Contacts of the helix formed by residues 116 - 124 (chain A) in PDB entry 3CPE
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A LYS* 3.0 30.2 + - + +
113A CYS* 3.5 7.5 + - - +
115A ASP* 1.3 78.8 - - - +
117A ILE* 1.3 63.7 + - - +
118A VAL* 3.7 8.5 + - - +
119A TYR* 3.2 30.0 + - + +
120A PHE 3.1 17.5 + - - -
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Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A CYS 4.2 0.4 + - - -
115A ASP 4.0 0.8 - - - -
116A ASP* 1.3 73.9 + - - +
118A VAL* 1.3 57.8 + - + +
120A PHE* 3.2 8.9 + - + +
121A ALA* 2.8 33.3 + - - +
147A LEU* 3.7 38.4 - - + +
148A LYS* 4.5 3.8 - - + +
151A SER* 3.8 24.9 - - - +
172A ILE* 5.1 0.9 - - + -
173A PHE* 3.4 35.9 - - + -
176A HIS* 3.5 42.8 + - + +
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A ASP* 3.3 8.1 + - - +
117A ILE* 1.3 78.3 - - + +
119A TYR* 1.3 57.5 + - - +
121A ALA* 3.3 5.5 + - - +
122A GLU* 2.9 55.1 + - + +
139A LEU* 5.0 0.9 - - + -
144A ARG* 3.8 33.0 - - + +
147A LEU* 4.5 11.2 - - + -
148A LYS* 4.0 30.5 - - + -
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Residues in contact with TYR 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLN* 4.0 10.9 + - - -
109A GLU* 2.8 31.2 + - - -
112A LYS* 3.6 39.0 - - + -
113A CYS* 4.5 10.3 - - - -
116A ASP* 3.2 29.9 + - - +
118A VAL* 1.3 77.1 - - - +
120A PHE* 1.3 66.6 + - - +
122A GLU* 3.3 4.3 + - + -
123A THR* 2.6 56.8 + - + +
124A TYR* 4.2 8.3 - + - -
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Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A CYS* 3.9 25.8 - - + +
116A ASP 3.1 12.1 + - - +
117A ILE* 3.2 9.8 + - - +
119A TYR* 1.3 76.7 - - - +
121A ALA* 1.3 61.7 + - - +
124A TYR* 3.0 38.7 + - + +
125A CYS* 3.6 22.3 + - - -
172A ILE* 4.0 9.2 - - + -
175A ALA* 4.9 3.1 - - + -
176A HIS* 3.7 36.8 - - + -
180A PHE* 3.5 33.9 - + - -
210A LEU* 3.6 40.8 - - + -
214A LEU* 4.2 5.8 - - + -
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ILE 2.8 20.7 + - - +
118A VAL 3.7 1.6 - - - +
120A PHE* 1.3 74.5 - - - +
122A GLU* 1.3 61.2 + - - +
123A THR 3.6 0.2 + - - -
125A CYS* 3.4 18.2 + - - +
137A VAL* 3.4 24.8 - - - +
139A LEU* 3.6 22.4 - - + -
147A LEU* 3.7 7.0 - - + -
172A ILE* 3.6 25.6 - - + -
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Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A VAL* 2.9 32.6 + - - +
119A TYR* 4.0 5.2 - - + +
121A ALA* 1.3 76.4 - - - +
123A THR* 1.3 60.6 + - - +
125A CYS 5.5 0.2 - - - -
136A LYS* 3.1 27.9 + - - +
137A VAL 4.8 6.4 - - - +
139A LEU* 3.8 19.7 - - + +
144A ARG* 3.0 31.5 + - - -
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Residues in contact with THR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 3.9 9.7 - - - +
75A GLN* 4.9 5.8 - - - +
119A TYR* 2.6 52.3 + - + +
122A GLU* 1.3 82.6 - - - +
124A TYR* 1.3 91.4 + - + +
125A CYS 3.9 0.2 - - - -
136A LYS* 3.3 33.9 + - - +
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Residues in contact with TYR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ILE* 4.5 5.6 - - - +
75A GLN* 3.1 56.6 + - + +
109A GLU* 3.1 26.5 + - - +
113A CYS* 3.4 27.6 - - - -
119A TYR* 4.2 1.6 - + - -
120A PHE* 3.0 15.9 + - + +
123A THR* 1.3 104.8 - - + +
125A CYS* 1.3 64.6 + - - +
126A ALA* 3.6 4.9 + - - +
206A ALA 5.3 0.3 - - - +
209A LEU 4.2 12.3 - - - +
210A LEU* 3.7 28.9 - - + +
211A PRO* 3.7 9.2 - - + +
213A PHE* 3.9 3.4 - + - -
214A LEU* 3.4 24.0 - - + -
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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