Contacts of the helix formed by residues 101 - 109 (chain B) in PDB entry 2B9R
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 GLU 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A GLU* 4.3 9.5 - - - +
102A ILE* 4.8 5.9 - - - +
119A ARG* 3.1 63.5 + - - +
122A GLU* 5.6 1.2 - - - +
89B PHE* 3.9 16.6 - - - -
93B LYS* 5.3 2.9 - - - -
99B PRO* 3.6 4.0 + - - +
100B PRO* 1.3 78.7 - - - +
102B ILE* 1.3 99.9 + - + +
103B GLY* 3.1 3.6 - - - +
104B ASP* 2.8 25.0 + - - +
105B PHE* 3.5 3.4 + - - -
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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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101A GLU* 4.6 10.3 - - - +
89B PHE* 3.6 28.7 - - + -
101B GLU* 1.3 94.8 + - + +
103B GLY* 1.3 73.6 + - - +
105B PHE* 2.9 7.4 + - - +
106B ALA* 2.9 19.6 + - - +
115B LYS* 3.2 41.3 - - + +
118B ILE* 3.5 29.1 - - + +
119B ARG* 3.4 22.9 - - + +
122B GLU* 5.4 0.2 - - - +
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Residues in contact with GLY 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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101B GLU* 2.9 3.8 + - - +
102B ILE* 1.3 83.5 - - - +
104B ASP* 1.3 62.7 + - - +
106B ALA* 2.8 20.7 + - - +
107B PHE* 3.0 12.2 + - - +
115B LYS* 5.3 4.0 - - - -
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Residues in contact with ASP 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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52B PHE* 3.5 23.4 - - + -
100B PRO* 3.1 34.7 - - + +
101B GLU* 2.8 19.0 + - - +
103B GLY* 1.3 69.6 - - - -
105B PHE* 1.3 61.8 + - - +
107B PHE* 3.2 16.9 + - - +
108B VAL 3.3 9.5 + - - -
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Residues in contact with PHE 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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48B VAL* 4.8 1.3 - - + -
52B PHE* 3.7 22.2 - + - -
54B LEU* 4.6 2.0 - - + -
85B VAL* 4.1 24.4 - - + +
88B MET* 3.8 27.8 - - + -
89B PHE* 3.4 49.6 - + + -
92B SER* 4.0 10.1 - - - -
100B PRO* 3.6 34.8 - - + -
101B GLU 3.8 8.7 - - - -
102B ILE* 2.9 7.2 + - - +
104B ASP* 1.3 77.6 - - - +
106B ALA* 1.3 68.4 + - - +
107B PHE 3.3 0.3 + - - -
108B VAL* 3.5 12.5 - - + +
109B THR* 3.0 20.1 - - - +
118B ILE* 4.1 12.3 - - + -
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Residues in contact with ALA 106 (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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102B ILE 2.9 9.9 + - - +
103B GLY* 2.8 17.4 + - - +
105B PHE* 1.3 78.0 - - - +
107B PHE* 1.3 59.2 + - - +
109B THR* 2.7 26.7 + - - -
110B ASP 4.0 0.3 + - - -
111B ASN* 4.4 3.6 + - - -
113B TYR 3.9 16.9 - - - +
114B THR* 5.1 0.4 - - - -
115B LYS* 4.3 13.7 - - + +
118B ILE* 3.9 15.0 - - + +
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Residues in contact with PHE 107 (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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103B GLY 3.0 9.3 + - - +
104B ASP* 3.4 13.5 - - - +
106B ALA* 1.3 78.0 - - - +
108B VAL* 1.3 59.8 + - + +
109B THR 3.0 0.4 - - - -
110B ASP* 2.5 31.7 + - - -
111B ASN 3.8 3.6 + - - +
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Residues in contact with VAL 108 (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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44B TRP* 3.5 18.3 + - + -
48B VAL* 4.2 24.9 - - + -
51B LYS* 4.0 35.5 + - + +
52B PHE* 4.0 28.7 - - + -
85B VAL* 4.5 3.4 - - + -
104B ASP 3.3 4.4 + - - +
105B PHE* 3.5 14.6 - - - +
107B PHE* 1.3 81.8 - - + +
109B THR* 1.3 59.0 + - - +
110B ASP* 2.8 13.1 + - - +
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Residues in contact with THR 109 (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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44B TRP* 4.3 9.2 - - + -
81B GLN* 4.7 7.6 - - + +
85B VAL* 3.9 24.2 - - + -
105B PHE 3.0 20.6 - - - +
106B ALA* 2.7 16.4 + - - +
107B PHE 3.0 0.6 - - - -
108B VAL* 1.3 73.7 - - - +
110B ASP* 1.3 68.7 + - - +
112B THR* 2.8 23.0 + - - -
113B TYR* 3.1 48.3 + - + -
118B ILE* 5.0 0.9 - - + -
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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