Contacts of the helix formed by residues 79 - 100 (chain P) 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 GLY 79 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159O TYR* 5.3 2.0 - - - -
75P TYR* 3.5 27.7 + - - -
77P GLY 3.6 3.0 + - - -
78P MET* 1.3 71.0 - - - +
80P PRO* 1.3 72.9 - - - +
81P ASP 3.2 0.9 + - - -
82P TYR* 3.3 16.8 + - - +
83P ARG* 2.8 19.6 + - - +
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Residues in contact with PRO 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123O GLN* 2.7 24.7 - - + +
157O ALA* 3.1 38.8 - - + +
158O GLY* 3.6 11.7 - - - +
159O TYR* 3.7 24.2 - - + +
78P MET* 3.8 10.1 - - + -
79P GLY* 1.3 90.3 - - - +
81P ASP* 1.3 55.0 + - - +
83P ARG* 3.5 25.0 + - - +
127P ARG* 6.2 1.1 - - - +
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Residues in contact with ASP 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123O GLN* 3.3 16.6 + - - +
127O GLN* 3.2 22.9 - - - +
78P MET* 4.0 18.8 - - + +
79P GLY 3.3 0.2 - - - -
80P PRO* 1.3 77.4 - - - +
82P TYR* 1.3 63.2 + - - +
83P ARG 3.3 0.4 + - - -
84P VAL 3.6 1.2 + - - -
85P LEU* 3.2 21.0 + - - +
127P ARG* 3.9 9.3 + - - +
129P PHE* 3.2 25.5 - - - +
130P GLY 3.2 25.3 + - - -
131P VAL* 3.5 20.2 + - + +
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Residues in contact with TYR 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61P VAL* 5.4 4.5 - - + -
62P HIS 4.0 5.2 - - - -
63P LYS 3.0 23.3 + - - -
65P GLU* 3.2 45.4 + - + +
73P LEU* 3.4 25.6 - - + +
75P TYR* 3.2 54.1 - + + -
78P MET 4.2 0.2 - - - +
79P GLY 3.3 11.9 - - - +
81P ASP* 1.3 77.2 - - - +
83P ARG* 1.3 63.7 + - + +
85P LEU* 4.3 4.3 - - + -
86P VAL* 3.0 52.6 + - + +
131P VAL* 3.7 18.1 - - + +
133P LEU* 4.4 5.4 - - + -
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Residues in contact with ARG 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116O LYS* 6.0 0.7 - - + -
119O ALA* 4.9 0.2 - - - -
120O ASP* 3.7 15.7 - - - +
158O GLY 3.2 18.6 - - - -
159O TYR* 2.7 41.3 - - - +
160O TYR* 2.8 54.1 + - + +
61P VAL* 3.4 28.9 - - + +
65P GLU* 5.1 3.8 - - - +
75P TYR* 4.9 2.2 + - - -
79P GLY* 2.8 41.1 + - - +
80P PRO* 3.4 9.8 - - - +
81P ASP 3.3 0.8 - - - -
82P TYR* 1.3 81.2 - - + +
84P VAL* 1.3 52.7 + - + +
86P VAL* 4.2 3.9 - - - +
87P HIS* 2.7 41.8 + - + +
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Residues in contact with VAL 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120O ASP* 4.0 36.1 - - + +
123O GLN* 3.0 37.9 + - - +
124O VAL* 6.3 0.7 - - + -
81P ASP 3.6 1.0 + - - -
82P TYR 3.2 0.2 - - - -
83P ARG* 1.3 76.2 - - + +
85P LEU* 1.3 67.3 + - - +
86P VAL 3.2 1.6 - - - -
87P HIS* 3.0 20.5 + - + +
88P ARG* 3.2 12.2 + - + +
120P TYR* 6.2 0.4 - - - +
129P PHE* 5.6 5.4 - - + -
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Residues in contact with LEU 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73P LEU* 4.5 6.7 - - + -
81P ASP* 3.2 17.7 + - - +
82P TYR* 3.3 6.3 + - - +
84P VAL* 1.3 78.9 - - - +
86P VAL* 1.3 61.9 + - + +
88P ARG* 3.3 7.5 + - - +
89P ALA* 3.0 19.5 + - + +
113P VAL* 4.1 19.1 - - + +
116P VAL* 5.9 4.5 - - + -
117P MET* 4.1 32.8 - - + -
