 1.3 64.0 + - - +
90Q LEU* 3.3 10.9 + - - +
91Q ARG* 3.0 56.0 + - - +
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Residues in contact with ASN 88 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84Q ASN 2.9 16.6 + - - +
85Q VAL* 3.6 11.0 - - - +
86Q LEU 3.2 0.2 - - - -
87Q THR* 1.3 75.1 - - - +
89Q GLU* 1.3 67.1 + - - +
91Q ARG* 3.2 14.6 + - - +
92Q LEU* 3.1 40.5 + - - +
72X LEU* 5.9 1.0 - - - +
76X LYS* 3.9 22.3 + - - +
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Residues in contact with GLU 89 (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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85Q VAL* 3.0 31.3 + - + +
86Q LEU* 3.7 4.7 - - + +
88Q ASN* 1.3 80.7 + - - +
90Q LEU* 1.3 57.2 + - - +
92Q LEU* 3.4 23.8 + - - +
93Q ILE* 3.0 37.3 + - - +
114Q LEU* 4.1 13.9 - - + -
117Q ILE* 3.9 27.5 - - + +
130Q PHE* 6.3 2.0 - - + -
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Residues in contact with LEU 90 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68Q LEU* 3.4 35.0 - - + -
74Q CYS* 4.2 6.7 - - - -
86Q LEU 2.9 24.4 + - - +
87Q THR* 3.5 5.2 - - - +
88Q ASN 3.2 0.2 - - - -
89Q GLU* 1.3 74.4 - - - +
91Q ARG* 1.3 64.9 + - - +
93Q ILE* 3.5 1.7 + - + -
94Q ALA* 3.1 22.2 + - - +
110Q LEU* 3.3 38.5 - - + +
114Q LEU* 3.7 42.2 - - + -
134Q LEU* 4.2 11.7 - - + -
136Q TYR* 3.9 13.0 - - + -
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Residues in contact with ARG 91 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111P GLN* 6.1 0.8 - - - +
66Q TYR* 3.7 25.3 - - - -
67Q LYS* 3.0 36.3 + - - +
68Q LEU* 4.1 13.7 - - - +
87Q THR* 3.0 36.2 + - + +
88Q ASN* 3.6 14.0 - - - +
90Q LEU* 1.3 73.9 - - - +
92Q LEU* 1.4 56.9 + - - +
94Q ALA* 3.6 0.7 + - - +
95Q GLN* 3.0 35.5 + - - +
72X LEU* 4.1 13.9 - - + -
75X LEU* 3.2 44.6 + - + +
76X LYS* 4.1 27.7 + - - +
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Residues in contact with LEU 92 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88Q ASN* 3.1 34.7 + - - +
89Q GLU* 3.7 28.5 - - - +
90Q LEU 3.2 0.2 - - - -
91Q ARG* 1.4 74.1 - - - +
93Q ILE* 1.3 65.5 + - + +
95Q GLN* 3.3 1.6 + - - +
96Q ARG* 2.9 37.7 + - + +
68X PHE* 4.2 12.3 - - + -
72X LEU* 3.7 35.2 - - + -
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Residues in contact with ILE 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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89Q GLU* 3.0 28.7 + - - +
90Q LEU* 3.9 8.1 - - - +
92Q LEU* 1.3 75.4 - - + +
94Q ALA* 1.3 58.2 + - - +
96Q ARG* 3.4 28.8 + - - +
97Q TYR* 3.0 27.7 + - + +
105Q ILE* 3.9 17.3 - - + -
110Q LEU* 4.1 6.7 - - + -
113Q ALA* 3.6 35.9 - - + -
114Q LEU* 4.1 9.9 - - + +
117Q ILE* 3.8 25.4 - - + -
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Residues in contact with ALA 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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68Q LEU 4.4 1.3 - - - +
69Q ASN* 3.3 36.2 + - - +
90Q LEU 3.1 16.5 + - - +
91Q ARG 3.9 3.4 - - - +
93Q ILE* 1.3 80.6 - - - +
95Q GLN* 1.4 58.5 + - - +
97Q TYR* 3.5 3.8 + - - +
98Q LEU* 3.0 25.3 + - - +
105Q ILE* 3.7 26.2 + - + +
110Q LEU* 4.2 3.8 - - + -
