Contacts of the helix formed by residues 83 - 106 (chain G) in PDB entry 5T0J
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 MET 83 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G ALA* 4.0 36.4 + - + +
34G GLN* 5.9 0.2 - - - +
35G GLY* 4.4 3.4 - - - -
81G THR 3.6 8.1 + - - +
82G GLY* 1.3 71.5 - - - -
84G THR* 1.3 63.6 + - - +
85G ALA* 3.6 8.5 + - + +
86G ASP* 3.3 30.3 - - - +
87G SER* 3.9 11.3 + - - -
132G ARG* 3.6 20.2 - - - +
135G GLY* 4.3 21.9 + - - +
136G CYS* 4.1 4.0 - - - +
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Residues in contact with THR 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68G HIS* 3.3 32.9 + - + +
70G PHE* 4.5 9.6 - - + -
82G GLY 3.4 4.5 + - - -
83G MET* 1.3 70.5 - - - +
85G ALA* 1.3 60.8 + - - +
87G SER* 2.8 30.5 + - - +
88G ARG* 2.6 50.4 + - - +
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Residues in contact with ALA 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G MET* 3.3 7.3 - - + -
84G THR* 1.3 80.9 - - - +
86G ASP* 1.3 72.2 + - - +
87G SER 3.4 0.2 + - - -
88G ARG* 3.6 17.9 + - - +
89G SER* 4.1 9.0 + - - -
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Residues in contact with ASP 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G MET* 3.3 22.7 + - + +
85G ALA* 1.3 82.6 - - - +
87G SER* 1.3 64.0 + - - +
88G ARG 3.3 0.2 - - - -
89G SER* 3.3 17.0 + - - -
90G GLN* 3.4 6.2 + - - +
132G ARG* 2.5 35.9 + - - -
134G LEU* 3.7 18.8 - - + +
135G GLY 3.3 7.6 + - - -
136G CYS* 3.3 31.3 - - + +
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Residues in contact with SER 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G PHE* 4.0 5.9 - - - -
80G MET* 3.6 37.7 - - - +
81G THR 5.0 0.7 - - - -
83G MET 3.9 11.9 + - - -
84G THR* 2.8 37.5 + - - +
86G ASP* 1.3 78.7 - - - +
88G ARG* 1.3 62.4 + - - +
90G GLN 3.1 2.6 + - - -
91G VAL* 3.0 25.5 + - - +
136G CYS* 3.3 14.2 - - - +
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Residues in contact with ARG 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G THR 5.1 9.9 + - - -
66G VAL* 6.0 1.6 - - - +
70G PHE* 4.5 15.8 - - + -
84G THR* 2.6 57.5 + - - +
85G ALA* 3.6 12.8 - - - +
86G ASP 3.3 0.4 - - - -
87G SER* 1.3 79.2 + - - +
89G SER* 1.3 61.4 + - - +
91G VAL* 3.1 17.3 + - - +
92G GLN* 2.8 36.1 + - - +
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Residues in contact with SER 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G ALA 4.1 8.9 + - - -
86G ASP* 3.3 13.2 + - - -
87G SER 3.2 0.6 - - - -
88G ARG* 1.3 79.3 - - - +
90G GLN* 1.3 60.2 + - - +
92G GLN* 3.6 10.6 + - - +
93G ARG* 3.3 27.4 + - - +
134G LEU* 5.6 7.1 - - - +
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Residues in contact with GLN 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G MET* 4.2 7.4 - - + -
86G ASP 3.4 7.8 + - - +
87G SER 3.1 9.4 + - - +
89G SER* 1.3 77.0 - - - +
91G VAL* 1.3 59.9 + - - +
93G ARG* 3.1 33.0 + - - +
94G ALA* 3.0 27.4 + - - +
118G ILE* 3.3 33.1 - - + +
122G SER* 3.3 22.8 + - - -
125G TYR* 4.2 9.5 - - - -
134G LEU* 6.2 0.8 - - - +
136G CYS* 4.2 17.5 - - - -
138G MET* 4.1 18.7 - - + +
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Residues in contact with VAL 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G PHE* 3.5 40.6 - - + -
72G ILE* 3.4 16.7 - - + +
78G CYS* 4.7 2.7 - - - -
80G MET* 4.4 10.5 - - - -
87G SER 3.0 17.2 + - - +
88G ARG* 3.1 11.4 + - - +
90G GLN* 1.3 77.6 - - - +
92G GLN* 1.3 66.6 + - + +
94G ALA 3.2 2.8 + - - -
95G ARG* 3.1 54.0 + - - +
138G MET* 4.8 0.9 - - - -
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Residues in contact with GLN 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G ARG* 2.8 43.1 + - - +
89G SER* 3.6 9.6 - - - +
91G VAL* 1.3 80.5 - - + +
93G ARG* 1.3 57.8 + - + +
95G ARG* 3.4 20.2 + - - +
96G TYR* 3.1 25.6 + - - +
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Residues in contact with ARG 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G SER* 3.3 16.6 + - - +
90G GLN* 3.1 36.6 + - - +
91G VAL 3.1 0.8 - - - -
92G GLN* 1.3 76.0 - - - +
94G ALA* 1.3 60.4 + - - +
96G TYR* 2.9 7.9 + - + +
97G GLU* 2.4 65.5 + - - +
117G ARG 4.2 1.6 + - - -
118G ILE* 3.8 9.9 + - + +
121G ILE* 3.3 32.3 - - - +
125G TYR* 3.0 41.9 + - - -
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Residues in contact with ALA 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G ILE* 3.6 26.8 - - + +
90G GLN 3.0 17.1 + - - +
91G VAL 3.2 4.9 + - - +
93G ARG* 1.3 77.1 - - - +
95G ARG* 1.3 58.1 + - - +
