Contacts of the helix formed by residues 123 - 132 (chain G) in PDB entry 2HPC
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 LYS 123 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120G GLU* 5.1 4.5 - - - +
122G LEU* 1.3 77.6 - - + +
124G ARG* 1.3 84.2 + - - +
126G VAL* 3.4 12.6 - - - +
127G ILE* 3.4 24.1 - - + +
151H LEU* 3.3 41.8 + - - +
153H ILE* 4.8 7.8 - - + +
154H ASP* 4.2 25.7 + - - +
95I LYS* 4.8 10.7 - - - +
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Residues in contact with ARG 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G GLU* 2.5 43.6 + - - -
121G VAL* 3.1 18.4 - - + +
122G LEU* 2.8 21.0 + - - +
123G LYS* 1.3 98.5 - - - +
125G LYS* 1.3 56.3 + - + +
126G VAL* 2.3 20.4 + - - -
127G ILE* 3.6 4.9 + - - +
128G GLU* 3.4 16.3 + - - +
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Residues in contact with LYS 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G LEU* 3.4 6.6 + - - +
124G ARG* 1.3 77.0 - - + +
126G VAL* 1.3 69.6 + - - +
128G GLU* 3.9 13.0 - - + +
129G LYS* 3.7 43.8 - - + +
101I LEU* 6.1 2.8 - - - +
104I ASP* 5.6 5.6 + - - +
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Residues in contact with VAL 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122G LEU* 3.3 23.8 - - + +
123G LYS* 3.4 14.4 - - - +
124G ARG 2.3 16.6 + - - -
125G LYS* 1.3 78.6 - - - +
127G ILE* 1.3 67.0 + - + +
128G GLU 2.6 13.6 + - - +
129G LYS* 2.8 27.8 + - - +
130G VAL* 3.1 11.2 + - + +
153H ILE* 5.7 6.1 - - + +
154H ASP* 5.5 7.9 - - - +
156H THR* 4.8 9.4 - - - +
157H VAL* 4.8 21.8 - - + -
100I ILE* 5.4 9.9 - - + -
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Residues in contact with ILE 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G LYS* 3.4 21.8 - - + +
124G ARG* 3.8 3.4 - - - +
126G VAL* 1.3 83.8 - - + +
128G GLU* 1.3 52.8 + - + +
130G VAL* 4.0 9.9 - - + +
131G GLN* 2.8 35.3 + - - +
192G ASP* 5.7 4.5 - - - +
153H ILE* 3.9 28.9 - - + -
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Residues in contact with GLU 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G ARG 3.4 17.7 - - - +
125G LYS* 3.9 9.5 - - + +
126G VAL 2.6 1.1 - - - +
127G ILE* 1.3 79.3 - - + +
129G LYS* 1.3 116.0 + - - +
130G VAL 2.6 16.6 + - - -
131G GLN* 2.7 30.5 + - - +
132G HIS* 3.0 23.9 + - + +
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Residues in contact with LYS 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G LYS* 3.7 43.4 - - + +
126G VAL* 2.8 12.8 + - - +
128G GLU* 1.3 119.6 + - - +
130G VAL* 1.3 66.6 + - - +
132G HIS* 5.5 1.8 - - + -
133G ILE* 3.2 18.6 - - + +
161H ILE* 5.0 1.4 - - - +
103I HIS* 5.7 4.8 - - + +
104I ASP* 3.9 29.2 - - - +
107I ILE* 5.2 9.7 - - + +
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Residues in contact with VAL 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126G VAL* 3.1 19.3 - - + +
127G ILE* 4.0 8.1 - - + +
128G GLU 2.6 1.6 + - - -
129G LYS* 1.3 81.9 - - - +
131G GLN* 1.3 66.0 + - - +
132G HIS 3.1 1.3 - - - -
133G ILE* 3.1 25.3 + - + +
134G GLN* 2.8 31.8 + - + +
192G ASP* 5.2 15.9 - - - +
156H THR* 5.2 6.1 - - - +
161H ILE* 3.5 31.6 - - + -
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Residues in contact with GLN 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G ILE 2.8 22.4 + - - +
128G GLU* 2.7 19.2 + - - +
130G VAL* 1.3 79.0 - - - +
132G HIS* 1.3 93.4 + - + +
133G ILE 3.2 3.1 + - - -
134G GLN* 3.1 35.7 + - - +
135G LEU* 4.0 4.2 + - - +
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Residues in contact with HIS 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G GLU* 3.0 23.4 + - + +
129G LYS* 5.5 1.1 - - + -
131G GLN* 1.3 111.1 + - + +
133G ILE* 1.3 69.7 + - + +
135G LEU* 3.9 21.0 - - + +
136G LEU* 3.8 13.2 - - - +
107I ILE* 5.1 1.4 - - - +
111I GLN* 5.3 2.9 + - - -
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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