Contacts of the helix formed by residues 1399 - 1404 (chain A) in PDB entry 6A5T
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 ALA1399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.7 28.7 - - + -
1398A GLY* 1.3 72.1 - - - -
1400A LEU* 1.3 61.1 + - - +
1402A ARG* 3.3 16.0 + - - +
1403A CYS* 2.9 26.1 + - - +
1411A ILE* 4.2 6.7 - - + +
1412A LEU* 5.5 2.7 - - + -
1415A ALA* 4.2 7.2 - - + -
1420A GLU* 3.2 24.2 + - + +
1422A ASP* 2.9 10.5 + - + +
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Residues in contact with LEU1400 (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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17A VAL* 4.2 22.4 - - + -
19A PHE* 4.0 24.5 - - + -
1399A ALA* 1.3 63.4 - - - +
1401A MET* 1.3 56.0 + - - +
1402A ARG 2.9 4.7 - - - -
1403A CYS* 2.2 54.3 + - + -
1404A SER* 3.4 3.3 + - - -
1412A LEU* 5.1 4.5 - - + -
1422A ASP* 2.3 31.5 + - - +
1424A CYS* 5.9 0.2 - - - -
1428A SER* 5.1 0.7 - - - -
1429A GLU* 3.1 25.8 - - + +
1432A MET* 3.9 31.9 - - + -
1433A LEU* 4.9 8.1 - - + -
1204B PHE* 6.4 3.8 - - + -
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Residues in contact with MET1401 (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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844A LYS* 4.2 10.7 + - - +
845A ALA 5.1 3.6 - - - +
847A GLU* 3.8 25.1 - - + +
848A ASP* 3.2 41.7 - - + +
860A SER* 4.7 6.7 - - - -
1392A ILE* 5.1 4.7 - - + +
1397A THR* 4.9 13.2 - - + -
1398A GLY 5.3 5.6 - - - +
1399A ALA 3.6 0.4 - - - -
1400A LEU* 1.3 68.2 - - - +
1402A ARG* 1.3 63.8 + - + +
1404A SER* 3.5 13.3 + - - -
1405A PHE* 4.9 1.4 + - - +
1426A GLY* 4.2 14.8 - - - -
1427A VAL 5.0 0.4 - - - -
1428A SER* 3.4 26.2 + - - +
1429A GLU* 2.4 37.3 + - - +
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Residues in contact with ARG1402 (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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132A LYS* 4.4 14.3 - - - +
1392A ILE* 3.7 24.7 - - + +
1393A ASN* 2.9 41.0 + - - +
1395A ALA 3.5 7.8 + - - -
1397A THR* 3.0 33.0 + - - +
1398A GLY 2.5 22.9 + - - +
1399A ALA* 3.3 11.3 + - - +
1400A LEU 2.7 4.0 + - - -
1401A MET* 1.3 74.0 - - + +
1403A CYS* 1.3 57.0 + - - +
1404A SER 2.9 11.6 + - - -
1405A PHE* 3.3 16.3 + - - +
1406A GLU 4.7 3.1 + - - +
1411A ILE* 3.8 30.7 - - + +
1420A GLU* 3.6 27.9 + - - -
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Residues in contact with CYS1403 (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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337A LEU* 3.6 22.9 - - - +
1399A ALA 2.9 12.1 + - - +
1400A LEU* 2.2 58.5 + - - +
1402A ARG* 1.3 67.6 - - - +
1404A SER* 1.3 55.4 + - - -
1405A PHE 3.4 0.7 - - - -
1406A GLU 5.3 0.4 - - - -
1408A THR* 2.6 45.5 + - + +
1411A ILE* 4.4 12.6 - - + -
1412A LEU* 4.3 19.5 - - + -
1432A MET* 4.6 5.8 - - - -
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Residues in contact with SER1404 (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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337A LEU* 4.9 8.3 - - - -
338A ARG* 4.3 15.3 - - - +
342A MET* 3.6 37.2 - - - +
840A ARG* 4.7 2.3 + - - -
844A LYS* 2.6 34.7 + - - -
1400A LEU 3.4 4.8 + - - -
1401A MET 3.5 8.2 + - - -
1402A ARG 2.9 1.0 + - - -
1403A CYS* 1.3 82.3 - - - +
1405A PHE* 1.3 62.3 + - - +
1408A THR* 4.5 3.4 - - - -
1428A SER* 4.3 3.6 + - - -
1132B GLU* 5.3 1.6 - - - +
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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