Contacts of the helix formed by residues 109 - 117 (chain C) in PDB entry 6VVT
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 SER 109 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108C ALA* 1.3 75.6 - - - +
110C VAL* 1.3 71.8 + - - +
111C ASP* 3.3 6.4 + - - +
112C GLU* 2.9 19.8 + - - -
113C CYS* 2.6 37.6 + - - -
120C TYR* 4.2 3.6 - - - -
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Residues in contact with VAL 110 (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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109C SER* 1.3 78.5 + - - +
111C ASP* 1.3 76.2 + - - +
113C CYS* 3.0 4.7 + - - +
114C LYS* 2.9 35.0 + - - +
120C TYR* 3.7 29.1 - - + +
152C THR* 3.3 35.7 - - + -
153C GLU* 5.2 11.2 - - - +
154C LYS* 5.7 7.4 - - - +
158C ILE* 4.0 9.3 - - + +
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Residues in contact with ASP 111 (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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109C SER* 3.3 6.0 + - - +
110C VAL* 1.3 87.4 - - - +
112C GLU* 1.3 62.1 + - - +
114C LYS* 3.5 19.4 + - - +
115C ASP* 3.0 25.2 + - - +
662C ARG* 5.2 10.9 + - - +
664C ARG* 5.9 4.8 - - - +
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Residues in contact with GLU 112 (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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108C ALA* 3.5 24.0 - - + +
109C SER* 2.9 24.2 + - - +
111C ASP* 1.3 80.4 - - - +
113C CYS* 1.3 57.8 + - - +
115C ASP* 3.6 6.9 + - - +
116C LYS* 3.1 30.7 + - + +
118C MET* 4.4 2.8 - - - +
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Residues in contact with CYS 113 (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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108C ALA* 3.7 25.8 - - - -
109C SER 2.6 26.2 + - - +
110C VAL* 3.0 5.8 + - - +
112C GLU* 1.3 71.9 - - - +
114C LYS* 1.3 61.8 + - - +
116C LYS 3.4 0.5 + - - -
117C ASP* 2.9 27.2 + - - -
118C MET* 3.1 28.7 + - - +
119C THR 4.1 2.0 - - - -
120C TYR* 3.7 28.5 - - - -
158C ILE* 3.6 20.0 - - + -
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Residues in contact with LYS 114 (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 VAL* 2.9 26.3 + - - +
111C ASP* 4.0 18.9 + - - +
113C CYS* 1.3 76.2 - - - +
115C ASP* 1.3 61.7 + - - +
117C ASP* 3.4 12.1 - - - +
154C LYS* 4.9 10.9 - - - +
158C ILE* 4.4 17.9 - - + +
161C GLY* 3.3 29.4 - - - +
162C THR* 5.0 1.6 - - - -
163C GLU* 3.5 32.0 + - + +
664C ARG* 5.6 7.7 - - - +
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Residues in contact with ASP 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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111C ASP 3.0 18.4 + - - +
112C GLU* 3.9 7.9 - - - +
113C CYS 3.1 0.2 - - - -
114C LYS* 1.3 80.2 - - - +
116C LYS* 1.3 60.1 + - - +
117C ASP* 3.2 10.4 + - - +
842C ARG* 3.5 39.8 + - - +
844C PHE* 3.9 13.4 - - - -
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Residues in contact with LYS 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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112C GLU* 3.1 18.6 + - + +
115C ASP* 1.3 79.8 - - - +
117C ASP* 1.3 69.9 + - - +
118C MET* 3.3 29.5 + - + +
844C PHE* 4.6 13.2 - - + -
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Residues in contact with ASP 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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113C CYS 2.9 8.3 + - - -
114C LYS 3.4 13.3 - - - +
115C ASP 3.2 7.1 - - - +
116C LYS* 1.3 79.2 - - - +
118C MET* 1.3 59.1 + - - +
160C ASN* 3.4 22.5 + - - +
161C GLY* 3.6 13.8 - - - +
747C GLU* 4.3 14.5 - - - +
844C PHE* 5.9 3.4 - - - -
859C LEU* 6.2 0.3 - - - +
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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