Contacts of the helix formed by residues 112 - 121 (chain C) in PDB entry 7BRU
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 112 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C SER* 3.4 15.1 + - - -
76C ASP* 4.0 15.0 - - - +
77C LEU 3.6 6.3 - - - -
78C THR* 4.1 5.8 - - + +
79C VAL* 4.5 0.4 - - - -
110C SER 4.6 4.7 - - - +
111C ALA* 1.3 78.0 - - - +
113C MET* 1.3 64.8 + - - +
114C GLY* 3.5 2.8 + - - -
115C GLN* 2.9 43.7 + - - +
116C LEU* 3.3 9.7 + - - +
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Residues in contact with MET 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C VAL* 4.1 15.6 - - + +
53C VAL* 3.8 28.7 - - + -
73C VAL* 4.0 20.9 - - + -
74C PRO 4.5 0.7 - - - +
75C SER* 3.5 9.1 + - - -
77C LEU 3.0 25.1 + - - +
78C THR 4.5 2.7 - - - +
79C VAL* 3.8 32.1 - - - -
82C PHE* 3.8 28.7 - - + -
111C ALA 3.8 0.4 + - - -
112C THR* 1.3 72.3 - - - +
114C GLY* 1.3 56.7 + - - +
116C LEU* 3.4 6.2 + - - +
117C TYR* 2.9 29.5 + - - +
127C LEU* 4.3 6.5 - - + +
129C ILE* 4.0 13.2 - - + -
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Residues in contact with GLY 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C VAL* 4.4 3.1 - - - -
75C SER* 3.1 32.3 + - - -
112C THR* 3.1 3.2 - - - -
113C MET* 1.3 77.3 - - - +
115C GLN* 1.3 59.6 + - - +
118C GLN* 2.6 50.2 + - - +
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Residues in contact with GLN 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C SER 4.5 0.7 - - - +
111C ALA* 3.3 16.3 - - + +
112C THR* 2.9 44.0 + - - +
114C GLY* 1.3 76.0 - - - +
116C LEU* 1.3 62.2 + - - +
118C GLN* 3.9 6.0 - - - +
119C GLU* 3.0 28.1 + - - +
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C VAL* 4.9 11.4 - - + -
102C VAL* 5.8 4.5 - - + -
107C PRO* 5.6 7.9 - - + -
111C ALA* 5.3 4.9 - - + +
112C THR 3.3 9.0 + - - +
113C MET* 3.8 10.8 - - - +
114C GLY 3.3 0.4 - - - -
115C GLN* 1.3 78.8 - - - +
117C TYR* 1.3 56.4 + - - +
119C GLU* 4.7 0.7 - - - -
120C HIS* 2.9 43.8 + - - +
127C LEU* 4.2 17.4 - - + +
129C ILE* 6.2 1.1 - - + -
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Residues in contact with TYR 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ARG* 4.2 12.8 - - + +
51C VAL* 3.9 27.1 - - + -
52C PRO* 3.8 13.9 - - + -
113C MET 2.9 17.2 + - - +
114C GLY 3.7 3.1 - - - +
116C LEU* 1.3 75.0 - - - +
118C GLN* 1.3 84.0 + - + +
119C GLU 3.1 0.2 + - - -
121C HIS* 2.7 66.0 + + + +
125C PHE* 2.9 46.6 + - - +
127C LEU* 3.9 24.8 - - + +
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Residues in contact with GLN 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C VAL* 4.2 3.8 - - - +
114C GLY* 2.6 45.0 + - - +
115C GLN* 4.0 4.4 - - - +
117C TYR* 1.3 103.9 - - + +
119C GLU* 1.3 57.8 + - - +
121C HIS* 3.7 19.2 + - + -
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Residues in contact with GLU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C GLN 3.0 19.4 + - - +
116C LEU* 4.7 0.4 - - - -
118C GLN* 1.3 79.9 - - - +
120C HIS* 1.3 82.8 + - + +
121C HIS* 3.9 0.7 - - - -
202C PO4 4.4 6.2 + - - -
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Residues in contact with HIS 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C VAL* 3.5 36.6 + - + +
103C ASN* 5.1 4.7 - - + -
107C PRO* 6.4 2.2 - - + -
116C LEU* 2.9 24.4 + - - +
117C TYR 3.7 0.2 - - - -
119C GLU* 1.3 94.9 + - + +
121C HIS* 1.3 67.0 + - - +
122C GLU* 3.6 1.7 + - - +
126C PHE 4.8 0.2 - - - +
127C LEU* 4.3 9.9 - - + +
128C TYR 5.2 1.2 + - - -
202C PO4 2.8 41.0 + - - -
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Residues in contact with HIS 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C TYR* 2.7 66.4 + + + +
118C GLN* 3.7 22.4 + - + -
119C GLU 3.9 0.4 - - - -
120C HIS* 1.3 75.0 - - - +
122C GLU* 1.3 83.1 + - - +
125C PHE* 4.3 10.8 - - + -
126C PHE 3.6 9.0 - - - +
127C LEU* 4.4 3.6 - - - +
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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