Contacts of the helix formed by residues 109 - 116 (chain B) in PDB entry 6V99
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 GLY 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B TYR* 3.2 8.0 + - - +
108B GLU* 1.3 79.1 - - - +
110B THR* 1.3 62.7 + - - -
112B ASP* 3.8 2.8 - - - +
113B ALA* 2.8 27.7 + - - +
230B SER 4.1 0.4 - - - -
231B ARG 3.1 14.8 - - - -
232B ASP* 3.6 8.7 - - - -
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Residues in contact with THR 110 (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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18B LEU* 3.6 26.7 - - + +
109B GLY* 1.3 72.3 - - - -
111B ALA* 1.3 60.4 + - - +
113B ALA* 3.3 19.1 + - - +
114B VAL* 3.5 6.6 + - - +
232B ASP* 2.8 19.4 + - - +
233B PHE* 2.6 51.7 + - + +
234B GLY 4.4 0.3 + - - -
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Residues in contact with ALA 111 (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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110B THR* 1.3 78.5 + - - +
112B ASP* 1.3 61.3 + - - +
114B VAL* 3.0 6.2 + - - +
115B TYR* 2.8 27.2 + - - +
220B LEU* 3.7 7.7 - - + +
223B ASP* 4.1 8.1 - - + +
231B ARG* 2.9 20.1 + - - +
232B ASP 4.0 6.5 - - - +
233B PHE* 3.6 12.4 - - + +
237B ILE* 3.6 31.2 - - + -
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Residues in contact with ASP 112 (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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104B THR* 5.7 1.4 - - - -
106B TRP 4.4 1.4 - - - +
107B TYR* 3.7 6.1 - - - -
108B GLU* 2.9 29.5 + - - +
109B GLY 3.2 11.0 + - - +
111B ALA* 1.3 79.0 - - - +
113B ALA* 1.3 63.5 + - - +
115B TYR* 3.9 3.9 - - - -
116B GLN* 3.0 53.7 + - - +
231B ARG* 3.1 51.8 + - + +
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Residues in contact with ALA 113 (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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16B TYR* 3.0 5.5 + - - -
18B LEU* 4.2 9.2 - - + -
65B ALA* 4.0 14.8 - - + +
107B TYR* 3.8 31.6 - - + -
109B GLY 2.8 14.0 + - - +
110B THR* 3.4 13.7 - - - +
111B ALA 3.1 0.4 - - - -
112B ASP* 1.3 77.5 - - - +
114B VAL* 1.3 57.1 + - - +
116B GLN 4.2 0.2 + - - -
117B ASN* 2.9 28.1 + - - -
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Residues in contact with VAL 114 (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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16B TYR* 3.5 34.3 - - + -
18B LEU* 4.3 3.8 - - + -
110B THR 3.7 14.6 - - - +
111B ALA 3.0 5.8 + - - +
113B ALA* 1.3 76.1 - - - +
115B TYR* 1.3 66.6 + - - +
116B GLN 3.2 0.2 - - - -
117B ASN* 3.0 13.9 + - - +
118B ILE* 3.5 8.7 + - - +
121B ILE* 3.8 22.3 - - + +
129B MET* 4.8 5.2 - - + -
131B ILE* 4.5 6.5 - - + -
216B LEU* 5.0 2.5 - - + -
217B MET* 4.8 3.6 - - + -
220B LEU* 3.5 20.0 - - + -
233B PHE* 3.7 19.1 - - + -
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Residues in contact with TYR 115 (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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111B ALA 2.8 16.2 + - - +
112B ASP* 3.2 17.0 + - - +
114B VAL* 1.3 75.9 - - - +
116B GLN* 1.3 79.2 + - - +
117B ASN 3.0 1.6 + - - -
118B ILE* 3.1 43.8 + - + +
220B LEU* 3.6 31.6 - - + +
221B ARG* 4.2 15.6 - - + +
224B ALA* 3.8 20.8 - - + +
231B ARG* 3.9 16.8 - - - +
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Residues in contact with GLN 116 (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 ARG* 3.9 8.0 + - - -
101B VAL* 4.3 8.8 - - - +
102B SER* 3.1 35.2 + - - -
104B THR* 5.7 6.2 - - - -
107B TYR* 3.9 23.1 - - + -
112B ASP* 3.0 42.4 + - - +
114B VAL 3.2 0.4 - - - -
115B TYR* 1.3 91.5 - - - +
117B ASN* 1.3 63.9 + - - +
118B ILE 3.5 0.4 - - - -
119B ASP* 3.6 9.7 - - - +
231B ARG* 5.4 0.8 - - - +
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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