129P PHE* 4.0 30.0 - - + -
131P VAL* 4.4 9.6 - - + -
133P LEU* 3.2 34.5 - - + -
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Residues in contact with VAL 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65P GLU* 3.3 18.6 - - - +
67P ILE* 3.8 11.4 - - + -
73P LEU* 3.7 8.7 - - + -
82P TYR* 3.0 59.7 + - + +
83P ARG 4.2 4.5 - - - +
85P LEU* 1.3 76.8 - - - +
87P HIS* 1.3 58.1 + - + +
89P ALA* 3.1 8.4 + - - +
90P ARG* 3.0 59.5 + - - +
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Residues in contact with HIS 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116O LYS* 4.1 22.0 + - + +
120O ASP* 2.5 39.1 + - - +
83P ARG* 2.7 28.9 + - - +
84P VAL* 3.0 17.2 + - + +
86P VAL* 1.3 78.5 - - + +
88P ARG* 1.3 58.1 + - - +
90P ARG* 3.4 28.1 + - - +
91P LYS* 3.0 25.7 + - - +
65W LEU* 5.5 0.9 - - - +
69W SER* 5.5 2.9 - - - -
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Residues in contact with ARG 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84P VAL* 3.2 9.0 + - + +
85P LEU* 3.9 7.2 - - - +
87P HIS* 1.3 80.3 - - - +
89P ALA* 1.4 60.5 + - - +
91P LYS* 3.2 38.8 + - - +
92P LEU* 3.1 35.1 + - + +
113P VAL* 5.3 0.2 - - - -
116P VAL* 3.5 41.3 - - + +
119P GLU* 3.0 37.0 + - - -
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Residues in contact with ALA 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67P ILE* 3.8 19.8 - - + +
73P LEU* 4.6 8.7 - - + -
85P LEU* 3.0 14.1 + - + +
86P VAL* 3.1 12.7 + - - +
88P ARG* 1.4 76.8 - - - +
90P ARG* 1.3 55.4 + - - +
92P LEU* 3.5 0.7 + - - -
93P ALA* 3.1 23.2 + - - +
109P LEU* 3.4 13.7 - - + +
113P VAL* 3.8 29.1 - - + +
135P ILE* 6.6 0.2 - - + -
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Residues in contact with ARG 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116O LYS* 6.2 1.0 - - - +
65P GLU* 3.9 26.5 + - - +
66P PRO* 3.4 25.1 + - - +
67P ILE* 3.8 18.6 - - + +
86P VAL* 3.0 33.1 + - + +
87P HIS* 3.5 23.4 + - - +
89P ALA* 1.3 72.4 - - - +
91P LYS* 1.3 59.4 + - - +
93P ALA* 3.8 1.3 - - - +
94P GLN* 3.0 33.8 + - - +
65W LEU* 3.7 16.7 - - + +
68W LEU* 3.3 43.1 + - + +
69W SER* 3.4 35.5 + - - +
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Residues in contact with LYS 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87P HIS 3.0 14.5 + - - +
88P ARG* 3.2 51.7 + - + +
90P ARG* 1.3 75.8 - - - +
92P LEU* 1.3 61.8 + - - +
94P GLN* 4.1 2.3 - - - +
95P GLN* 3.0 47.6 + - + +
65W LEU* 4.8 10.3 - - + +
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Residues in contact with LEU 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88P ARG* 3.1 33.1 + - + +
89P ALA 3.7 5.4 - - - +
91P LYS* 1.3 82.8 - - - +
93P ALA* 1.3 57.2 + - - +
95P GLN* 4.0 13.9 - - - +
96P TYR* 3.1 28.8 + - - +
104P ILE* 4.7 2.6 - - + +
109P LEU* 3.7 9.6 - - + -
112P ARG* 3.8 40.9 - - + +
113P VAL* 3.6 34.1 - - + +
116P VAL* 4.2 10.1 - - + -
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Residues in contact with ALA 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67P ILE 3.9 17.3 - - - +
68P THR* 4.1 18.8 - - - +
89P ALA 3.1 16.5 + - - +
90P ARG 3.8 4.5 - - - +
91P LYS 3.3 0.4 - - - -
