Contacts of the helix formed by residues 135 - 142 (chain 6) in PDB entry 5U8T
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 VAL 135 (chain 6).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1236 SER 3.1 10.2 + - - +
1246 VAL* 3.3 7.0 - - + +
1316 GLU* 5.3 15.5 - - - +
1326 VAL 4.9 10.1 - - - +
1336 GLU 3.6 3.6 - - - +
1346 LYS 1.3 74.6 + - - +
1366 TYR* 1.3 80.9 + - + +
1386 ALA* 3.1 15.3 + - + +
1396 GLN* 2.9 28.8 + - + +
1576 HIS* 6.5 0.7 - - + -
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Residues in contact with TYR 136 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1186 PHE* 4.0 20.9 - + - -
1196 LEU* 3.6 28.9 - - + +
1236 SER* 3.3 34.9 - - - -
1346 LYS* 3.0 3.7 - - + +
1356 VAL* 1.3 95.6 - - + +
1376 ARG* 1.3 60.6 + - - +
1396 GLN* 3.8 9.4 - - + -
1406 ILE* 2.7 48.8 + - + +
1526 TYR 4.3 8.1 - - - -
1536 ILE* 3.2 43.5 - - + +
1546 ASP 3.5 11.9 + - - -
1576 HIS* 4.4 11.6 + - - +
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Residues in contact with ARG 137 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196 LEU 5.8 0.4 - - - +
1206 GLU* 4.1 19.5 + - - +
1336 GLU 5.1 1.1 - - - -
1346 LYS* 3.2 44.5 - - + +
1366 TYR* 1.3 76.0 - - + +
1386 ALA* 1.3 63.2 + - - +
1406 ILE* 4.4 3.5 - - - +
1416 GLU* 2.9 34.9 + - + +
1926 TYR* 2.2 62.9 + - + -
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Residues in contact with ALA 138 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1336 GLU 3.8 16.3 + - - +
1346 LYS 4.0 1.8 - - - +
1356 VAL* 3.1 20.9 + - + +
1376 ARG* 1.3 79.2 - - - +
1396 GLN* 1.3 57.5 + - - +
1416 GLU* 4.4 1.9 - - - +
1426 PHE* 2.9 31.9 + - - +
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Residues in contact with GLN 139 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1356 VAL* 2.9 18.2 + - + +
1366 TYR* 3.0 16.8 + - + +
1386 ALA* 1.3 78.1 - - - +
1406 ILE* 1.3 60.0 + - + +
1426 PHE* 3.4 25.7 - - - -
1436 MET* 2.8 32.1 + - + +
1516 ILE* 6.0 3.1 - - + -
1526 TYR* 4.7 29.2 - - + +
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Residues in contact with ILE 140 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196 LEU 5.9 0.2 - - - +
1366 TYR* 2.7 47.2 + - + +
1376 ARG* 4.4 3.1 - - - +
1396 GLN* 1.3 75.9 - - + +
1416 GLU* 1.3 63.0 + - + +
1426 PHE 3.2 1.3 - - - -
1436 MET* 2.9 11.0 + - + +
1446 LYS* 2.6 30.8 + - - +
1516 ILE* 4.3 26.5 - - + -
1536 ILE* 6.2 2.5 - - + -
1856 LEU* 5.2 8.1 - - + -
1896 VAL* 3.7 43.5 - - + -
1926 TYR* 5.4 4.7 - - + -
1936 ALA* 5.4 0.7 - - + -
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Residues in contact with GLU 141 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1376 ARG* 2.9 24.2 + - + +
1386 ALA* 4.4 2.0 - - - +
1406 ILE* 1.3 79.2 - - + +
1426 PHE* 1.3 58.0 + - - +
1436 MET 3.1 0.4 - - - -
1446 LYS* 3.3 27.3 + - - +
1456 ILE* 3.2 26.2 + - - +
1926 TYR* 3.1 42.2 - - + +
1936 ALA* 4.0 5.7 + - - +
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Residues in contact with PHE 142 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1386 ALA 2.9 23.0 + - - +
1396 GLN* 3.4 30.1 - - - +
1416 GLU* 1.3 75.7 - - - +
1436 MET* 1.3 56.3 + - - +
1446 LYS 3.2 2.7 - - - -
1456 ILE* 3.2 34.3 + - + +
1466 TYR* 3.3 52.6 - + - -
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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