Contacts of the helix formed by residues 81 - 102 (chain U) 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 LEU 81 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152T ASN* 3.2 29.3 - - - +
154T PHE* 5.0 9.9 - - + -
33U SER* 4.9 9.0 - - - +
77U VAL* 4.5 17.9 - - + +
78U ALA* 5.7 1.1 - - - -
79U GLY 3.7 13.0 - - - +
80U LEU* 1.4 72.8 - - - +
82U ALA* 1.3 65.4 + - - +
83U ASP 3.4 0.2 - - - -
84U ALA* 3.2 15.6 + - + +
85U ARG* 3.4 32.8 + - - +
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Residues in contact with ALA 82 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117T GLN* 2.9 20.1 + - - +
120T THR* 5.8 2.7 - - + +
150T SER* 3.9 13.5 - - - +
151T ALA* 3.6 38.1 - - + +
152T ASN* 3.9 11.7 - - + +
80U LEU* 3.2 11.8 - - + -
81U LEU* 1.3 80.5 - - - +
83U ASP* 1.3 59.1 + - - +
84U ALA 3.6 0.2 + - - -
85U ARG* 3.8 15.3 + - - +
86U SER 4.1 1.7 + - - -
129U ARG* 5.9 0.9 - - - +
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Residues in contact with ASP 83 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117T GLN* 3.5 13.4 - - - +
121T GLN* 3.0 20.1 - - - +
80U LEU* 3.6 20.6 - - + -
82U ALA* 1.3 75.9 - - - +
84U ALA* 1.3 62.2 + - - +
85U ARG 3.3 0.2 - - - -
86U SER* 2.7 24.5 + - - -
87U LEU* 3.4 7.6 + - - +
129U ARG* 3.6 17.0 - - - +
131U PHE* 3.3 22.2 - - - -
132U GLY 3.1 26.7 + - - -
133U CYS* 3.3 11.2 - - - -
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Residues in contact with ALA 84 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67U PHE* 5.1 0.4 - - + -
75U MET* 4.7 0.3 - - - +
77U VAL* 3.8 41.7 - - + +
79U GLY 4.9 1.3 - - - +
80U LEU 3.5 7.1 + - - +
81U LEU* 3.2 12.5 + - - +
83U ASP* 1.3 76.1 - - - +
85U ARG* 1.3 59.0 + - + +
87U LEU* 3.4 7.8 + - - +
88U ALA* 3.0 25.7 + - - +
133U CYS* 3.3 22.1 - - + -
135U PHE* 6.0 0.4 - - - -
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Residues in contact with ARG 85 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113T GLY* 5.6 0.2 - - - -
151T ALA* 4.0 4.8 - - + +
152T ASN* 3.2 58.4 + - - +
153T TYR* 3.3 50.0 + - - -
154T PHE* 5.7 0.2 - - - -
67U PHE* 4.0 28.1 - - + -
81U LEU* 3.4 28.4 + - + +
82U ALA* 4.0 10.3 - - - +
83U ASP 3.3 0.4 - - - -
84U ALA* 1.3 74.3 - - + +
86U SER* 1.4 58.3 + - - +
88U ALA* 3.1 9.1 + - + +
89U ASP* 3.0 38.8 + - - +
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Residues in contact with SER 86 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117T GLN* 4.0 26.3 - - - +
121T GLN* 5.9 0.5 - - - +
82U ALA 4.1 1.6 + - - -
83U ASP* 2.7 31.1 + - - -
85U ARG* 1.4 76.0 - - - +
87U LEU* 1.3 60.1 + - - +
89U ASP* 3.3 8.2 + - - +
90U ILE* 3.0 35.5 + - - +
118U TYR* 6.0 1.1 - - - -
131U PHE* 4.7 4.7 - - - -
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Residues in contact with LEU 87 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75U MET* 4.0 4.4 - - + +
83U ASP 3.4 3.3 + - - +
84U ALA* 3.4 6.2 + - - +
85U ARG 3.3 0.2 - - - -
86U SER* 1.3 77.9 + - - +
88U ALA* 1.3 60.3 + - - +
90U ILE* 3.5 5.0 + - + +
91U ALA* 3.0 28.1 + - - +
115U VAL* 4.6 8.6 - - + +
118U TYR* 4.1 15.3 - - + -
119U VAL* 3.5 22.4 - - + -
