Contacts of the helix formed by residues 124 - 133 (chain E) in PDB entry 3CQ6
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 124 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E TYR* 3.9 15.7 - - - -
120E GLN* 6.2 0.2 - - - +
122E SER 3.3 5.5 + - - -
123E TYR* 1.3 77.3 - - - +
125E MET* 1.3 61.4 + - - +
127E PRO* 3.4 17.3 - - - +
128E ILE* 3.5 16.7 - - - +
333E ARG* 5.0 4.0 - - - -
402E PO4 2.7 31.8 + - - -
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Residues in contact with MET 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E TYR* 3.8 41.5 - - + -
99E ASN* 3.6 28.5 - - - +
123E TYR* 3.1 41.9 + - + +
124E SER* 1.3 78.0 + - - +
126E HIS* 1.3 57.5 + - - +
127E PRO 3.4 0.2 - - - -
128E ILE* 3.1 25.2 + - + -
129E LEU* 2.7 57.3 + - + +
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Residues in contact with HIS 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E LEU* 3.6 24.9 - - + +
122E SER* 4.9 3.8 + - - -
123E TYR* 3.3 26.0 + + + +
125E MET* 1.3 76.9 - - - +
127E PRO* 1.3 67.5 - - + +
129E LEU* 3.3 4.5 + - - +
130E ALA* 2.9 28.3 + - - +
137E PHE* 4.5 6.9 - - + -
166E PHE* 3.8 51.0 - + + +
168E THR* 3.3 26.7 + - - -
197E ASP* 3.1 30.6 + - + +
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Residues in contact with PRO 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120E GLN* 4.0 17.5 - - - +
123E TYR 3.5 9.2 - - - +
124E SER* 3.4 15.5 - - - +
126E HIS* 1.3 97.4 - - + +
128E ILE* 1.3 56.2 + - + +
130E ALA* 3.4 1.7 + - - +
131E LYS* 2.9 29.6 + - - +
137E PHE* 3.9 42.1 - - + +
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Residues in contact with ILE 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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21E TYR* 3.9 39.5 - - + +
124E SER* 3.5 19.3 - - - +
125E MET* 3.1 26.5 + - + +
127E PRO* 1.3 79.8 - - + +
129E LEU* 1.3 57.9 + - + +
131E LYS* 3.5 7.6 + - + +
132E GLY* 2.9 23.9 + - - -
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Residues in contact with LEU 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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99E ASN* 3.7 35.9 - - + +
102E LEU* 3.7 38.4 - - + -
103E GLN* 4.5 17.3 - - + +
106E LEU* 3.6 16.6 - - + -
125E MET* 2.7 43.9 + - + +
126E HIS* 3.8 3.6 - - - +
128E ILE* 1.3 70.5 - - + +
130E ALA* 1.3 65.9 + - - +
132E GLY* 3.2 2.4 + - - +
133E THR* 3.0 30.5 + - - +
166E PHE* 6.5 0.2 - - + -
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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
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106E LEU* 3.8 7.5 - - + +
116E ALA* 4.7 8.1 - - + -
126E HIS 2.9 13.7 + - - +
127E PRO* 3.4 13.5 - - + +
129E LEU* 1.3 76.0 - - - +
131E LYS* 1.3 60.6 + - - +
133E THR* 3.0 10.9 + - - -
135E THR* 2.7 47.8 + - - +
137E PHE* 4.0 20.6 - - + -
166E PHE* 5.4 0.7 - - + -
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Residues in contact with LYS 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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14E GLU* 4.6 10.9 - - - +
15E LEU* 5.8 5.8 - - + -
18E GLU* 2.7 44.2 + - - -
127E PRO 2.9 17.6 + - - +
128E ILE* 3.7 8.1 - - - +
130E ALA* 1.3 75.0 - - - +
132E GLY* 1.3 63.1 + - - +
134E HIS* 3.0 21.2 + - - +
135E THR 3.9 5.6 + - - -
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Residues in contact with GLY 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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103E GLN* 6.1 2.5 - - - -
128E ILE 2.9 15.7 + - - -
129E LEU* 3.2 5.5 + - - -
131E LYS* 1.3 76.9 - - - +
133E THR* 1.3 60.6 + - - +
134E HIS* 3.4 12.0 + - - -
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Residues in contact with THR 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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103E GLN* 4.1 27.8 - - + +
106E LEU* 3.6 30.7 - - + +
107E GLN* 4.4 11.4 - - + -
111E GLY* 3.4 14.4 - - - -
112E PRO* 4.0 2.4 - - - +
129E LEU* 3.0 18.7 + - - +
130E ALA 3.0 4.2 + - - -
131E LYS 3.1 0.2 - - - -
132E GLY* 1.3 77.3 - - - +
134E HIS* 1.3 73.2 + - - +
135E THR* 2.9 21.8 + - - -
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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