Contacts of the helix formed by residues 72 - 88 (chain B) in PDB entry 3QEO
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 THR 72 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B LEU* 1.3 77.9 - - - +
73B MET* 1.3 65.7 + - - +
74B GLU* 3.7 6.6 + - - +
75B GLN* 3.0 36.1 + - - +
76B LYS* 2.9 20.8 + - - +
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Residues in contact with MET 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A THR* 3.4 37.7 - - + +
156A GLN* 5.6 4.9 - - + +
157A ASP* 3.9 37.5 - - + +
160A ASP* 5.7 3.6 - - - +
71B LEU 4.2 0.4 + - - -
72B THR* 1.3 71.9 - - - +
74B GLU* 1.3 64.2 + - - +
76B LYS* 3.0 17.1 + - + +
77B ASN* 3.0 15.9 + - - +
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ASP* 4.6 3.1 + - - +
54B PRO* 3.9 7.6 - - - +
58B TRP* 3.5 22.5 + - + +
72B THR* 3.4 6.1 + - - +
73B MET* 1.3 78.1 - - - +
75B GLN* 1.3 52.8 - - - +
77B ASN* 3.8 0.7 - - - +
78B GLY* 2.7 32.4 + - - -
99B TYR* 3.3 19.1 + - - +
103B SER* 3.0 39.0 + - - +
106B ARG* 2.8 32.6 + - - +
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Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B ARG* 3.6 38.7 + - + +
58B TRP* 4.6 10.7 - - + +
60B ASN* 4.3 16.7 + - - +
71B LEU* 4.6 7.1 + - - -
72B THR* 3.0 39.8 + - - +
74B GLU* 1.3 80.5 - - - +
76B LYS* 1.3 57.1 + - - +
79B GLY* 2.9 25.6 + - - -
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Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A GLU* 5.7 9.2 + - - -
153A THR* 6.4 0.9 - - + -
71B LEU* 5.5 10.7 - - + +
72B THR 2.9 12.3 + - - +
73B MET* 3.7 8.7 - - + +
75B GLN* 1.3 73.9 - - - +
77B ASN* 1.3 71.1 + - - +
79B GLY* 3.5 0.7 + - - -
80B ASN* 3.2 47.7 + - - +
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Residues in contact with ASN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A THR* 3.7 17.2 + - - +
153A THR* 3.1 55.6 + - - +
154A ILE* 3.6 15.2 - - + +
157A ASP* 4.6 0.2 + - - -
73B MET* 3.0 17.1 + - - +
74B GLU 3.8 0.2 - - - +
76B LYS* 1.3 79.4 - - - +
78B GLY* 1.3 56.9 + - - +
80B ASN* 5.0 1.0 + - - +
81B VAL* 2.9 35.8 + - - +
99B TYR* 3.4 31.7 + - + -
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Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B TRP* 3.3 36.3 - - - -
74B GLU 2.7 22.8 + - - -
77B ASN* 1.3 72.7 - - - +
79B GLY* 1.3 64.2 + - - +
81B VAL* 3.9 3.8 - - - -
82B LEU* 3.0 27.0 + - - +
99B TYR* 4.7 0.4 - - - -
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Residues in contact with GLY 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B TRP* 3.8 20.7 - - - +
75B GLN 2.9 15.5 + - - -
76B LYS 4.0 0.9 - - - -
78B GLY* 1.3 76.7 - - - +
80B ASN* 1.3 61.9 + - - +
82B LEU* 3.5 4.3 - - - +
83B GLN* 3.0 25.4 + - - +
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Residues in contact with ASN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A THR* 3.4 27.2 + - - +
76B LYS* 3.2 46.2 + - - +
77B ASN* 3.7 2.9 + - - +
79B GLY* 1.3 76.1 - - - +
81B VAL* 1.3 58.0 + - - +
83B GLN* 3.2 11.8 + - - +
84B MET* 3.0 36.5 + - + +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A THR* 4.4 1.1 - - + -
154A ILE* 4.4 15.5 - - + -
58B TRP* 4.2 6.7 - - + -
77B ASN 2.9 30.2 + - - +
78B GLY* 3.6 11.4 - - - +
80B ASN* 1.3 70.8 - - - +
82B LEU* 1.3 68.4 + - - +
84B MET* 3.3 10.6 + - + +
85B MET* 2.9 24.7 + - + +
92B TRP* 4.7 13.0 - - + +
95B THR* 4.4 15.0 - - + -
96B PHE* 3.8 43.1 - - + +
99B TYR* 4.5 4.7 - - + -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B VAL* 3.7 22.0 - - + -
58B TRP* 4.0 11.9 - - + +
59B SER* 3.8 36.8 - - - +
78B GLY 3.0 18.2 + - - +
79B GLY* 3.5 5.2 - - - +
81B VAL* 1.3 78.7 - - - +
83B GLN* 1.3 62.3 + - - +
85B MET* 3.2 2.9 - - + +
86B TYR* 3.1 57.2 + - + +
96B PHE* 3.7 19.3 - - + -
196B GLU* 5.7 3.1 - - - +
261B LLT 3.5 14.1 - - + +
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Residues in contact with GLN 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B GLY 3.0 17.3 + - - +
80B ASN* 3.6 10.1 - - - +
82B LEU* 1.3 76.4 - - - +
84B MET* 1.3 62.8 + - - +
86B TYR* 3.3 9.8 + - + +
87B GLU* 3.1 43.5 + - - +
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Residues in contact with MET 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ASN* 4.4 7.4 - - - +
150A THR* 4.4 16.4 - - + +
80B ASN* 3.0 41.3 + - + +
81B VAL* 3.7 12.3 - - + +
83B GLN* 1.3 76.8 - - - +
85B MET* 1.3 53.2 + - - +
87B GLU* 3.6 5.2 - - - +
88B LYS* 2.7 31.7 + - - +
92B TRP* 3.3 64.9 - - + +
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Residues in contact with MET 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B VAL 2.9 9.5 + - - +
82B LEU* 3.2 11.9 - - + +
84B MET* 1.3 74.5 - - - +
86B TYR* 1.3 68.5 + - + +
87B GLU 3.3 0.3 + - - -
88B LYS 4.7 0.7 - - - -
89B PRO* 3.3 32.6 - - + +
92B TRP* 3.7 9.1 - - + +
93B SER* 3.5 44.2 - - - +
96B PHE* 3.4 51.1 - - + -
141B LEU* 4.1 18.6 - - + -
261B LLT 4.2 13.5 - - + +
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Residues in contact with TYR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LEU* 3.1 50.4 + - + +
83B GLN* 3.3 11.0 + - + +
85B MET* 1.3 82.3 - - + +
87B GLU* 1.3 67.1 + - - +
89B PRO* 4.4 6.9 - - - +
196B GLU* 3.9 37.9 - - + -
197B GLU* 4.0 19.3 + - + +
200B ILE* 5.0 12.0 - - + +
261B LLT 2.4 34.0 + - + -
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLN* 3.1 41.5 + - + +
84B MET* 3.6 7.0 - - - +
85B MET 3.1 0.2 - - - -
86B TYR* 1.3 85.3 - - - +
88B LYS* 1.3 62.0 + - + +
89B PRO* 3.9 3.9 - - - +
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Residues in contact with LYS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B MET 2.7 14.9 + - - +
87B GLU* 1.3 76.7 + - + +
89B PRO* 1.3 67.8 - - - +
90B GLU* 3.4 20.3 + - - +
91B ARG* 3.2 27.0 + - + -
92B TRP* 3.3 23.2 + - + +
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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