Contacts of the helix formed by residues 87 - 98 (chain B) in PDB entry 2QH5
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 ASN 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B GLU* 5.3 2.1 + - - +
85B SER* 3.4 5.3 + - - -
86B LYS* 1.3 86.0 + - - +
88B THR* 1.3 81.5 + - - +
89B ALA 3.6 1.5 + - - -
90B ASN* 3.8 1.4 + - - +
91B ALA* 3.5 18.9 + - - +
241B ASP* 3.6 18.6 + - - +
242B MET* 3.3 13.6 - - - +
243B SER* 3.6 28.1 - - - +
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Residues in contact with THR 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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8B LEU* 3.7 25.4 - - + -
87B ASN* 1.3 86.8 + - - +
89B ALA* 1.3 66.4 + - - +
90B ASN 3.3 1.6 - - - -
91B ALA* 3.8 6.7 - - + -
92B ILE* 2.9 38.8 + - - +
189B PHE* 6.4 0.2 - - - -
242B MET 3.4 0.2 + - - -
243B SER* 3.3 8.5 - - - -
244B ILE* 3.0 28.3 + - - +
245B ASP* 4.2 2.6 + - - -
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Residues in contact with ALA 89 (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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88B THR* 1.3 77.9 + - - +
90B ASN* 1.3 55.0 + - - +
92B ILE* 3.8 1.4 - - - +
93B ALA* 2.8 37.9 + - - +
200B LEU* 5.9 0.2 - - + -
207B ILE* 4.3 19.3 - - + -
211B CYS* 5.0 0.4 - - - -
242B MET* 3.0 20.5 + - + +
244B ILE* 3.5 21.6 - - + +
247B ALA* 4.0 26.7 - - + -
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Residues in contact with ASN 90 (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 GLU* 5.5 0.7 - - - +
86B LYS* 2.6 39.3 + - + +
87B ASN 4.2 2.0 - - - +
88B THR 3.3 0.2 - - - -
89B ALA* 1.3 72.8 - - - +
91B ALA* 1.3 67.5 + - - +
94B LEU* 2.9 35.7 + - + +
207B ILE* 4.4 10.4 - - - +
211B CYS* 3.4 26.9 - - - -
236B MET* 5.4 3.1 - - + -
239B LEU* 3.8 25.5 - - + +
240B GLU* 2.8 21.6 + - - +
242B MET 4.6 2.4 + - - +
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Residues in contact with ALA 91 (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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8B LEU* 4.0 22.9 - - + -
55B VAL* 4.0 10.0 - - + +
80B LEU* 4.3 3.6 - - - +
82B GLU* 3.9 23.0 + - - +
87B ASN 3.5 15.4 + - - +
88B THR* 3.5 8.0 + - + +
89B ALA 3.4 0.2 - - - -
90B ASN* 1.3 81.1 - - - +
92B ILE* 1.3 53.5 + - - +
94B LEU* 4.1 4.2 - - - +
95B SER* 2.4 32.3 + - - -
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Residues in contact with ILE 92 (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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6B ILE* 5.3 2.2 - - + -
8B LEU* 4.4 11.0 - - + -
88B THR* 2.9 27.6 + - - +
89B ALA* 3.9 2.0 - - - +
91B ALA* 1.3 72.2 - - - +
93B ALA* 1.3 60.4 + - - +
95B SER* 3.1 9.2 + - - -
96B ALA* 2.9 26.1 + - + +
105B LEU* 5.0 0.7 - - + +
107B VAL* 3.8 34.1 - - + -
189B PHE* 4.4 7.6 - - + -
191B PHE* 3.9 21.8 - - + -
196B PHE* 3.4 26.5 - - + -
244B ILE* 3.7 28.3 - - + -
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Residues in contact with ALA 93 (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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89B ALA 2.8 22.8 + - - +
90B ASN 3.9 2.2 - - - +
92B ILE* 1.3 74.6 - - - +
94B LEU* 1.3 56.6 + - - +
96B ALA* 3.1 4.7 + - - +
97B LEU* 2.9 33.1 + - - +
196B PHE* 3.6 10.8 - - + -
197B LEU* 4.1 4.3 - - + +
200B LEU* 3.7 27.8 - - + -
207B ILE* 5.6 0.2 - - + -
208B LEU* 5.1 0.9 - - + -
211B CYS* 4.0 18.8 - - + -
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Residues in contact with LEU 94 (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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80B LEU* 4.5 5.2 - - + -
82B GLU* 4.9 9.6 - - - +
90B ASN* 2.9 31.6 + - + +
91B ALA 4.1 3.4 - - - +
93B ALA* 1.3 76.5 - - - +
95B SER* 1.3 52.5 + - - +
97B LEU* 3.1 7.7 + - - +
98B MET* 2.7 53.1 + - + +
211B CYS* 3.4 30.7 - - + +
214B ALA* 4.3 8.5 - - + +
215B PHE* 3.9 28.0 - - + +
218B LEU* 5.3 0.4 - - + -
231B LEU* 3.8 27.8 - - + -
236B MET* 5.4 1.8 - - + -
239B LEU* 5.2 4.5 - - + -
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Residues in contact with SER 95 (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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4B LYS* 4.7 0.2 + - - -
6B ILE* 3.6 31.4 - - - +
53B LEU* 3.8 25.4 - - - +
55B VAL* 4.4 1.4 - - - +
80B LEU* 4.4 4.3 - - - +
91B ALA 2.4 28.9 + - - -
92B ILE* 3.1 8.6 + - - -
94B LEU* 1.3 73.4 - - - +
96B ALA* 1.3 59.1 + - - +
98B MET* 3.3 11.4 + - - +
99B SER* 2.7 27.7 + - - -
105B LEU* 4.3 2.4 - - - +
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Residues in contact with ALA 96 (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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92B ILE 2.9 12.7 + - - +
93B ALA 3.4 9.0 - - - +
95B SER* 1.3 75.8 - - - +
97B LEU* 1.3 63.3 + - - +
99B SER* 3.2 20.6 + - - +
105B LEU* 3.8 18.6 - - + +
193B ALA* 4.0 9.7 - - + +
196B PHE* 3.8 24.0 - - + -
197B LEU* 3.8 23.9 - - + +
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Residues in contact with LEU 97 (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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93B ALA 2.9 18.2 + - - +
94B LEU* 3.4 10.3 - - - +
96B ALA* 1.3 78.3 - - - +
98B MET* 1.3 56.1 + - - +
99B SER 3.1 8.0 + - - +
197B LEU* 4.0 22.2 - - + -
208B LEU* 4.8 4.0 - - + -
211B CYS* 3.6 38.4 - - + +
212B GLU* 4.0 26.5 - - + +
215B PHE* 3.5 38.7 - - + -
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Residues in contact with MET 98 (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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4B LYS* 3.3 13.3 + - - +
53B LEU* 4.3 24.0 - - + -
79B PHE 5.8 0.2 - - - +
80B LEU* 3.7 32.3 - - + -
94B LEU* 2.7 49.5 + - + +
95B SER* 3.8 6.5 - - - +
96B ALA 3.2 0.8 - - - -
97B LEU* 1.3 72.3 - - - +
99B SER* 1.3 59.5 + - - +
215B PHE* 3.6 17.5 - - + -
218B LEU* 3.8 21.8 - - + -
229B ALA* 5.1 5.8 - - - -
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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
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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