Contacts of the helix formed by residues 115 - 123 (chain C) in PDB entry 2V5Q
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 115 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C HIS* 3.6 4.0 - - - -
106C VAL 4.6 1.3 - - - -
107C ASN* 4.0 13.5 + - - +
108C ALA 3.3 5.2 - - - +
109C PHE* 3.7 31.9 - - + -
114C SER* 1.3 73.3 - - - +
116C PRO* 1.3 77.4 - - - +
117C LEU* 3.2 20.7 + - - +
118C HIS* 3.0 39.2 + - + +
119C LEU* 3.3 11.6 + - - +
138C ASP 5.1 2.1 + - - +
141C ALA* 4.0 13.0 - - + -
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Residues in contact with PRO 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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82C THR* 4.8 0.4 - - - +
84C LEU* 3.8 33.2 - - + +
85C HIS* 3.5 28.2 - - + +
88C ALA* 3.4 27.5 - - + +
105C ASP 4.7 2.2 - - - +
106C VAL 3.4 14.6 - - - +
108C ALA* 3.4 13.5 - - + +
115C THR* 1.3 87.8 - - - +
117C LEU* 1.3 54.9 + - - +
119C LEU* 3.4 2.9 + - + +
120C ALA* 2.9 25.8 + - - +
132C LEU* 3.7 11.4 - - + -
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Residues in contact with LEU 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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106C VAL 5.1 0.4 + - - -
115C THR* 3.0 10.6 + - - +
116C PRO* 1.3 77.0 - - - +
118C HIS* 1.3 59.5 + - + +
120C ALA* 3.4 2.0 + - - +
121C ALA* 2.9 29.5 + - - +
129C VAL* 3.8 44.4 - - + +
132C LEU* 3.6 13.8 - - + +
133C LEU* 4.1 23.6 - - + -
137C ALA* 4.1 20.0 - - + -
138C ASP 4.1 15.9 - - - +
139C VAL* 4.1 8.5 - - + -
126D LEU* 3.7 26.9 - - + -
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Residues in contact with HIS 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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113C GLY 4.1 10.8 - - - -
114C SER* 3.6 16.4 - - - +
115C THR* 3.0 49.6 + - + +
117C LEU* 1.3 77.7 - - + +
119C LEU* 1.3 60.1 + - + +
121C ALA* 3.4 3.3 + - - +
122C ASP* 2.9 30.4 + - - +
138C ASP 5.5 1.8 - - - -
139C VAL 4.6 9.0 + - - -
141C ALA* 4.6 11.2 - - + -
124D GLY* 5.6 4.3 - - - -
126D LEU* 3.5 27.8 - - + +
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Residues in contact with LEU 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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135B ARG* 4.6 6.5 - - - +
316B ILE* 4.5 20.0 - - + -
81C PHE* 3.7 21.1 - - + -
85C HIS* 3.7 39.5 - - + +
89C MET* 4.1 26.9 - - + -
114C SER* 4.2 21.1 - - - +
115C THR 3.3 11.3 + - - +
116C PRO 3.8 5.2 - - - +
118C HIS* 1.3 75.0 - - + +
120C ALA* 1.3 61.9 + - - +
122C ASP* 3.3 6.5 + - + +
123C GLU* 3.0 33.6 + - - +
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Residues in contact with ALA 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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88C ALA* 3.8 14.9 + - + +
89C MET* 4.9 0.2 - - - +
116C PRO 2.9 17.8 + - - +
117C LEU 3.7 4.5 - - - +
119C LEU* 1.3 73.2 - - - +
121C ALA* 1.3 64.9 + - - +
123C GLU 3.2 1.9 + - - -
124C GLY 3.1 4.0 + - - -
125C HIS* 2.8 33.0 + - - +
128C ILE* 3.7 28.5 - - + -
129C VAL* 3.9 13.0 - - + -
132C LEU* 4.3 3.4 - - + -
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Residues in contact with ALA 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 LEU 2.9 17.2 + - - +
118C HIS* 3.7 4.5 - - - +
120C ALA* 1.3 76.4 - - - +
122C ASP* 1.3 64.0 + - - +
124C GLY* 3.0 14.2 + - - +
125C HIS 5.0 0.2 - - - +
126C LEU* 5.1 0.9 - - - -
129C VAL* 3.7 15.8 - - + +
121D ALA* 4.0 30.9 - - + +
122D ASP* 4.7 3.8 - - - +
124D GLY* 5.8 0.9 - - - -
126D LEU* 3.6 28.7 - - + -
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Residues in contact with ASP 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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313B ARG* 4.8 17.9 + - - -
315B PRO* 5.7 0.5 - - - +
316B ILE* 4.3 21.9 + - + +
118C HIS 2.9 18.3 + - - +
119C LEU* 3.8 8.8 - - + +
120C ALA 3.2 0.4 - - - -
121C ALA* 1.3 78.0 - - - +
123C GLU* 1.3 64.7 + - + +
124C GLY 3.4 0.7 + - - -
121D ALA 5.1 3.1 - - - -
122D ASP* 5.3 9.2 - - - +
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Residues in contact with GLU 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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315B PRO* 3.3 26.0 - - - +
316B ILE* 3.9 16.5 + - + +
317B THR* 3.6 24.9 + - + +
89C MET* 3.3 15.5 - - + +
119C LEU 3.0 17.2 + - - +
120C ALA 3.2 0.4 + - - -
122C ASP* 1.3 82.1 - - - +
124C GLY* 1.3 63.0 + - - +
125C HIS* 3.2 33.1 + - + -
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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