Contacts of the helix formed by residues 77 - 97 (chain R) 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 THR 77 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155Q ASN* 3.9 22.7 - - - +
73R PHE* 3.3 28.6 - - - -
75R GLY 3.9 3.2 + - - -
76R LEU* 1.4 66.6 - - - +
78R ALA* 1.4 64.7 + - + +
79R ASP 3.2 2.7 - - - -
80R ALA* 3.1 18.0 + - - -
81R ARG* 3.2 22.7 + - - +
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Residues in contact with ALA 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119Q GLN* 3.5 26.4 + - - +
153Q SER* 4.6 5.6 - - - +
154Q GLY 2.8 31.9 - - - +
155Q ASN* 5.2 0.2 - - - +
76R LEU* 3.2 6.0 - - + -
77R THR* 1.4 82.3 - - + +
79R ASP* 1.3 62.2 + - - +
81R ARG* 3.9 10.0 + - - +
82R ILE* 3.4 20.4 - - - +
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Residues in contact with ASP 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12Q PHE* 5.8 0.2 - - - -
119Q GLN* 3.4 12.6 + - - +
123Q GLN* 3.1 23.9 + - - +
76R LEU* 3.3 24.3 + - - +
78R ALA* 1.3 82.2 - - - +
80R ALA* 1.3 60.0 + - - +
81R ARG 3.4 1.1 - - - -
82R ILE* 3.2 8.6 + - - +
83R VAL* 3.0 29.3 + - - +
125R ARG* 3.1 30.2 + - - -
127R PHE* 4.3 5.2 - - + -
128R GLY* 3.3 13.8 + - - +
129R ILE* 3.8 12.1 - - + -
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Residues in contact with ALA 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71R MET* 4.0 4.7 - - - +
73R PHE* 3.3 48.4 - - + -
76R LEU 3.3 1.8 + - - -
77R THR* 3.1 9.0 + - - +
79R ASP* 1.3 76.7 - - - +
81R ARG* 1.3 60.9 + - - +
83R VAL* 3.4 4.0 + - - +
84R ILE* 3.1 25.6 + - - +
129R ILE* 3.6 23.8 - - + -
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Residues in contact with ARG 81 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112Q THR* 3.8 9.1 + - - -
115Q CYS* 2.8 47.3 + - - +
116Q ASP* 2.9 23.6 + - - -
154Q GLY* 3.9 12.5 - - - -
155Q ASN* 4.5 2.1 - - - +
156Q TYR* 3.7 36.3 + - - +
63R CYS* 6.1 0.2 - - - -
73R PHE* 4.7 5.9 - - + -
77R THR* 3.2 19.6 + - - +
78R ALA* 3.9 13.5 + - - +
80R ALA* 1.3 73.5 - - - +
82R ILE* 1.3 68.3 + - - +
84R ILE* 3.0 13.1 + - + +
85R ASN* 2.8 45.6 + - - +
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Residues in contact with ILE 82 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116Q ASP* 3.0 44.6 - - + +
119Q GLN* 3.8 17.7 - - + -
120Q ALA* 6.3 0.7 - - - +
123Q GLN* 5.5 2.9 - - + +
78R ALA 3.4 22.2 - - - +
79R ASP* 3.2 9.6 + - - +
81R ARG* 1.3 92.4 - - + +
83R VAL* 1.4 61.4 + - - +
85R ASN* 3.8 9.1 + - - +
86R ARG* 3.9 15.4 + - - +
127R PHE* 4.6 15.8 - - + -
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Residues in contact with VAL 83 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71R MET* 4.4 5.4 - - + -
79R ASP 3.0 12.2 + - - +
80R ALA 3.6 7.6 - - - +
82R ILE* 1.4 76.8 - - - +
84R ILE* 1.3 64.0 + - - +
85R ASN 3.3 0.3 + - - -
86R ARG* 3.3 6.2 + - - +
87R ALA* 3.1 17.7 + - - +
111R ILE* 4.0 27.6 - - + -
114R LEU* 4.2 15.0 - - + +
115R LYS* 4.7 4.0 - - + -