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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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69Q ASN* 3.3 26.8 - - - +
91Q ARG 3.0 21.1 + - - +
92Q LEU 3.7 0.7 - - - +
94Q ALA* 1.4 74.1 - - - +
96Q ARG* 1.3 58.4 + - - +
97Q TYR 3.4 0.2 - - - -
98Q LEU* 3.7 27.7 - - - +
99Q LEU* 3.1 17.7 + - - +
67X LYS* 4.5 3.5 - - - +
68X PHE* 3.3 36.0 - - + +
71X ASN* 3.2 36.2 - - + +
72X LEU* 4.0 13.2 - - + -
75X LEU* 4.1 15.8 - - + +
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Residues in contact with ARG 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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92Q LEU* 2.9 28.2 + - + +
93Q ILE* 3.8 32.1 - - - +
95Q GLN* 1.3 73.2 - - - +
97Q TYR* 1.3 66.0 + - - +
99Q LEU* 3.0 19.9 + - + +
100Q GLN* 2.7 26.4 + - - +
68X PHE* 4.1 18.8 - - + -
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Residues in contact with TYR 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 ILE* 3.0 18.1 + - + +
94Q ALA 3.6 4.7 - - - +
96Q ARG* 1.3 77.4 - - - +
98Q LEU* 1.3 56.4 + - - +
100Q GLN* 4.2 9.0 - - - +
101Q TYR* 3.1 52.1 + + + +
103Q GLU* 2.9 36.8 + - + -
105Q ILE* 3.4 39.9 - - + -
106Q PRO* 3.6 13.0 - - + +
109Q GLN* 3.2 20.6 - - - -
67Y TYR* 2.8 35.3 + + - -
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Residues in contact with LEU 98 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69Q ASN* 6.0 0.2 - - - +
94Q ALA 3.0 17.8 + - - +
95Q GLN* 3.7 32.7 + - - +
96Q ARG 3.2 0.2 - - - -
97Q TYR* 1.3 73.8 - - - +
99Q LEU* 1.3 62.8 + - - +
102Q GLN* 2.8 36.3 + - - +
103Q GLU* 3.3 37.0 - - - +
104Q PRO* 3.9 12.1 - - + -
67X LYS* 5.7 7.9 - - + -
71X ASN* 4.8 7.9 - - - +
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Residues in contact with LEU 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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95Q GLN 3.1 16.2 + - - +
96Q ARG* 3.0 16.6 + - + +
98Q LEU* 1.3 77.9 - - - +
100Q GLN* 1.4 64.9 + - + +
102Q GLN* 3.5 3.6 - - - +
64X GLN* 2.8 75.2 - - + +
65X ARG* 3.9 21.8 - - - +
68X PHE* 4.2 22.2 - - + -
86Y ARG* 3.7 13.1 + - - +
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Residues in contact with GLN 100 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96Q ARG* 2.7 37.1 + - - +
97Q TYR* 4.2 8.7 - - - +
99Q LEU* 1.4 82.8 - - + +
101Q TYR* 1.3 95.8 + - + +
102Q GLN* 3.3 0.4 - - - +
82Y ASN* 3.0 31.0 - - - +
83Y PHE* 3.6 13.6 + - + -
86Y ARG* 3.8 33.2 + - + +
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Residues in contact with TYR 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 TYR* 3.1 47.6 + + + +
100Q GLN* 1.3 112.3 - - + +
102Q GLN* 1.4 68.7 + - - +
103Q GLU* 3.4 3.4 + - + +
63Y ASN* 4.9 5.9 + - - +
64Y VAL 5.5 0.2 + - - -
67Y TYR* 4.2 16.4 - + - +
75Y LEU* 3.5 39.3 - - + +
79Y ALA* 3.5 37.5 - - - +
80Y ALA* 5.2 0.4 - - - -
82Y ASN* 3.8 2.0 - - - +
83Y PHE* 3.8 40.6 - + + -
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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
------------------------------------------------------------
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) + - + + + + + -
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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