Contacts of the helix formed by residues 247 - 256 (chain A) in PDB entry 3L6B
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 ASN 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ASP* 3.1 37.2 + - + +
155A GLN* 2.8 52.1 + - - +
157A PRO* 4.7 6.5 - - - +
160A ILE* 4.5 4.9 - - + +
246A LEU* 1.3 82.9 - - - +
248A THR* 1.3 60.7 + - - +
250A PRO* 3.6 8.2 - - - +
251A ILE* 3.8 16.8 - - - +
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Residues in contact with THR 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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154A ASN 3.3 25.1 - - - +
155A GLN* 3.0 12.2 + - - +
160A ILE* 3.8 15.0 - - + -
186A GLY 2.8 18.9 + - - -
187A GLY* 3.3 30.6 - - - +
188A GLY* 3.8 0.9 - - - +
191A ALA* 3.9 8.5 - - + -
244A ILE* 4.1 2.4 - - - +
245A GLY 3.4 5.9 + - - -
247A ASN* 1.3 78.2 - - - +
249A TRP* 1.3 66.6 + - - +
250A PRO 3.4 0.2 - - - -
251A ILE* 3.2 5.2 + - - +
252A ILE* 3.0 27.7 + - - +
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Residues in contact with TRP 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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220A SER* 3.3 35.7 - - - -
221A LYS* 3.9 20.6 - - + -
224A GLY* 3.6 9.6 + - - -
225A LYS* 3.5 22.4 - - - +
226A LEU* 3.8 33.9 - - + +
244A ILE* 3.7 28.0 - - + -
245A GLY 3.0 18.6 + - - +
246A LEU* 4.8 2.0 - - + +
248A THR* 1.3 76.4 + - - +
250A PRO* 1.3 69.5 - - + +
252A ILE* 3.2 7.3 + - + -
253A ARG* 2.7 73.3 + - + +
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Residues in contact with PRO 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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5A TYR* 3.9 14.6 - - + -
6A ASP* 5.9 1.1 - - - +
246A LEU 3.1 24.2 - - - +
247A ASN* 3.6 7.2 - - - +
248A THR 3.6 3.4 - - - -
249A TRP* 1.3 100.0 - - + +
251A ILE* 1.3 60.3 + - + +
253A ARG* 3.5 29.0 + - - +
254A ASP* 3.1 30.8 + - - +
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Residues in contact with ILE 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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5A TYR* 3.6 40.8 - - + -
6A ASP* 4.7 4.5 - - + +
7A ILE* 4.5 10.8 - - + +
160A ILE* 5.1 5.4 - - + -
191A ALA* 3.6 42.6 - - + +
194A ALA* 4.1 5.8 - - + -
195A ILE* 3.9 20.0 - - + -
247A ASN 3.8 17.9 - - - +
248A THR* 3.2 6.4 + - - +
250A PRO* 1.3 76.4 - - + +
252A ILE* 1.3 58.8 + - - +
255A LEU* 2.8 41.1 + - + +
256A VAL 3.9 0.2 + - - -
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Residues in contact with ILE 252 (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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187A GLY* 3.9 15.5 - - - +
190A LEU* 3.7 33.0 - - + -
191A ALA* 4.6 7.9 - - + +
217A CYS* 3.8 21.5 - - - -
221A LYS* 3.0 30.9 + - + -
244A ILE* 3.9 27.6 - - + -
248A THR* 3.0 27.5 + - - +
249A TRP* 3.7 9.4 - - + +
251A ILE* 1.3 74.3 - - - +
253A ARG* 1.3 65.5 + - - +
256A VAL* 3.2 23.3 + - + -
259A ILE* 4.7 1.1 - - + -
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Residues in contact with ARG 253 (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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5A TYR* 4.8 2.0 - - - -
221A LYS* 2.9 28.4 + - + -
224A GLY* 4.8 8.7 - - - +
249A TRP* 2.7 64.0 + - + +
250A PRO* 3.5 26.3 - - - +
252A ILE* 1.3 73.4 - - - +
254A ASP* 1.3 90.8 + - - +
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Residues in contact with ASP 254 (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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3A ALA 5.2 0.7 + - - -
5A TYR* 2.6 34.9 + - + +
250A PRO 3.1 11.9 + - - +
251A ILE 4.1 0.2 - - - +
253A ARG* 1.3 120.3 + - - +
255A LEU* 1.3 67.2 - - + +
256A VAL 3.8 1.3 - - - +
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Residues in contact with LEU 255 (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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5A TYR* 4.2 16.8 - - + +
194A ALA* 4.0 15.2 - - + +
195A ILE* 3.8 40.2 - - + -
198A LYS* 3.3 46.6 - - + +
206A VAL* 4.5 1.4 - - - +
251A ILE* 2.8 25.6 + - + +
254A ASP* 1.3 89.3 - - + +
256A VAL* 1.3 63.8 + - - +
257A ASP* 3.8 1.0 + - - -
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Residues in contact with VAL 256 (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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190A LEU* 3.7 33.2 - - + -
194A ALA* 4.0 14.6 - - + -
206A VAL* 3.4 15.7 - - + +
208A ALA* 4.2 12.8 - - + +
221A LYS* 2.9 24.7 + - - -
252A ILE* 3.2 30.4 + - + +
253A ARG 4.8 0.2 - - - +
254A ASP 5.1 0.7 - - - -
255A LEU* 1.3 80.1 + - - +
257A ASP* 1.3 63.8 + - - +
258A ASP 3.6 19.3 - - - +
259A ILE* 4.5 6.7 - - + -
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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