92P LEU* 1.3 77.2 - - - +
94P GLN* 1.4 59.5 + - + +
96P TYR* 3.3 5.9 + - - +
97P TYR* 3.1 24.6 + - - +
104P ILE* 4.3 16.2 + - + +
109P LEU* 4.2 10.3 - - + +
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Residues in contact with GLN 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90P ARG 3.0 19.7 + - - +
91P LYS* 4.3 2.7 - - - +
93P ALA* 1.4 74.9 + - + +
95P GLN* 1.4 59.8 + - - +
97P TYR* 3.2 24.4 + - - +
98P LEU* 3.1 31.0 + - - +
61W SER* 2.8 39.1 - - - +
64W GLU* 3.2 20.7 + - - +
65W LEU* 3.1 34.4 + - + -
68W LEU* 4.8 9.0 - - + -
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Residues in contact with GLN 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91P LYS* 3.0 37.3 + - + +
92P LEU* 4.0 13.1 - - - +
94P GLN* 1.4 72.9 - - - +
96P TYR* 1.3 65.4 + - - +
98P LEU* 3.4 17.2 - - + +
99P VAL* 3.2 32.7 + - + +
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Residues in contact with TYR 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92P LEU 3.1 20.6 + - - +
93P ALA 3.4 5.6 - - - +
95P GLN* 1.3 78.5 - - - +
97P TYR* 1.3 56.0 + - - +
100P TYR* 2.9 62.0 + + + +
102P GLU* 3.2 30.5 + - - -
104P ILE* 3.3 39.0 - - + -
105P PRO* 3.2 9.7 - - - +
108P GLN* 4.6 0.3 - - - +
112P ARG* 3.3 39.0 - - - -
73X TYR* 2.4 34.0 + + - -
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Residues in contact with TYR 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69P LYS* 3.9 29.5 + - - -
93P ALA 3.1 13.3 + - - +
94P GLN* 3.2 26.6 + - - +
96P TYR* 1.3 76.3 - - - +
98P LEU* 1.4 59.6 + - - +
101P GLN* 2.9 70.6 + - - +
102P GLU* 3.6 26.9 - - - +
103P PRO* 4.0 7.2 - - + -
36W PHE* 5.8 7.2 - + - -
60W SER* 5.0 11.2 - - - -
61W SER* 5.6 5.8 - - - -
64W GLU* 5.1 8.7 - - - -
84X TYR* 5.6 1.6 + - - -
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Residues in contact with LEU 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94P GLN 3.1 18.3 + - - +
95P GLN* 3.4 18.6 - - + +
97P TYR* 1.4 79.1 - - - +
99P VAL* 1.4 77.6 + - + +
101P GLN* 3.5 19.9 + - - +
57W GLN* 3.9 20.3 - - + +
58W LEU* 5.2 11.0 - - + -
61W SER* 3.4 30.1 - - - +
88X SER* 5.4 0.3 - - - -
92X ASN* 3.9 18.7 - - - +
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Residues in contact with VAL 99 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95P GLN* 3.2 25.1 + - + +
96P TYR* 5.1 0.2 - - - -
98P LEU* 1.4 92.7 - - + +
100P TYR* 1.4 88.8 + - + +
101P GLN 3.7 0.2 - - - -
69X ARG* 4.9 10.5 - - - +
88X SER* 3.5 28.3 - - - +
89X MET* 4.2 6.4 + - + -
92X ASN* 4.2 24.7 - - + +
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Residues in contact with TYR 100 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96P TYR* 2.9 57.5 + + + +
99P VAL* 1.4 95.5 - - + +
101P GLN* 1.3 69.2 + - - +
102P GLU* 3.2 17.5 - - - +
112P ARG* 4.3 10.7 + - - -
69X ARG 5.4 2.9 + - - -
73X TYR* 4.0 25.6 - + + +
85X THR* 3.2 45.6 + - + +
88X SER* 3.8 2.1 - - - -
89X MET* 3.7 23.3 - - + -
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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
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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