Contacts of the helix formed by residues 116 - 127 (chain C) in PDB entry 2P5V
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 ASP 116 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C LEU* 3.5 14.0 - - - +
114C PHE* 3.5 1.3 - - - +
115C THR* 1.3 92.5 + - - +
117C MSE 1.3 65.5 + - - +
118C ASN* 3.6 12.8 - - - +
119C ALA* 3.1 15.4 + - - +
120C PHE 3.1 17.7 + - - -
1009C CL 3.7 16.8 - - + -
116F ASP* 5.7 2.7 - - + -
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Residues in contact with MSE 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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68C LEU* 3.5 12.0 - - + +
116C ASP* 1.3 75.4 - - - +
118C ASN* 1.3 53.1 + - - +
120C PHE* 3.5 26.3 - - - +
121C SER* 2.7 38.5 + - - -
141C PHE* 3.9 13.5 - - + -
1009C CL 3.4 8.6 - - + +
103E THR* 4.0 15.7 - - - -
67F GLY 4.5 10.5 - - - +
68F LEU* 3.5 28.7 - - + -
117F MSE 3.3 34.1 - - + -
141F PHE* 3.8 13.5 - - + -
142F VAL 3.9 19.5 - - - +
143F LEU* 5.0 1.1 - - - -
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Residues in contact with ASN 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C ASP* 3.2 15.3 - - - +
117C MSE 1.3 80.1 - - - +
119C ALA* 1.3 58.1 + - - +
121C SER* 3.4 7.1 + - - -
122C HIS* 3.1 26.3 + - - +
62F GLU* 2.8 29.3 + - - -
67F GLY* 5.2 5.1 + - - -
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Residues in contact with ALA 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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114C PHE* 4.0 15.8 - - + -
115C THR* 3.6 22.9 - - + +
116C ASP* 3.1 11.1 + - - +
118C ASN* 1.3 76.3 - - - +
120C PHE* 1.3 66.4 + - - +
122C HIS* 3.3 8.8 + - - +
123C PHE* 3.1 22.2 + - - +
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Residues in contact with PHE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 3.6 17.9 - - + -
70C ALA* 3.4 21.8 - - + -
72C ILE* 4.0 12.8 - - + -
114C PHE* 3.4 34.6 - + + -
116C ASP 3.1 4.8 + - - -
117C MSE 3.5 17.0 - - - +
119C ALA* 1.3 76.9 - - - +
121C SER* 1.3 58.6 + - - +
123C PHE* 3.1 4.7 + - - +
124C VAL* 2.9 53.3 + - + +
139C SER* 3.3 23.8 - - - -
141C PHE* 3.5 26.7 - + - -
103E THR* 4.1 5.2 - - + -
143F LEU* 3.9 17.7 - - + -
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Residues in contact with SER 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C MSE 2.7 22.1 + - - -
118C ASN* 3.6 7.6 - - - -
119C ALA 3.3 0.2 - - - -
120C PHE* 1.3 74.1 - - - +
122C HIS* 1.3 56.8 + - - +
124C VAL 4.6 0.2 - - - +
125C LEU* 2.9 46.2 + - - +
142F VAL 5.3 1.1 - - - -
143F LEU* 2.6 50.6 + - - -
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Residues in contact with HIS 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 ASN 3.1 13.6 + - - +
119C ALA* 3.7 10.5 - - - +
120C PHE 3.3 0.4 - - - -
121C SER* 1.3 74.7 - - - +
123C PHE* 1.3 59.5 + - - +
125C LEU* 5.2 0.4 - - - -
126C ASP* 2.5 69.3 + - + +
127C THR* 3.9 2.6 + - - -
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Residues in contact with PHE 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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72C ILE* 3.7 25.6 - - + -
93C TRP* 3.8 28.0 - + - -
95C GLU* 3.8 29.4 - - + +
96C VAL* 3.8 20.9 - - + -
110C LEU* 5.3 0.9 - - + -
114C PHE* 3.5 32.1 - + + -
119C ALA 3.1 8.3 + - - +
120C PHE 3.3 6.3 - - - +
122C HIS* 1.3 79.5 - - - +
124C VAL* 1.3 67.7 + - + +
127C THR* 2.9 33.5 + - + -
128C LEU* 2.9 38.2 + - + -
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Residues in contact with VAL 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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120C PHE* 2.9 58.7 + - + +
121C SER 3.9 2.9 - - - +
123C PHE* 1.3 81.6 - - + +
125C LEU* 1.3 61.5 + - - +
128C LEU* 3.9 17.9 - - + -
129C LEU* 2.8 57.4 + - + +
137C ALA* 5.9 1.8 - - + -
139C SER* 5.1 1.3 - - - +
143F LEU* 3.9 21.5 - - + -
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Residues in contact with LEU 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 SER* 2.9 34.9 + - - +
122C HIS* 5.6 0.2 - - - -
124C VAL* 1.3 79.7 - - - +
126C ASP* 1.3 74.1 + - - +
129C LEU* 4.5 10.8 - - + +
130C SER* 4.0 15.6 + - - -
83E ARG* 4.0 28.0 - - - +
101E ALA* 4.9 4.3 - - + -
143F LEU* 4.1 31.4 - - + +
144F LYS* 4.1 35.0 - - + +
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Residues in contact with ASP 126 (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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122C HIS* 2.5 50.9 + - + +
125C LEU* 1.3 87.5 - - - +
127C THR* 1.3 62.3 + - - +
130C SER* 2.9 17.5 + - - -
144F LYS* 5.9 0.3 + - - -
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Residues in contact with THR 127 (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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93C TRP* 3.5 38.9 - - + +
122C HIS* 3.9 3.3 + - - -
123C PHE* 2.9 32.0 + - + -
125C LEU 3.6 0.6 - - - -
126C ASP* 1.3 82.1 + - - +
128C LEU* 1.3 67.0 + - - +
130C SER* 3.1 12.5 + - - -
131C HIS* 3.2 12.6 + - - +
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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