Contacts of the helix formed by residues 235 - 240 (chain A) in PDB entry 2CT8
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 PHE 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A HIS* 4.1 6.3 - - + -
105A PHE* 3.7 27.6 - + + -
106A VAL* 4.7 6.3 - - + -
109A VAL* 3.4 20.2 - - + -
231A PHE* 3.3 54.3 + + - +
232A ASP 4.4 3.8 - - - +
233A ALA 3.2 1.6 + - - -
234A LEU* 1.3 74.0 - - + +
236A ASN* 1.3 64.8 + - - +
237A TYR 3.1 0.7 - - - -
238A ILE* 3.1 9.7 + - + +
239A SER* 3.0 22.0 + - - -
268A TRP* 3.6 28.0 - + - -
271A PHE* 4.1 17.9 - + + -
272A LEU* 4.6 5.4 - - + -
275A LEU* 3.5 27.4 - - + -
277A TYR* 4.5 5.4 - + - -
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Residues in contact with ASN 236 (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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13A ILE* 3.4 37.3 - - + +
48A LEU* 3.4 19.2 - - - +
95A ILE* 3.6 12.0 - - + +
97A THR* 5.0 1.6 - - + -
102A HIS* 3.7 13.1 - - + -
233A ALA 2.9 20.5 + - - +
234A LEU 2.9 0.6 + - - -
235A PHE* 1.3 76.9 - - - +
237A TYR* 1.3 92.4 + - - +
238A ILE 3.0 1.4 + - - -
239A SER* 3.4 8.0 + - - -
240A ALA* 3.1 25.6 + - - +
501A MSP 3.6 8.1 - - - +
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Residues in contact with TYR 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A TYR* 2.7 29.1 + - - +
10A THR* 3.4 27.6 - - + -
11A THR 3.5 15.2 + - - -
12A PRO* 3.8 8.4 - - + +
48A LEU* 4.1 1.9 - - + +
234A LEU* 3.1 27.1 - - + +
236A ASN* 1.3 102.4 - - - +
238A ILE* 1.3 58.4 + - - +
241A LEU* 3.9 5.0 + - - +
249A TRP* 3.6 13.9 - - + -
254A HIS* 3.2 33.8 - + + +
255A LEU 5.1 0.2 + - - -
256A VAL* 4.3 4.2 - - - +
264A HIS* 2.6 43.1 + + - -
268A TRP* 3.9 8.1 - + + -
501A MSP 3.5 11.6 - - + -
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Residues in contact with ILE 238 (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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105A PHE* 3.7 23.2 - - + -
235A PHE* 3.1 11.4 + - + +
237A TYR* 1.3 77.9 - - - +
239A SER* 1.3 69.3 + - - +
240A ALA 3.2 1.3 - - - -
241A LEU* 3.1 19.5 + - - +
242A GLU 3.8 1.2 + - - -
245A VAL* 3.5 24.7 - - + +
249A TRP* 3.5 48.5 - - + +
268A TRP* 4.1 11.7 - - + -
272A LEU* 3.9 21.8 - - + -
277A TYR* 4.1 15.9 - - + -
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Residues in contact with SER 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 3.5 5.8 - - - +
101A TYR* 4.9 3.4 - - - +
102A HIS* 2.8 36.6 + - - -
105A PHE* 3.7 37.8 - - - -
235A PHE 3.0 8.8 + - - -
236A ASN 3.4 6.9 + - - -
238A ILE* 1.3 76.1 - - - +
240A ALA* 1.3 55.8 + - - +
242A GLU* 2.7 35.2 + - - +
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Residues in contact with ALA 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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8A TYR* 5.0 0.4 - - - +
46A PHE* 4.7 3.0 - - + -
48A LEU* 3.5 37.0 - - + -
93A LYS* 3.4 32.2 + - + +
95A ILE* 3.8 20.0 - - + -
236A ASN 3.1 15.3 + - - +
237A TYR 4.8 1.1 - - - +
239A SER* 1.3 81.9 + - - +
241A LEU* 1.3 63.0 + - + +
242A GLU* 3.0 1.5 + - - +
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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