127R PHE* 3.3 46.9 - - + -
129R ILE* 3.7 25.4 - - + -
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Residues in contact with ILE 84 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63R CYS* 3.2 41.5 - - + -
65R LEU* 3.7 35.2 - - + -
71R MET* 3.8 22.9 - - + -
73R PHE* 5.7 0.2 - - + -
80R ALA 3.1 11.5 + - - +
81R ARG* 3.0 25.5 + - + +
83R VAL* 1.3 76.5 - - - +
85R ASN* 1.3 61.2 + - - +
87R ALA* 3.4 3.5 - - + +
88R ARG* 2.9 53.8 + - - +
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Residues in contact with ASN 85 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116Q ASP* 4.1 12.3 - - - +
81R ARG* 2.8 31.0 + - - +
82R ILE* 3.8 18.5 - - - +
83R VAL 3.3 0.2 - - - -
84R ILE* 1.3 75.0 - - - +
86R ARG* 1.3 63.1 + - - +
88R ARG* 3.1 23.5 + - - +
89R VAL* 3.1 19.7 + - - +
70Y ARG* 3.3 45.8 + - - +
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Residues in contact with ARG 86 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82R ILE 3.9 9.2 + - - +
83R VAL 3.3 7.9 + - - +
85R ASN* 1.3 75.1 - - - +
87R ALA* 1.3 63.2 + - - +
89R VAL* 3.4 32.6 + - - +
90R GLU* 3.1 24.9 + - - +
110R TYR* 3.2 30.5 + - - +
114R LEU* 4.0 18.1 - - + +
117R ARG* 5.7 2.2 - - - +
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Residues in contact with ALA 87 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R LEU* 3.4 21.1 - - + -
83R VAL 3.1 14.0 + - - +
84R ILE* 3.4 10.5 - - - +
85R ASN 3.2 0.2 - - - -
86R ARG* 1.3 76.4 - - - +
88R ARG* 1.4 55.4 + - - +
90R GLU* 3.3 10.7 + - - +
91R CYS* 3.1 30.7 + - - -
107R ILE* 4.4 1.5 - - + +
110R TYR* 4.6 7.3 - - + -
111R ILE* 3.6 26.5 - - + -
114R LEU* 4.9 0.4 - - - +
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Residues in contact with ARG 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63R CYS* 4.0 18.6 - - - +
64R ALA 3.2 26.5 + - - +
65R LEU* 4.3 19.9 - - + +
84R ILE* 2.9 42.2 + - - +
85R ASN* 3.1 21.1 + - - +
87R ALA* 1.4 71.5 - - - +
89R VAL* 1.4 64.7 + - - +
91R CYS* 3.2 17.5 + - - +
92R GLN* 3.2 19.8 + - - +
66Y LEU* 3.8 14.8 - - + -
69Y MET* 3.0 35.5 + - + +
70Y ARG* 3.8 20.9 + - - +
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Residues in contact with VAL 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85R ASN 3.1 9.4 + - - +
86R ARG* 3.6 35.0 - - - +
88R ARG* 1.4 74.8 - - - +
90R GLU* 1.3 60.5 + - - +
92R GLN* 4.2 2.3 - - - +
93R SER* 2.9 39.7 + - - +
66Y LEU* 4.2 15.7 - - + -
70Y ARG* 3.4 23.8 - - - +
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Residues in contact with GLU 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R ARG* 3.1 17.2 + - - +
87R ALA* 3.4 8.3 - - - +
88R ARG 3.2 0.2 - - - -
89R VAL* 1.3 79.2 - - - +
91R CYS* 1.4 58.8 + - - +
93R SER* 4.0 4.6 - - - -
94R HIS* 3.2 17.8 + - - +
102R VAL* 3.9 2.9 - - - +
106R TYR* 3.2 31.6 - - + -
107R ILE* 3.2 27.9 - - - +
110R TYR* 3.1 52.4 - - + +
111R ILE* 5.3 0.2 - - - +
