Contacts of the helix formed by residues 117 - 125 (chain C) 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 ASN 117 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C TYR* 3.1 20.0 + - + +
95C LEU* 3.7 20.7 - - + +
100C ARG* 3.2 24.9 + - - -
107C TYR* 2.9 27.2 + - - -
113C ALA 3.0 20.2 + - - -
114C VAL 2.9 6.8 + - - +
116C GLN* 1.3 80.2 - - - +
118C ILE* 1.3 60.6 + - - +
119C ASP* 3.1 8.4 - - - +
120C ILE* 2.8 29.9 + - + +
121C ILE* 3.2 12.6 + - - +
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Residues in contact with ILE 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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114C VAL 3.8 8.5 - - - +
115C TYR* 3.2 42.0 + - + +
116C GLN 3.5 0.4 - - - -
117C ASN* 1.3 77.5 - - - +
119C ASP* 1.3 62.5 + - - +
121C ILE* 3.0 7.9 + - + -
122C GLU* 2.9 57.5 + - + +
217C MET* 3.6 32.1 - - + +
220C LEU* 4.2 14.1 - - + -
221C ARG* 3.6 19.3 - - + +
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Residues in contact with ASP 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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101C VAL* 4.4 18.3 - - - +
116C GLN 3.7 7.0 - - - +
117C ASN* 3.3 16.6 - - - +
118C ILE* 1.3 76.4 - - - +
120C ILE* 1.3 73.4 + - - +
122C GLU* 5.3 2.9 - - - -
123C PRO* 3.1 24.8 - - - +
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Residues in contact with ILE 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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71B HIS* 4.9 13.9 - - + -
75B ARG* 6.1 1.6 - - - +
14C MET* 5.1 4.5 - - + -
93C ASP* 3.8 33.4 - - + +
95C LEU* 4.0 26.7 - - + -
117C ASN* 2.8 19.7 + - + +
119C ASP* 1.3 96.6 + - - +
121C ILE* 1.3 65.0 + - + +
123C PRO* 3.4 9.8 - - - +
124C TYR* 3.4 22.7 - - + +
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Residues in contact with ILE 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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14C MET* 4.0 18.8 - - + -
16C TYR* 4.2 10.5 - - + -
114C VAL* 3.7 30.1 - - + -
117C ASN 3.6 14.8 - - - +
118C ILE* 3.0 13.1 + - - +
120C ILE* 1.3 79.0 - - + +
122C GLU* 1.3 66.2 + - - +
124C TYR* 3.1 21.8 + - - +
125C ALA 3.1 8.3 + - - -
126C PRO* 3.4 12.5 - - + +
129C MET* 3.8 31.2 - - + -
213C THR* 4.2 11.0 - - + -
217C MET* 4.3 11.7 - - + -
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Residues in contact with GLU 122 (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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118C ILE* 2.9 33.9 + - + +
119C ASP* 5.3 2.1 - - - -
121C ILE* 1.3 77.1 - - + +
123C PRO* 1.3 63.5 - - + +
125C ALA* 2.9 26.2 + - - +
126C PRO* 5.4 0.2 - - - -
213C THR* 6.3 1.3 - - + -
217C MET* 4.2 17.0 - - + +
221C ARG* 3.0 34.3 + - - -
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Residues in contact with PRO 123 (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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119C ASP* 3.1 25.8 - - - +
120C ILE* 3.4 9.2 - - - +
122C GLU* 1.3 93.7 - - + +
124C TYR* 1.3 65.6 + - + +
125C ALA* 3.3 3.6 + - - +
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Residues in contact with TYR 124 (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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79B ARG* 5.6 2.6 + - - -
14C MET* 4.3 17.9 - - + -
61C ARG* 3.5 52.0 + - - +
91C SER* 3.4 17.8 - - - -
93C ASP* 2.8 36.1 + - - -
120C ILE* 3.4 26.7 - - + +
121C ILE 3.1 7.5 + - - +
123C PRO* 1.3 81.5 - - + +
125C ALA* 1.3 66.8 + - - +
126C PRO* 3.3 9.7 - - + +
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Residues in contact with ALA 125 (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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121C ILE 4.1 0.2 - - - -
122C GLU* 2.9 20.2 + - - +
123C PRO 4.2 3.4 - - - +
124C TYR* 1.3 80.4 - - - +
126C PRO* 1.3 74.8 - - - +
127C GLU* 3.6 2.9 + - - +
213C THR* 5.8 1.1 - - - -
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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