Contacts of the helix formed by residues 1376 - 1384 (chain B) in PDB entry 5XA0
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 HIS1376 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1372B MET 4.1 5.8 + - - +
1373B TYR 5.2 0.8 + - - -
1374B HIS 3.4 0.2 - - - -
1375B ILE* 1.3 75.2 - - - +
1377B LEU* 1.3 59.5 + - - +
1378B VAL 3.2 1.6 - - - -
1379B GLU* 3.7 9.3 + - + +
1380B LEU* 2.8 34.2 + - + +
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Residues in contact with LEU1377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1331B MET* 5.2 1.6 - - + -
1332B ALA* 3.4 35.7 - - + +
1335B VAL* 6.2 0.7 - - + -
1373B TYR 5.7 0.4 + - - -
1374B HIS* 3.5 21.7 + - + +
1375B ILE 3.3 1.2 - - - -
1376B HIS* 1.3 74.3 - - - +
1378B VAL* 1.3 53.2 + - - +
1380B LEU* 3.9 6.3 - - - -
1381B LEU* 2.0 48.4 + - + +
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Residues in contact with VAL1378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1374B HIS 4.8 0.4 + - - -
1375B ILE 4.0 11.7 + - - +
1376B HIS 3.2 0.2 - - - -
1377B LEU* 1.3 75.7 - - - +
1379B GLU* 1.3 52.3 + - - +
1381B LEU* 4.4 2.7 - - - -
1382B ALA* 2.0 50.4 + - + +
1423B ILE* 5.4 0.7 - - + -
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Residues in contact with GLU1379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1375B ILE 5.0 0.2 + - - -
1376B HIS* 3.7 11.3 + - + +
1377B LEU 3.6 0.2 - - - -
1378B VAL* 1.3 76.0 - - - +
1380B LEU* 1.3 54.2 + - - +
1382B ALA* 3.8 7.0 - - - -
1383B VAL* 2.3 41.6 + - - +
1419B LYS* 5.0 12.3 - - + +
1423B ILE* 4.4 13.6 - - + +
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Residues in contact with LEU1380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332B ALA* 5.6 4.5 - - + -
1336B ASN* 5.1 0.4 - - - -
1376B HIS* 2.8 28.8 + - + +
1377B LEU* 3.6 4.5 - - - +
1379B GLU* 1.3 72.1 - - - +
1381B LEU* 1.3 56.1 + - - +
1383B VAL* 3.3 7.0 + - - +
1384B CYS* 2.9 30.3 + - - +
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Residues in contact with LEU1381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1332B ALA* 4.7 4.2 - - + +
1335B VAL* 5.0 7.9 - - + -
1336B ASN* 3.3 31.4 - - + +
1377B LEU* 2.0 42.8 + - + +
1378B VAL* 3.9 2.2 - - - +
1380B LEU* 1.3 67.6 - - - +
1382B ALA* 1.3 56.0 + - - +
1384B CYS 2.4 21.6 - - - +
1385B THR* 3.7 6.9 + - - +
1386B GLU* 4.5 0.3 - - - -
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Residues in contact with ALA1382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1378B VAL* 2.0 37.7 + - + +
1379B GLU 3.6 2.0 - - - +
1381B LEU* 1.3 67.4 - - - +
1383B VAL* 1.3 61.8 + - - +
1384B CYS 2.9 5.3 + - - -
1386B GLU* 2.9 39.8 + - + +
1423B ILE* 3.7 25.6 - - + -
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Residues in contact with VAL1383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1339B GLU* 4.6 4.2 - - - +
1379B GLU 2.3 33.7 + - - +
1380B LEU* 3.6 7.9 - - - +
1382B ALA* 1.3 66.6 - - - +
1384B CYS* 1.3 56.7 + - + +
1385B THR 4.0 1.1 + - - -
1423B ILE* 5.5 0.8 - - - +
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Residues in contact with CYS1384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1336B ASN* 3.3 18.7 - - + +
1337B SER* 5.7 0.9 - - - +
1339B GLU* 3.6 16.2 - - + +
1340B ASP* 5.7 3.6 - - + -
1380B LEU 2.9 14.7 + - - +
1381B LEU 2.4 23.2 - - - +
1383B VAL* 1.3 80.1 - - + +
1385B THR* 1.3 64.1 + - - +
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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