Contacts of the helix formed by residues 96 - 105 (chain B) in PDB entry 2QB0
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 ILE 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B GLN* 5.6 1.3 - - - +
94B PRO* 3.7 18.2 - - + +
95B ASN 1.3 62.2 + - - -
97B PHE* 1.3 65.8 + - - +
98B GLU 3.5 1.3 - - - +
99B MET* 3.9 17.2 - - - +
100B LEU* 3.1 40.5 + - + +
160B PHE* 3.7 16.0 - - + -
164B VAL* 4.4 14.8 - - + -
190B ALA* 3.3 39.5 - - + +
193B ILE* 3.6 30.7 - - + -
194B ASN* 4.0 2.7 - - - +
251B TRP* 4.0 7.1 - - - -
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Residues in contact with PHE 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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24B LEU* 3.9 28.3 - - + -
25B GLN* 4.6 4.1 - - - +
28B TYR* 3.7 43.5 - + + -
95B ASN* 3.9 6.1 + - - +
96B ILE* 1.3 77.6 - - - +
98B GLU* 1.3 62.1 + - + +
100B LEU* 3.8 1.6 - - - +
101B ARG* 2.9 38.7 + - + +
106B LEU* 4.6 11.4 - - + -
122B ILE* 3.3 28.3 - - + +
153B LYS* 4.6 18.6 - - - -
157B GLU* 4.4 10.1 - - + -
160B PHE* 3.6 32.0 - + + -
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Residues in contact with GLU 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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28B TYR* 3.5 29.6 + - + +
96B ILE 4.9 0.4 - - - +
97B PHE* 1.3 79.3 - - + +
99B MET* 1.3 65.5 + - - +
101B ARG* 3.8 10.8 - - + -
102B ILE* 2.9 52.0 + - + +
254B TYR 4.7 5.2 - - - +
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Residues in contact with MET 99 (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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96B ILE* 3.6 26.3 + - - +
98B GLU* 1.3 79.7 - - - +
100B LEU* 1.3 57.2 + - - +
102B ILE 3.5 0.2 + - - -
103B ASP* 3.1 31.2 + - - -
190B ALA 4.0 14.1 - - - +
191B ALA* 3.8 24.2 - - + +
194B ASN* 3.3 28.7 - - + +
242B VAL* 4.4 4.3 - - + -
245B THR* 4.0 10.1 - - - +
251B TRP* 3.6 26.9 - - + -
254B TYR* 3.4 47.7 - - + +
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Residues in contact with LEU 100 (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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96B ILE* 3.1 35.1 + - + +
99B MET* 1.3 76.2 - - - +
101B ARG* 1.3 57.9 + - - +
102B ILE 3.2 0.7 - - - -
103B ASP* 3.7 2.2 - - + +
104B GLU* 2.7 45.0 + - + +
122B ILE* 3.5 7.6 - - + +
160B PHE* 3.5 31.2 - - + -
164B VAL* 5.0 1.3 - - + -
194B ASN* 3.6 22.0 - - - +
197B PHE* 3.7 29.6 - - + -
238B ARG* 3.4 29.4 - - - +
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Residues in contact with ARG 101 (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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97B PHE* 2.9 30.5 + - + +
98B GLU* 3.3 16.6 + - + +
100B LEU* 1.3 75.1 - - - +
102B ILE* 1.3 61.4 + - + +
105B GLY* 2.8 34.8 + - - +
106B LEU* 3.4 54.4 + - - +
122B ILE* 4.3 12.9 - - + +
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Residues in contact with ILE 102 (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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98B GLU* 2.9 43.3 + - + +
99B MET 3.7 3.8 - - - +
101B ARG* 1.3 82.6 - - + +
103B ASP* 1.3 66.4 + - - +
105B GLY* 4.3 2.3 + - - -
241B ARG* 4.5 16.8 + - - +
254B TYR* 3.9 45.8 - - + +
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Residues in contact with ASP 103 (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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99B MET 3.1 16.4 + - - +
100B LEU* 4.2 5.6 - - - +
102B ILE* 1.3 77.8 - - - +
104B GLU* 1.3 59.3 + - - +
194B ASN* 2.8 20.1 + - - +
238B ARG* 3.4 41.1 + - - +
241B ARG* 3.0 36.9 + - - +
254B TYR* 2.7 25.8 + - - -
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Residues in contact with GLU 104 (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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100B LEU* 2.7 37.1 + - + +
102B ILE 4.8 0.2 - - - -
103B ASP* 1.3 74.8 - - - +
105B GLY* 1.3 57.9 + - - +
107B ARG* 6.0 0.2 - - - +
111B TYR* 4.0 16.5 + - - -
122B ILE* 3.7 13.0 - - + -
123B GLY* 3.4 11.4 + - - +
197B PHE* 3.5 26.9 - - + -
198B GLN* 4.4 4.3 - - - -
238B ARG* 2.8 33.6 + - - +
256B MN 2.3 35.1 + - - -
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Residues in contact with GLY 105 (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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100B LEU 3.6 0.2 + - - -
101B ARG* 2.8 28.4 + - - -
102B ILE 4.3 2.3 + - - -
103B ASP 3.8 0.6 - - - -
104B GLU* 1.3 81.8 - - - +
106B LEU* 1.3 60.1 + - - -
107B ARG* 4.1 3.4 - - - -
111B TYR* 5.8 0.2 - - - -
121B GLY 3.3 2.2 - - - +
122B ILE* 3.3 26.2 - - - +
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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