Contacts of the helix formed by residues 1403 - 1407 (chain A) in PDB entry 6BM0
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 LEU1403 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PHE* 4.1 12.8 - - + -
1363A GLN* 3.9 23.6 - - + +
1366A LEU* 3.4 24.8 - - + +
1367A THR* 3.4 28.5 - - - +
1370A LEU* 5.5 0.9 - - + -
1372A HIS* 3.6 28.9 - - + +
1378A PRO* 3.9 15.5 - - + -
1400A ASP* 2.9 26.2 + - + +
1402A GLU* 1.3 78.4 - - - +
1404A LEU* 1.3 58.6 + - - +
1405A ASN 3.1 1.6 - - - -
1406A ARG* 3.0 30.0 + - + +
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Residues in contact with LEU1404 (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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4A VAL* 4.6 5.6 - - + -
1359A LEU* 4.0 22.7 - - + +
1362A LEU* 3.8 25.6 - - + -
1363A GLN* 4.3 11.2 - - + -
1366A LEU* 4.0 11.2 - - + -
1399A LEU* 4.0 33.4 - - + -
1400A ASP 2.9 19.5 + - - +
1401A GLY* 4.0 11.0 - - - +
1403A LEU* 1.3 75.4 - - - +
1405A ASN* 1.3 56.7 + - - +
1406A ARG 3.2 0.2 - - - -
1407A TYR* 3.2 22.9 + - - +
1408A LEU* 4.1 1.2 + - - +
1433A LEU* 3.6 32.6 - - + +
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Residues in contact with ASN1405 (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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6A LYS* 5.8 3.4 - - - +
896A PRO* 5.3 10.8 - - - +
897A HIS 3.8 19.5 + - - +
898A ASN* 6.2 1.4 - - - +
1401A GLY 3.3 20.3 + - - +
1402A GLU* 4.2 21.3 + - - +
1403A LEU 3.1 0.8 - - - -
1404A LEU* 1.3 75.3 - - - +
1406A ARG* 1.3 59.7 + - + +
1407A TYR 3.2 2.9 - - - -
1408A LEU* 3.3 35.1 + - - +
1409A TYR* 3.6 9.5 + - - +
1437A ASP* 6.0 0.7 - - - -
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Residues in contact with ARG1406 (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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75A PHE* 5.0 8.7 - - - -
816A ARG* 4.2 21.3 + - - +
1366A LEU* 4.5 3.7 - - - +
1370A LEU* 4.1 31.4 - - + +
1371A PRO* 4.3 9.1 + - - +
1372A HIS* 3.0 41.2 + - - +
1373A HIS* 5.1 1.4 - - - +
1402A GLU 4.3 10.5 - - - +
1403A LEU* 3.0 25.4 + - + +
1405A ASN* 1.3 76.8 - - + +
1407A TYR* 1.3 61.5 + - - +
1408A LEU 3.3 1.1 - - - -
1409A TYR* 3.8 21.8 - - + +
1410A LEU* 3.4 24.4 + - - +
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Residues in contact with TYR1407 (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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1362A LEU* 3.6 30.3 - - + -
1366A LEU* 4.1 19.5 - - + +
1403A LEU 3.9 1.6 + - - -
1404A LEU 3.2 16.2 + - - +
1406A ARG* 1.3 77.5 - - - +
1408A LEU* 1.3 55.9 + - - +
1409A TYR 3.2 0.4 + - - -
1410A LEU* 3.7 16.9 + - + +
1415A ARG* 2.5 79.9 + - + +
1418A LEU* 4.5 10.5 - - + -
1419A ALA* 4.1 1.8 - - - +
1426A PRO* 3.9 10.9 - - - +
1429A ILE* 3.3 36.6 - - + +
1430A LEU* 4.4 8.5 - - + -
1433A LEU* 3.6 20.4 - - + -
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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