Contacts of the helix formed by residues 84 - 95 (chain M) in PDB entry 3Q2K
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 84 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80M THR* 4.0 14.1 - - - -
81M PRO* 2.9 20.9 + - + +
83M GLY* 1.3 75.1 - - - +
85M HIS* 1.3 66.1 + - - +
86M PRO* 3.2 4.7 - - - -
87M TRP* 3.3 12.4 + - + +
88M GLN* 3.0 35.9 + - + +
180M TRP* 4.0 24.0 - - + -
500M NAI 3.5 46.7 - - + +
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Residues in contact with HIS 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78M LEU* 3.6 25.9 + - + +
80M THR* 2.7 39.3 + - - -
81M PRO 3.6 2.9 - - - -
82M SER* 3.0 16.1 + - - +
84M LEU* 1.3 76.2 - - - +
86M PRO* 1.3 61.6 - - + +
88M GLN* 4.6 0.7 - - - -
89M ALA* 2.8 32.2 + - - +
101M SER* 3.7 12.3 - - - +
102M GLU* 3.4 21.6 + - + +
104M PRO 2.9 24.6 + - - -
105M MET 3.1 17.0 - - - +
115M MET* 4.3 1.6 - - + -
500M NAI 3.1 20.6 + - - -
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Residues in contact with PRO 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82M SER 3.6 5.8 - - - +
83M GLY 3.4 14.1 - - - +
84M LEU 3.2 4.9 - - - -
85M HIS* 1.3 96.8 - - + +
87M TRP* 1.3 67.6 + - + +
89M ALA* 3.7 1.4 - - - +
90M ILE* 2.8 34.8 + - + +
105M MET 3.6 3.1 - - - +
106M ALA* 3.6 13.7 - - + -
107M THR* 5.0 1.1 - - - +
111M ASP* 3.6 35.4 - - + +
115M MET* 3.1 26.5 - - + -
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Residues in contact with TRP 87 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117K LYS* 5.7 11.9 - - + -
121K GLU* 5.4 8.5 - - - -
83M GLY 3.5 22.2 + - - -
84M LEU* 3.3 12.7 + - + +
85M HIS 3.3 0.4 - - - -
86M PRO* 1.3 79.9 - - + +
88M GLN* 1.3 61.6 + - + +
90M ILE* 3.3 15.9 + - + +
91M GLU* 3.2 20.7 + - - +
108M ARG* 6.4 0.4 - - - -
111M ASP* 3.1 36.5 + - + -
114M ARG* 3.4 35.0 - - - -
180M TRP* 5.8 2.7 - + - -
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Residues in contact with GLN 88 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16M VAL* 4.0 9.9 - - - +
64M LEU* 3.8 25.1 - - + +
78M LEU* 3.9 22.0 - - + +
80M THR* 2.7 32.3 + - - +
84M LEU* 3.0 26.9 + - + +
85M HIS* 3.9 2.2 - - - +
87M TRP* 1.3 73.2 - - + +
89M ALA* 1.3 54.5 + - - +
91M GLU* 3.1 4.9 + - - +
92M VAL* 2.6 40.3 + - - +
500M NAI 3.5 34.5 + - - -
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Residues in contact with ALA 89 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78M LEU* 3.9 5.0 - - + +
85M HIS 2.8 22.3 + - - +
86M PRO 3.7 4.0 - - - +
88M GLN* 1.3 72.4 - - - +
90M ILE* 1.3 58.1 + - - +
92M VAL* 3.7 1.3 - - - +
93M ALA* 2.8 30.1 + - - +
99M VAL* 3.9 30.0 - - + +
115M MET* 3.8 26.5 - - + -
119M CYS* 4.4 7.8 - - - -
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Residues in contact with ILE 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86M PRO* 2.8 26.3 + - + +
87M TRP* 3.6 22.4 - - + +
88M GLN 3.1 0.2 - - - -
89M ALA* 1.3 73.7 - - - +
91M GLU* 1.3 65.2 + - - +
93M ALA* 3.2 2.4 + - - +
94M GLN* 3.1 49.3 + - - +
111M ASP* 6.3 0.2 - - - -
114M ARG* 4.0 34.3 - - + +
115M MET* 4.2 18.6 - - - +
118M ALA* 3.9 21.5 - - + -
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Residues in contact with GLU 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64M LEU* 3.6 18.2 - - + +
65M SER* 3.2 32.7 + - - -
68M LEU* 4.0 15.7 - - + +
87M TRP 3.2 10.3 + - - +
88M GLN* 3.1 7.6 + - - +
90M ILE* 1.3 78.0 - - - +
92M VAL* 1.3 65.5 + - - +
93M ALA 3.1 0.2 + - - -
94M GLN* 3.2 13.2 + - + +
95M ALA* 3.1 20.8 + - - +
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Residues in contact with VAL 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64M LEU* 4.2 15.3 - - + -
68M LEU* 4.0 7.2 - - - +
76M LEU* 4.0 31.6 - - + -
78M LEU* 4.4 10.1 - - + -
88M GLN 2.6 29.4 + - - +
91M GLU* 1.3 72.2 - - - +
93M ALA* 1.3 60.3 + - - +
95M ALA* 3.2 11.6 + - - +
97M ARG* 3.4 25.0 + - + +
98M HIS 3.8 13.5 - - - +
99M VAL* 3.5 26.7 - - + -
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Residues in contact with ALA 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89M ALA 2.8 19.0 + - - +
90M ILE* 3.7 5.6 - - - +
91M GLU 3.2 0.4 - - - -
92M VAL* 1.3 78.6 - - - +
94M GLN* 1.3 58.2 + - + +
96M GLY* 2.8 17.3 + - - -
97M ARG 4.0 10.1 - - - +
99M VAL* 5.1 0.4 - - + -
118M ALA* 4.3 4.7 - - + +
119M CYS* 3.9 29.4 - - - +
122M ALA* 3.2 33.6 - - + +
124M VAL* 4.9 0.9 - - + -
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Residues in contact with GLN 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90M ILE* 3.1 35.8 + - + +
91M GLU* 3.7 13.5 - - + +
93M ALA* 1.3 77.8 - - + +
95M ALA* 1.3 56.5 + - - +
96M GLY 3.2 1.3 + - - -
118M ALA* 5.5 4.3 - - + +
122M ALA* 5.1 1.8 - - - -
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Residues in contact with ALA 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68M LEU* 3.9 33.9 - - + -
91M GLU 3.1 11.6 + - - +
92M VAL 3.5 9.2 - - - +
93M ALA 3.1 0.8 - - - -
94M GLN* 1.3 76.2 - - - +
96M GLY* 1.3 60.7 + - - -
97M ARG* 3.2 22.2 + - + +
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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