Contacts of the helix formed by residues 246 - 255 (chain A) in PDB entry 3ROT
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 THR 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ASP* 3.9 4.0 - - - +
35A PRO* 3.8 24.6 - - + +
36A TYR* 4.1 7.9 - - - +
216A SER* 3.7 29.4 - - - +
220A ASP* 4.8 2.1 + - - -
244A ASP* 3.1 14.0 + - + +
245A LYS* 1.3 75.1 - - - +
247A PRO* 1.3 71.6 - - - +
248A ASN* 3.9 5.9 + - - +
249A THR* 2.6 28.0 + - - -
250A VAL* 2.8 27.2 + - - +
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Residues in contact with PRO 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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35A PRO* 4.2 15.7 - - + -
245A LYS 4.6 0.7 - - - +
246A THR* 1.3 87.7 - - - +
248A ASN* 1.3 62.7 + - - +
250A VAL* 3.3 8.4 + - + +
251A SER* 3.0 22.9 + - - -
220B ASP 5.9 0.7 - - - +
224B GLN* 4.2 29.2 - - + +
227B LEU* 3.8 31.0 - - + -
228B HIS* 5.7 5.2 - - + +
248B ASN* 4.0 22.7 + - - +
251B SER* 5.1 1.2 + - - -
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Residues in contact with ASN 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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219A LEU* 6.1 0.2 - - - +
220A ASP* 3.3 37.9 + - - +
223A GLY* 5.2 1.8 - - - -
227A LEU* 5.2 0.7 - - - +
246A THR* 3.3 3.9 + - - +
247A PRO* 1.3 79.5 - - - +
249A THR* 1.3 57.3 + - - +
251A SER* 3.2 9.0 + - - -
252A LEU* 3.0 52.9 + - - +
247B PRO* 3.5 30.4 - - - +
248B ASN* 3.8 19.3 + - + +
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Residues in contact with THR 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A SER* 4.2 6.8 - - - -
219A LEU* 3.6 30.4 - - + +
220A ASP* 5.3 1.4 + - - -
242A SER* 5.0 0.4 - - - -
243A PHE 5.2 0.2 + - - -
244A ASP 3.4 18.2 + - - +
245A LYS* 4.2 3.1 - - - -
246A THR* 2.6 32.2 + - - -
248A ASN* 1.3 77.4 - - - +
250A VAL* 1.3 58.3 + - - +
252A LEU* 3.2 4.8 + - - +
253A ILE* 3.0 33.2 + - + +
258A VAL* 4.9 0.8 - - + +
261A VAL* 3.5 32.3 - - + -
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Residues in contact with VAL 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LYS* 3.7 30.5 - - + +
246A THR 2.8 18.5 + - - +
247A PRO* 3.6 9.9 - - + +
249A THR* 1.3 74.8 - - - +
251A SER* 1.3 62.8 - - - +
253A ILE* 3.2 10.5 + - + +
254A HIS* 3.1 50.7 + - + +
255B LYS* 5.8 4.9 - - - -
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Residues in contact with SER 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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247A PRO 3.0 14.3 + - - -
248A ASN* 3.5 15.0 - - - -
249A THR 3.2 0.2 - - - -
250A VAL* 1.3 78.9 - - - +
252A LEU* 1.3 62.8 + - - +
254A HIS* 3.2 10.3 + - - +
255A LYS* 3.1 42.1 + - - +
247B PRO 5.2 1.3 + - - -
251B SER* 3.5 32.4 + - - -
255B LYS* 6.3 1.3 - - - +
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Residues in contact with LEU 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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219A LEU* 4.2 22.4 - - + -
223A GLY* 4.0 23.1 - - - +
226A LEU* 5.0 1.1 - - + -
227A LEU* 4.0 22.9 - - + -
248A ASN* 3.0 43.3 + - - +
249A THR 3.7 4.3 - - - +
251A SER* 1.3 77.0 - - - +
253A ILE* 1.3 61.2 + - - +
255A LYS* 3.3 6.0 + - + +
256A LYS 3.2 3.1 + - - -
257A LEU* 2.9 56.8 + - + +
258A VAL* 3.4 18.0 + - + -
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Residues in contact with ILE 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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245A LYS* 4.7 16.4 - - + -
249A THR* 3.0 21.2 + - + +
250A VAL* 3.4 16.4 - - + +
251A SER 3.2 0.2 - - - -
252A LEU* 1.3 76.8 - - - +
254A HIS* 1.3 68.0 + - + +
256A LYS* 2.9 23.6 + - - +
258A VAL* 3.7 31.0 - - + +
259A ASN 5.4 4.7 - - - +
260A TYR* 5.4 2.7 - - - +
261A VAL* 3.6 28.3 - - + +
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Residues in contact with HIS 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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250A VAL* 3.1 37.1 + - + +
251A SER* 3.2 10.8 + - - +
253A ILE* 1.3 85.2 - - + +
255A LYS* 1.3 60.3 + - + +
256A LYS* 3.2 7.0 + - - +
255B LYS* 4.4 21.7 + - - -
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Residues in contact with LYS 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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227A LEU* 3.6 31.9 - - + -
251A SER* 3.1 32.1 + - - +
252A LEU* 3.9 6.1 - - + +
253A ILE 3.1 0.4 - - - -
254A HIS* 1.3 77.6 - - + +
256A LYS* 1.3 70.3 + - - +
257A LEU* 3.2 18.3 + - + +
250B VAL* 5.7 10.2 - - - +
251B SER* 6.1 2.2 - - - +
254B HIS* 6.0 3.8 - - - -
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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