Contacts of the helix formed by residues 238 - 243 (chain A) in PDB entry 6CNC
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 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ILE* 3.4 46.9 + - + +
120A LYS* 5.5 4.5 - - - +
124A LEU* 5.0 1.9 - - - +
234A ILE* 3.5 19.6 - - - +
235A LYS 4.2 3.3 + - - +
236A SER 2.8 12.8 - - - +
237A ALA* 1.3 87.3 - - - +
239A CYS* 1.3 76.5 + - - -
240A GLU* 2.6 27.1 + - - +
241A LEU* 3.1 26.8 + - + +
242A LEU* 3.4 21.4 - - + +
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Residues in contact with CYS 239 (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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234A ILE* 6.0 0.4 - - - -
235A LYS* 4.8 1.1 - - - +
236A SER* 3.7 24.0 - - - +
237A ALA 4.3 0.2 - - - +
238A ASP* 1.3 86.4 + - - +
240A GLU* 1.3 95.6 + - - +
241A LEU 3.4 0.2 - - - -
242A LEU* 3.5 16.8 + - - +
244A ILE* 3.2 27.7 + - - +
246A ALA* 2.8 40.4 - - + -
252A ARG* 4.5 7.6 - - + -
253A PRO* 5.3 9.7 - - + +
70O ALA 4.4 2.2 - - - +
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Residues in contact with GLU 240 (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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124A LEU* 4.4 7.6 - - + +
127A LEU* 4.1 16.3 - - + +
128A ARG* 2.6 34.4 + - - +
137A ARG* 5.5 1.1 + - - +
237A ALA 3.9 3.3 - - - +
238A ASP 2.6 13.3 + - - +
239A CYS* 1.3 93.6 - - - +
241A LEU* 1.3 57.8 + - - +
242A LEU 3.0 1.8 - - - -
243A GLY* 2.6 24.4 + - - -
244A ILE 3.1 24.9 - - - +
245A ASP* 3.9 17.3 - - - +
246A ALA 5.5 0.2 - - - -
71O LEU* 3.5 21.9 - - - +
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Residues in contact with LEU 241 (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 ILE* 4.1 27.4 - - + -
115A LEU* 5.5 3.6 - - + -
120A LYS* 3.8 30.1 - - + +
123A PHE* 4.1 14.1 - - + -
124A LEU* 3.7 26.2 - - + +
127A LEU* 4.8 9.4 - - + +
141A LEU* 3.6 14.9 - - - +
144A ILE* 3.6 38.4 - - + +
238A ASP* 3.1 21.1 + - + +
240A GLU* 1.3 79.1 - - - +
242A LEU* 1.3 60.1 + - + +
243A GLY 3.3 0.2 - - - -
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Residues in contact with LEU 242 (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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101A GLN 5.4 1.6 - - - +
102A ILE* 3.4 44.7 - - + +
105A GLY* 4.9 10.8 - - - +
106A ILE* 5.5 2.5 - - + -
113A ILE* 4.0 22.9 - - + -
141A LEU* 4.3 5.3 - - - +
144A ILE* 6.0 3.8 - - + -
145A LEU* 6.2 7.9 - - + -
234A ILE* 4.3 11.7 - - + -
238A ASP* 3.4 28.5 - - + +
239A CYS* 3.5 11.7 + - - +
240A GLU 3.0 0.8 - - - -
241A LEU* 1.3 81.8 - - + +
243A GLY* 1.3 58.0 + - - +
244A ILE* 3.6 9.3 - - + +
253A PRO* 5.7 0.7 - - + -
1401A PHE* 4.7 1.9 - - - -
1402A TYR* 3.8 12.8 - - - -
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Residues in contact with GLY 243 (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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127A LEU* 5.9 0.2 - - - -
137A ARG* 3.5 12.0 + - - -
141A LEU* 3.9 14.8 - - - +
240A GLU* 2.6 21.5 + - - -
241A LEU 3.3 1.2 + - - -
242A LEU* 1.3 71.9 - - - +
244A ILE* 1.3 61.9 + - - +
245A ASP 4.0 0.4 - - - -
1402A TYR* 3.3 41.6 - - - +
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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