131U PHE* 3.5 46.7 - - + -
133U CYS* 4.0 23.6 - - + -
135U PHE* 3.5 35.0 - - + -
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Residues in contact with ALA 88 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67U PHE* 3.9 36.3 - - + -
69U VAL* 4.6 2.2 - - + +
75U MET* 3.9 15.2 - - - +
84U ALA 3.0 14.0 + - - +
85U ARG* 3.1 12.3 + - - +
87U LEU* 1.3 74.9 - - - +
89U ASP* 1.4 56.2 + - - +
91U ALA* 3.2 5.4 + - - +
92U ARG* 3.0 39.4 + - - +
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Residues in contact with ASP 89 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114T SER* 4.6 11.3 + - - +
85U ARG* 3.0 26.7 + - - +
86U SER* 3.3 8.0 + - - +
88U ALA* 1.4 70.3 - - - +
90U ILE* 1.4 61.9 + - + +
92U ARG* 3.2 34.3 + - - +
93U GLU* 3.1 25.3 + - - +
77b LEU* 4.5 8.1 - - - +
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Residues in contact with ILE 90 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86U SER* 3.0 21.9 + - - +
87U LEU* 3.9 7.2 - - - +
89U ASP* 1.4 75.8 - - + +
91U ALA* 1.3 59.6 + - - +
93U GLU* 3.2 24.0 + - - +
94U GLU* 2.9 56.8 + - + +
115U VAL* 5.2 3.1 - - + -
118U TYR* 3.9 46.4 - - + +
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Residues in contact with ALA 91 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69U VAL* 3.7 23.2 - - + +
75U MET* 3.9 14.6 - - + -
87U LEU 3.0 15.6 + - - +
88U ALA 3.2 8.9 + - - +
90U ILE* 1.3 75.9 - - - +
92U ARG* 1.4 53.8 + - - +
94U GLU* 3.3 13.1 + - - +
95U ALA* 3.0 28.4 + - - +
111U LEU* 4.2 3.0 - - + +
115U VAL* 4.0 15.0 - - + -
137U LEU* 4.3 2.2 - - + -
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Residues in contact with ARG 92 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67U PHE* 3.8 30.2 - - - +
68U ASN 3.1 25.9 + - - +
69U VAL* 3.0 27.7 - - - +
88U ALA* 3.0 23.3 + - - +
89U ASP* 3.2 34.8 + - - +
90U ILE 3.3 0.2 - - - -
91U ALA* 1.4 73.5 - - - +
93U GLU* 1.4 60.5 + - - +
95U ALA* 3.5 2.9 + - - +
96U SER* 3.2 23.6 + - - -
73b ASP* 5.1 7.6 - - - +
76b LEU* 3.3 42.2 + - + +
77b LEU* 4.1 16.1 + - - +
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Residues in contact with GLU 93 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89U ASP 3.1 12.8 + - - +
90U ILE* 3.2 32.3 + - - +
92U ARG* 1.4 72.5 - - - +
94U GLU* 1.3 61.6 + - + +
96U SER* 2.7 21.4 + - - +
97U ASN* 2.9 35.4 + - - +
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Residues in contact with GLU 94 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90U ILE* 2.9 43.2 + - + +
91U ALA 3.6 3.8 - - - +
93U GLU* 1.3 78.4 - - + +
95U ALA* 1.3 59.9 + - - +
97U ASN* 4.0 5.7 - - - +
98U PHE* 3.3 23.7 + - - +
106U ILE* 4.0 6.2 - - + +
111U LEU* 3.4 9.0 - - + +
114U ARG* 3.9 21.4 - - + +
115U VAL* 2.1 55.2 + - - +
118U TYR* 4.2 5.4 - - - +
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Residues in contact with ALA 95 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69U VAL* 4.3 4.3 - - + +
70U ASP* 3.7 37.9 - - + +
91U ALA 3.0 16.7 + - - +
92U ARG 3.8 5.4 - - - +
93U GLU 3.3 0.2 - - - -
94U GLU* 1.3 76.2 - - - +
96U SER* 1.4 55.2 + - - +
