Contacts of the helix formed by residues 127 - 136 (chain E) in PDB entry 2C2V
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 127 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82E PRO 4.0 7.2 + - - +
84E VAL 4.2 11.4 - - - +
85E ASP* 5.2 5.5 - - - +
86E LYS* 5.4 2.4 + - - +
124E PRO* 3.1 50.8 + - + +
128E ASP* 1.4 65.2 + - + +
129E VAL* 2.9 14.0 - - - +
130E ALA* 2.8 27.3 + - - +
131E GLU* 3.0 17.7 + - - +
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Residues in contact with ASP 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E LYS* 3.3 37.7 + - - +
127E ASN* 1.4 70.0 - - + +
129E VAL* 1.3 60.3 + - + +
131E GLU* 2.5 35.7 + - - +
132E GLN* 2.9 13.6 + - - +
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Residues in contact with VAL 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E TYR* 3.3 50.9 - - + -
81E HIS 4.4 15.9 - - - +
82E PRO* 4.3 9.0 - - + -
84E VAL 5.2 4.0 - - - +
85E ASP* 6.5 0.2 - - - -
86E LYS* 3.1 32.1 - - - +
127E ASN* 2.9 12.4 - - - +
128E ASP* 1.3 77.4 - - + +
130E ALA* 1.3 65.0 + - - +
131E GLU 3.1 0.5 + - - -
132E GLN* 3.5 2.9 + - - +
133E TRP* 3.3 22.9 + - + +
147E TRP* 6.4 0.4 - - + -
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Residues in contact with ALA 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E PRO* 3.7 16.7 - - + +
121E PRO* 3.5 25.2 - - + +
122E ASP* 3.5 12.1 - - - +
124E PRO 4.2 10.5 - - - -
127E ASN* 2.8 20.8 - - - +
129E VAL* 1.3 74.6 - - - +
131E GLU* 1.3 71.6 + - - +
132E GLN 3.3 0.2 + - - -
133E TRP* 3.6 4.4 - - - +
134E LYS* 3.3 20.8 + - - +
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Residues in contact with GLU 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E ASN 3.0 10.8 + - - +
128E ASP* 2.5 28.5 + - - +
130E ALA* 1.3 79.2 - - - +
132E GLN* 1.4 62.2 + - + +
134E LYS* 2.9 30.1 + - - +
135E THR* 3.0 23.2 + - - +
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Residues in contact with GLN 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ARG* 6.3 0.8 - - - +
80E TYR* 4.3 18.3 + - - +
128E ASP 3.4 12.8 - - - +
129E VAL* 4.0 4.7 - - - +
131E GLU* 1.4 77.8 - - + +
133E TRP* 1.3 65.2 + - - +
134E LYS 2.8 2.0 - - - -
135E THR* 2.7 8.1 + - - +
136E ASN* 2.4 50.5 + - - +
139E GLN* 4.7 11.8 + - - +
140E ALA* 4.7 5.7 + - + +
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Residues in contact with TRP 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E PRO* 4.6 4.5 - - + -
51E PHE* 4.5 7.6 - + - -
80E TYR* 3.3 46.9 - + - -
81E HIS* 3.8 2.2 - - - -
82E PRO* 3.5 30.5 - - + -
119E PRO* 3.6 32.6 - - + +
121E PRO* 4.3 17.7 - - + -
129E VAL* 3.3 15.1 + - + +
130E ALA* 3.6 10.1 - - - +
132E GLN* 1.3 83.0 - - - +
134E LYS* 1.3 57.4 + - - +
137E GLU* 3.3 34.0 + - - +
140E ALA* 3.9 20.5 - - + +
141E ILE* 4.5 19.5 - - + +
144E ALA* 4.1 14.8 - - + -
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Residues in contact with LYS 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E PRO* 3.8 14.8 - - + -
122E ASP* 2.7 58.9 + - - +
130E ALA* 3.5 7.0 - - - +
131E GLU* 2.9 19.1 + - - +
132E GLN 2.8 0.6 - - - -
133E TRP* 1.3 77.4 - - - +
135E THR* 1.3 67.5 + - + +
137E GLU 4.9 0.4 - - - -
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Residues in contact with THR 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E GLU* 3.0 28.7 + - - +
132E GLN* 2.7 10.7 + - - -
134E LYS* 1.3 88.1 - - + +
136E ASN* 1.3 63.3 + - - +
137E GLU 3.8 1.6 - - - -
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Residues in contact with ASN 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E GLN* 2.4 25.9 + - - +
133E TRP 3.9 0.2 - - - -
135E THR* 1.3 79.2 + - - +
137E GLU* 1.4 56.8 + - - +
138E ALA* 3.2 12.2 - - - +
139E GLN* 3.3 41.4 + - + +
140E ALA* 2.7 34.0 + - - +
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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