97G GLU* 4.5 1.3 - - - +
98G ALA* 3.1 30.3 + - - +
114G LEU* 4.0 22.0 - - + +
118G ILE* 4.0 13.2 - - + +
138G MET* 4.5 9.0 - - + -
140G LEU* 5.8 0.4 - - + -
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Residues in contact with ARG 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G PHE* 4.9 3.0 - - - +
71G LYS* 2.8 39.6 + - - +
72G ILE* 3.6 27.2 + - + +
91G VAL* 3.1 36.3 + - - +
92G GLN* 3.6 19.0 - - - +
93G ARG 3.1 0.2 - - - -
94G ALA* 1.3 78.1 - - - +
96G TYR* 1.3 57.5 + - - +
98G ALA* 4.1 3.0 - - - +
99G ALA* 3.1 26.5 + - - +
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Residues in contact with TYR 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G GLN 3.1 13.0 + - - +
93G ARG* 2.9 11.5 + - - +
95G ARG* 1.3 77.6 - - - +
97G GLU* 1.3 59.3 + - + +
99G ALA* 3.3 8.5 + - + +
100G ASN* 2.4 67.9 + - - -
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Residues in contact with GLU 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G ARG* 2.4 52.0 + - - +
94G ALA* 4.4 3.8 - - - +
96G TYR* 1.3 75.2 - - + +
98G ALA* 1.3 64.9 + - - +
100G ASN* 3.4 13.4 + - - +
101G TRP* 3.3 18.4 + - - +
109G ILE* 5.2 3.0 - - - +
114G LEU* 4.3 7.5 - - + +
117G ARG* 3.2 31.3 - - + +
118G ILE* 3.2 26.0 + - - +
121G ILE* 3.5 11.3 - - - +
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Residues in contact with ALA 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G ILE* 4.7 0.4 - - + -
73G THR* 4.3 18.6 - - + +
94G ALA 3.1 20.8 + - - +
95G ARG* 4.1 4.9 - - - +
97G GLU* 1.3 77.5 - - - +
99G ALA* 1.3 57.3 + - - +
101G TRP* 3.2 9.3 + - - +
102G LYS* 2.9 31.8 + - + +
108G GLU* 5.3 2.0 - - - +
109G ILE* 4.3 11.3 - - + +
114G LEU* 3.8 19.4 - - + +
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Residues in contact with ALA 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G ARG 3.1 19.6 + - - +
96G TYR* 3.6 11.0 - - + +
97G GLU 3.3 0.2 - - - -
98G ALA* 1.3 73.5 - - - +
100G ASN* 1.3 54.9 + - - +
102G LYS* 3.1 10.3 + - + +
103G TYR* 2.6 36.7 + - - +
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Residues in contact with ASN 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G TYR* 2.4 62.1 + - - -
97G GLU* 3.5 12.4 - - - +
98G ALA 3.3 0.4 - - - -
99G ALA* 1.3 76.7 - - - +
101G TRP* 1.3 57.6 + - - +
103G TYR* 4.4 6.8 - - - +
104G LYS* 2.9 60.5 + - + +
105G TYR* 5.5 0.2 - - - -
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Residues in contact with TRP 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G GLU 3.3 9.9 + - - +
98G ALA 3.2 10.0 + - - +
100G ASN* 1.3 78.7 - - - +
102G LYS* 1.3 60.2 - - - +
105G TYR* 3.2 59.6 + + + +
106G GLY 3.3 3.3 + - - -
107G TYR* 3.1 58.3 - + - +
109G ILE* 3.4 43.3 - - + +
110G PRO* 3.7 16.6 - - + -
113G MET* 3.9 35.2 - - + -
117G ARG* 5.7 9.9 - - + -
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Residues in contact with LYS 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G THR* 6.1 2.2 - - + -
98G ALA* 2.9 20.6 + - + +
99G ALA* 3.1 11.6 + - - +
101G TRP* 1.3 75.2 - - - +
103G TYR* 1.3 66.1 + - - +
106G GLY* 3.0 28.3 + - - +
107G TYR* 3.2 21.3 - - - +
108G GLU* 3.5 42.8 + - - +
109G ILE* 5.0 0.7 - - + +
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Residues in contact with TYR 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G ALA 2.6 20.1 + - - +
100G ASN* 4.0 7.4 - - - +
102G LYS* 1.3 77.0 - - - +
104G LYS* 1.3 95.9 + - + +
106G GLY* 3.8 3.5 + - - -
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Residues in contact with LYS 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G ASN* 2.9 46.0 + - + +
103G TYR* 1.3 99.1 - - + +
105G TYR* 1.3 79.9 + - + +
106G GLY* 3.6 0.3 + - - -
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Residues in contact with TYR 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G ASN 5.5 0.2 - - - -
101G TRP* 3.2 74.8 + + - +
104G LYS* 1.3 92.8 - - + +
106G GLY* 1.3 56.0 + - - +
107G TYR* 3.2 33.8 - - + -
117G ARG* 4.9 11.1 + - - -
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Residues in contact with GLY 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G TRP 3.3 1.2 + - - -
102G LYS* 3.0 33.2 + - - +
103G TYR 4.3 3.1 - - - -
104G LYS 3.4 2.3 - - - -
105G TYR* 1.3 75.6 - - - +
107G TYR* 1.3 59.8 + - - +
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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
------------------------------------------------------------
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