98U PHE* 3.5 2.9 + - - +
99U ARG* 3.0 31.4 + - - +
106U ILE* 4.1 22.1 + - + +
111U LEU* 4.7 1.8 - - + +
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Residues in contact with SER 96 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92U ARG 3.2 12.5 + - - -
93U GLU* 2.7 28.2 + - - +
95U ALA* 1.4 74.2 - - - +
97U ASN* 1.4 61.8 + - - +
98U PHE 3.2 0.4 - - - -
99U ARG* 3.3 12.4 + - - +
100U SER* 3.0 29.5 + - - -
69b GLN* 3.3 37.7 + - - -
72b ILE* 6.4 1.8 - - - -
73b ASP* 4.8 4.5 + - - -
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Residues in contact with ASN 97 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93U GLU* 2.9 36.1 + - - +
94U GLU* 4.0 5.8 - - - +
95U ALA 3.5 0.2 - - - -
96U SER* 1.4 75.9 + - - +
98U PHE* 1.3 59.0 + - - +
100U SER* 3.1 8.5 + - - -
101U ASN* 3.0 43.3 + - - +
102U PHE* 5.4 0.4 - - - -
69b GLN* 5.3 2.1 + - - -
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Residues in contact with PHE 98 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94U GLU 3.3 16.1 + - - +
95U ALA 3.6 5.4 - - - +
96U SER 3.2 0.6 - - - -
97U ASN* 1.3 78.0 - - - +
99U ARG* 1.3 63.3 + - - +
102U PHE* 3.1 52.2 + + - +
103U GLY 3.7 0.3 + - - +
104U TYR* 3.1 66.6 - + - -
106U ILE* 3.6 28.5 - - + -
107U PRO* 3.7 6.7 - - + -
110U HIS* 3.4 32.3 - + - -
66V HIS* 4.7 1.8 - + - -
70V LEU* 4.3 7.4 - - + -
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Residues in contact with ARG 99 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70U ASP* 3.0 29.4 + - - -
71U ARG* 3.4 26.3 - - - +
95U ALA 3.0 20.3 + - - +
96U SER* 3.3 10.6 + - - +
98U PHE* 1.3 77.9 - - - +
100U SER* 1.3 56.6 + - - +
103U GLY* 2.7 42.4 + - - +
104U TYR 4.3 3.1 - - - +
105U ASN* 2.6 44.4 + - - +
106U ILE 4.5 0.8 - - - +
65b GLN* 4.9 1.0 - - - +
72b ILE* 4.1 30.5 - - - +
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Residues in contact with SER 100 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96U SER 3.0 14.4 + - - -
97U ASN* 3.1 16.3 + - - -
99U ARG* 1.3 79.7 - - - +
101U ASN* 1.4 69.8 + - - +
102U PHE 3.4 0.3 + - - -
103U GLY* 3.9 3.1 + - - -
81V SER* 4.9 4.0 - - - -
84V LYS* 5.5 0.9 + - - -
85V GLU* 3.0 15.7 - - - +
65b GLN* 3.5 29.1 - - - +
69b GLN* 5.8 2.2 + - - -
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Residues in contact with ASN 101 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97U ASN* 3.0 31.5 + - - +
100U SER* 1.4 82.6 + - - +
102U PHE* 1.3 79.6 + - + +
103U GLY 3.6 0.2 - - - -
81V SER* 4.0 10.6 - - - -
82V LEU* 3.4 27.3 + - + +
85V GLU* 3.7 19.1 - - - +
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Residues in contact with PHE 102 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97U ASN 4.8 0.2 - - - -
98U PHE* 3.1 68.9 + + + +
101U ASN* 1.3 101.1 - - + +
103U GLY* 1.3 59.6 + - - +
104U TYR* 3.0 7.4 + - + -
110U HIS* 5.7 1.6 - - - -
62V GLN* 5.6 3.8 - - + -
66V HIS* 3.9 17.3 - + + -
77V HIS* 4.4 1.6 - - - +
78V THR* 3.0 57.4 + - + +
81V SER* 4.0 8.3 + - - -
82V LEU* 4.2 18.4 - - + -
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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