Contacts of the helix formed by residues 84 - 95 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80H THR* 4.4 0.9 - - - +
81H PRO* 3.0 26.7 + - + +
83H GLY* 1.3 78.1 - - - +
85H HIS* 1.3 67.2 + - - +
86H PRO* 3.2 1.9 - - - -
87H TRP* 3.4 11.6 + - + +
88H GLN* 3.0 41.6 + - + +
180H TRP* 3.9 26.4 - - + -
500H NAI 3.8 44.0 - - + +
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Residues in contact with HIS 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H LEU* 3.4 21.4 + - + +
80H THR* 2.8 40.2 + - - -
81H PRO 3.6 5.6 - - - -
82H SER* 2.9 13.4 + - - +
84H LEU* 1.3 77.6 - - - +
86H PRO* 1.3 56.6 - - - +
88H GLN* 4.7 0.4 - - - +
89H ALA* 2.9 28.2 + - - +
101H SER* 3.1 11.6 + - - +
102H GLU* 3.1 31.4 + - + +
104H PRO 2.9 22.2 + - - -
105H MET 3.0 18.4 - - - +
115H MET* 4.4 0.9 - - + -
500H NAI 3.2 20.6 + - - -
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Residues in contact with PRO 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H SER 3.6 5.4 - - - +
83H GLY 3.6 14.1 - - - +
84H LEU 3.5 3.6 - - - -
85H HIS* 1.3 95.4 - - + +
87H TRP* 1.3 64.4 + - + +
90H ILE* 3.0 37.7 + - + +
105H MET 3.6 4.7 - - - +
106H ALA* 3.7 9.4 - - + -
107H THR 5.1 0.9 - - - +
111H ASP* 3.5 35.7 - - + +
115H MET* 3.1 29.3 - - + +
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Residues in contact with TRP 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E LYS* 6.3 5.2 - - + -
121E GLU* 6.1 0.9 - - - -
83H GLY 3.7 21.7 + - - -
84H LEU* 3.4 12.1 + - + +
85H HIS 3.3 0.2 - - - -
86H PRO* 1.3 76.6 - - + +
88H GLN* 1.3 67.4 + - + +
90H ILE* 3.2 19.4 + - + +
91H GLU* 3.0 23.6 + - - +
111H ASP* 3.6 36.0 + - + -
114H ARG* 3.6 37.9 - - - -
180H TRP* 6.0 1.6 - + - -
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Residues in contact with GLN 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H VAL* 4.1 6.1 - - - +
64H LEU* 3.6 28.1 - - + +
78H LEU* 3.8 22.5 - - + +
80H THR* 2.8 32.4 + - - +
84H LEU* 3.0 31.2 + - + +
85H HIS 4.1 0.4 - - - +
87H TRP* 1.3 76.4 - - + +
89H ALA* 1.3 57.6 + - - +
91H GLU* 3.1 6.5 + - - +
92H VAL* 2.8 34.1 + - - +
500H NAI 3.6 32.4 + - - -
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Residues in contact with ALA 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H LEU* 3.6 14.2 - - + +
85H HIS 2.9 19.5 + - - +
86H PRO 3.8 3.6 - - - +
88H GLN* 1.3 75.7 - - - +
90H ILE* 1.3 53.9 - - - +
92H VAL* 3.5 2.0 + - - +
93H ALA* 2.8 34.9 + - - +
99H VAL* 3.8 22.7 - - + +
115H MET* 3.8 26.5 - - + -
119H CYS* 4.4 6.5 - - - -
126H LEU* 5.1 0.7 - - + -
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Residues in contact with ILE 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H PRO* 3.0 18.9 + - + +
87H TRP* 3.5 36.6 - - + +
89H ALA* 1.3 74.1 - - - +
91H GLU* 1.3 65.8 + - - +
93H ALA* 3.3 6.6 + - - +
94H GLN* 3.0 48.6 + - + +
111H ASP* 6.2 0.2 - - - -
114H ARG* 3.9 29.4 - - + +
115H MET* 4.0 9.2 - - + +
118H ALA* 3.9 25.4 - - + -
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Residues in contact with GLU 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64H LEU* 3.9 13.4 - - + +
65H SER* 3.2 41.1 + - - -
68H LEU* 3.3 17.4 - - + +
87H TRP 3.0 14.5 + - - +
88H GLN* 3.6 8.7 - - - +
90H ILE* 1.3 74.4 - - - +
92H VAL* 1.3 63.7 + - - +
94H GLN* 2.9 28.1 + - + +
95H ALA* 3.1 12.3 + - - +
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Residues in contact with VAL 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64H LEU* 4.2 13.5 - - + -
68H LEU* 3.9 7.6 - - + -
76H LEU* 3.8 33.7 - - + -
78H LEU* 4.6 7.9 - - + -
88H GLN 2.8 26.4 + - - +
89H ALA 3.6 3.8 - - - +
91H GLU* 1.3 75.0 - - - +
93H ALA* 1.3 62.7 + - - +
94H GLN 3.3 0.2 + - - -
95H ALA* 3.4 3.6 + - - +
96H GLY 3.3 4.3 + - - -
97H ARG* 3.2 34.8 + - + +
98H HIS 3.6 8.3 - - - +
99H VAL* 3.4 23.1 - - + -
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Residues in contact with ALA 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89H ALA 2.8 22.0 + - - +
90H ILE* 3.7 6.7 - - - +
91H GLU 3.3 0.2 - - - -
92H VAL* 1.3 74.4 - - - +
94H GLN* 1.3 59.0 + - + +
95H ALA 3.2 0.2 - - - -
96H GLY* 3.1 13.3 + - - -
97H ARG 4.0 11.2 - - - +
118H ALA* 4.2 10.8 - - + +
119H CYS* 3.8 32.3 - - - -
122H ALA* 3.2 24.5 - - + +
124H VAL* 5.1 1.8 - - + -
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Residues in contact with GLN 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90H ILE* 3.0 37.9 + - + +
91H GLU* 2.9 21.4 + - + +
93H ALA* 1.3 76.5 - - + +
95H ALA* 1.3 57.6 + - - +
96H GLY* 3.2 4.4 + - - -
118H ALA* 6.1 1.6 - - + -
122H ALA* 5.4 0.7 - - - -
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Residues in contact with ALA 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68H LEU* 3.7 35.7 - - + +
91H GLU 3.1 7.1 + - - +
92H VAL 3.7 8.7 - - - +
94H GLN* 1.3 76.3 - - - +
96H GLY* 1.3 60.8 - - - +
97H ARG* 3.3 21.9 + - + +
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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