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Residues in contact with CYS 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65R LEU* 3.7 25.1 - - - +
66R ASP* 3.2 37.6 - - - +
87R ALA 3.1 28.5 + - - -
88R ARG* 3.2 8.2 + - - +
90R GLU* 1.4 77.1 - - - +
92R GLN* 1.3 66.8 + - + +
94R HIS* 3.3 4.9 + - - +
95R ARG* 3.2 21.1 + - - +
102R VAL* 4.0 13.0 - - + +
107R ILE* 3.4 16.8 - - - -
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Residues in contact with GLN 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65R LEU 4.8 3.9 - - - +
66R ASP* 4.1 13.9 - - - +
88R ARG* 3.2 15.0 + - + +
89R VAL* 4.2 3.1 - - - +
91R CYS* 1.3 78.3 - - + +
93R SER* 1.3 64.5 + - - +
95R ARG* 3.3 21.9 + - - +
96R LEU* 3.3 16.6 + - - +
62Y LYS* 3.4 60.1 + - + +
65Y GLN* 3.5 25.1 + - - +
66Y LEU* 3.9 20.4 - - + -
69Y MET* 5.0 10.7 - - + +
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Residues in contact with SER 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89R VAL* 2.9 31.4 + - - +
90R GLU* 4.0 5.2 - - - -
91R CYS 3.3 0.2 - - - -
92R GLN* 1.3 74.3 - - - +
94R HIS* 1.3 61.4 + - - +
96R LEU* 3.6 6.6 + - - +
97R THR* 3.1 32.2 + - - +
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Residues in contact with HIS 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90R GLU* 3.2 21.2 + - - +
91R CYS 3.5 4.9 - - - +
92R GLN 3.2 0.6 - - - -
93R SER* 1.3 77.0 - - - +
95R ARG* 1.3 58.3 + - - +
97R THR* 3.1 20.7 + - - -
98R VAL* 3.0 56.6 + - + +
100R ASP 3.8 6.3 + - - -
101R PRO 4.1 2.7 - - - -
102R VAL* 3.5 39.5 + - + -
103R THR 5.3 0.4 - - - -
106R TYR* 4.0 34.7 - + + +
66Z TYR* 5.0 5.4 + - - -
70Z ASN* 5.1 3.9 + - - -
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Residues in contact with ARG 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66R ASP* 3.0 36.2 + - - +
67R ASP* 4.5 7.5 - - - +
68R ASN* 4.6 0.4 + - - -
91R CYS 3.2 12.2 + - - +
92R GLN* 3.3 26.0 + - - +
94R HIS* 1.3 76.3 + - - +
96R LEU* 1.3 56.1 + - - +
98R VAL 2.7 16.4 - - - +
99R GLU* 3.4 18.6 - - - +
100R ASP 3.8 11.2 - - - +
101R PRO* 3.7 33.8 - - + +
58Y GLU* 5.3 0.3 - - - +
61Y GLN* 6.3 0.7 - - - +
62Y LYS* 3.9 23.4 + - + +
65Y GLN* 6.6 0.2 - - - -
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Residues in contact with LEU 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92R GLN 3.3 11.4 + - - +
93R SER* 3.9 9.2 - - - +
94R HIS 3.2 0.6 - - - -
95R ARG* 1.3 75.8 - - - +
97R THR* 1.3 69.3 + - + +
98R VAL 3.9 0.7 - - - -
55Y GLN* 5.5 5.4 - - - +
58Y GLU* 3.7 45.5 - - + +
59Y TYR* 3.9 10.5 - - + +
62Y LYS* 3.8 18.6 - - + +
81Z LYS* 3.1 32.3 - - - +
85Z ASN* 4.4 10.3 - - - +
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Residues in contact with THR 97 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93R SER* 3.1 17.2 + - - +
94R HIS* 3.1 19.1 + - - -
96R LEU* 1.3 86.9 - - + +
98R VAL* 1.3 69.3 + - - +
81Z LYS* 3.3 21.3 - - - +
82Z LEU* 3.3 23.9 + - - +
85Z ASN* 4.1 13.3 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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