Contacts of the helix formed by residues 243 - 251 (chain A) in PDB entry 4CBS
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 243 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ASN* 3.7 4.3 - - - -
236A LYS* 5.8 0.7 - - - +
237A PRO* 3.7 28.3 - - - +
239A SER 3.5 14.1 + - - +
240A PHE* 3.0 18.9 + - + +
241A TYR 3.5 0.4 - - - -
242A LEU* 1.3 75.6 - - - +
244A ILE* 1.3 64.0 + - - +
245A LYS* 3.1 24.8 + - - +
246A TRP* 3.2 31.8 + - + +
247A LEU* 3.1 23.1 + - - +
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Residues in contact with ILE 244 (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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74A LEU* 4.2 15.7 - - + -
76A LEU* 4.4 16.8 - - + -
78A ILE* 5.4 3.6 - - + -
88A ALA* 6.2 1.6 - - + -
92A ASN* 2.8 30.8 + - + +
222A PHE* 3.7 33.0 - - + -
230A MET* 3.9 31.4 - - + +
231A TYR* 4.6 7.2 - - + -
242A LEU 3.3 1.7 + - - +
243A ASP* 1.3 73.6 + - - +
245A LYS* 1.3 68.5 + - + +
247A LEU* 4.3 15.5 - - + -
248A ALA* 2.8 35.6 + - + +
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Residues in contact with LYS 245 (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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230A MET 4.1 6.7 - - - -
231A TYR* 3.7 68.5 + - + +
233A ARG* 5.5 6.8 + - - +
243A ASP* 3.1 14.0 + - - +
244A ILE* 1.3 83.6 - - + +
246A TRP* 1.3 65.1 + - + +
248A ALA* 3.9 1.6 - - - +
249A ASN* 3.2 22.7 + - - +
254A ASP* 4.4 2.8 - - - +
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Residues in contact with TRP 246 (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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236A LYS* 6.0 2.0 - - - +
240A PHE* 3.6 30.1 - + - -
243A ASP* 3.2 37.7 + - + +
245A LYS* 1.3 80.3 - - + +
247A LEU* 1.3 64.8 + - - +
249A ASN* 3.3 7.0 + - - +
250A PHE* 3.1 23.7 + - - +
259A MET* 3.9 27.9 - - + +
260A TYR 3.4 20.0 - - - -
261A HIS* 3.3 45.8 - + + +
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Residues in contact with LEU 247 (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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76A LEU* 3.8 15.0 - - + -
77A VAL 5.3 2.5 - - - +
78A ILE* 4.6 22.0 - - + -
241A TYR 3.6 10.3 - - - +
242A LEU* 3.5 26.7 - - + +
243A ASP 3.1 21.4 + - - +
244A ILE* 3.8 9.0 - - + +
246A TRP* 1.3 73.6 - - - +
248A ALA* 1.3 67.4 + - - +
250A PHE* 3.2 4.7 + - + -
251A TRP* 2.9 37.7 + - + +
261A HIS* 3.3 29.2 - - + +
262A HIS* 3.8 19.1 - - + -
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Residues in contact with ALA 248 (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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74A LEU* 3.5 26.0 - - + -
76A LEU* 3.8 12.2 - - - +
231A TYR* 3.5 19.7 - - - +
244A ILE* 2.8 23.7 + - + +
245A LYS 3.9 0.9 - - - +
247A LEU* 1.3 74.8 - - - +
249A ASN* 1.3 60.9 + - - +
251A TRP 3.3 1.9 + - - -
252A GLY 3.2 4.3 + - - -
253A CYS* 2.9 34.4 + - + +
254A ASP* 4.2 3.8 - - - +
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Residues in contact with ASN 249 (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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245A LYS 3.2 12.8 + - - +
246A TRP* 3.7 6.1 - - - +
247A LEU 3.2 0.2 - - - -
248A ALA* 1.3 79.6 - - - +
250A PHE* 1.3 63.9 + - - +
252A GLY* 3.0 12.6 + - - -
254A ASP* 3.4 23.1 + - - +
256A GLN* 3.5 27.5 + - - +
257A PRO 2.9 21.4 + - - -
258A ARG* 3.7 9.2 - - - +
259A MET* 2.7 42.9 + - - +
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Residues in contact with PHE 250 (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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48A HIS* 3.7 23.1 - - - -
49A MET* 3.7 26.7 - - + -
54A TYR* 3.9 18.8 - + - -
57A MET* 3.6 17.0 - - + +
246A TRP 3.1 14.9 + - - +
247A LEU* 3.2 4.7 + - + +
249A ASN* 1.3 81.5 + - - +
251A TRP* 1.3 65.8 + + + +
258A ARG* 2.9 31.4 + - + -
259A MET 3.5 24.7 - - - +
260A TYR* 4.5 3.6 - + - -
261A HIS* 4.6 10.5 - - + -
262A HIS* 4.5 14.6 - + - -
264A ILE* 3.6 30.7 - - + -
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Residues in contact with TRP 251 (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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57A MET* 3.4 62.1 - - + +
58A ASP* 4.5 0.7 - - - +
60A ILE* 4.6 3.6 - - + -
61A LYS* 2.8 34.1 + - + +
64A ILE* 6.0 0.2 - - + -
76A LEU* 3.8 32.3 - - + -
77A VAL* 3.5 52.3 + - + -
79A SER* 5.5 0.6 + - - -
247A LEU* 2.9 39.5 + - + +
248A ALA 4.0 1.6 - - - +
249A ASN 3.2 0.4 - - - -
250A PHE* 1.3 82.0 - + + +
252A GLY* 1.3 56.7 + - - +
253A CYS* 3.3 5.4 - - - -
258A ARG* 3.3 12.6 + - - +
262A HIS* 5.3 0.8 - - - -
264A ILE* 4.1 27.2 - - + +
269A LEU* 4.0 15.5 - - + -
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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