Contacts of the helix formed by residues 1341 - 1349 (chain A) in PDB entry 5D9Y
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 ALA1341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1150A HIS 4.5 3.6 - - - +
1151A LEU* 4.0 24.9 - - + -
1167A ARG* 4.1 2.9 - - - +
1230A ILE* 4.5 7.6 - - + -
1337A TYR* 2.8 31.6 + - + +
1340A LEU* 1.3 81.2 - - - +
1342A PRO* 1.3 66.9 - - - +
1343A ASP 3.3 1.8 - - - -
1344A ALA* 3.2 3.8 + - + -
1345A TYR* 3.0 21.0 + - - +
1873A ILE* 4.5 5.8 - - + -
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Residues in contact with PRO1342 (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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1167A ARG* 3.5 36.1 - - + +
1338A LYS* 3.3 20.1 - - + +
1339A LYS 4.2 4.3 - - - +
1340A LEU 3.5 1.6 - - - -
1341A ALA* 1.3 89.3 - - - +
1343A ASP* 1.3 65.5 + - - +
1345A TYR* 3.3 6.4 + - + +
1346A ASN* 2.8 33.0 + - - +
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Residues in contact with ASP1343 (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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1149A THR 4.4 9.5 - - - +
1150A HIS* 3.7 21.0 + - + +
1152A GLY* 5.6 0.5 - - - -
1167A ARG* 4.5 12.0 + - - -
1341A ALA 3.3 0.8 - - - -
1342A PRO* 1.3 84.0 - - - +
1344A ALA* 1.3 62.6 + - - +
1346A ASN* 3.4 4.2 + - - +
1347A ASN* 3.0 33.4 + - - +
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Residues in contact with ALA1344 (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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1150A HIS* 3.3 35.5 + - + +
1151A LEU* 4.1 9.4 - - + -
1337A TYR* 3.3 26.3 + - + +
1341A ALA 3.2 5.9 + - - +
1343A ASP* 1.3 75.4 - - - +
1345A TYR* 1.3 67.5 + - - +
1347A ASN* 3.3 5.9 + - - +
1348A GLN* 3.1 21.0 + - - +
1390A ASN 4.0 10.4 - - - +
1391A GLY 4.5 0.9 - - - -
1392A SER* 4.2 2.0 - - - +
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Residues in contact with TYR1345 (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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1334A ALA* 3.4 21.9 - - + +
1335A PRO* 5.9 0.4 - - + +
1337A TYR* 3.8 18.0 - + + -
1338A LYS* 3.4 58.9 + - + +
1341A ALA 3.0 17.3 + - - +
1342A PRO 3.5 4.7 - - - +
1344A ALA* 1.3 76.7 - - - +
1346A ASN* 1.3 70.9 + - - +
1348A GLN* 2.8 19.8 + - - +
1349A ILE* 3.2 36.8 + - + +
1365A GLY* 3.2 27.5 + - - -
1367A PRO* 3.8 27.8 - - + -
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Residues in contact with ASN1346 (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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1338A LYS* 5.5 6.7 - - - +
1342A PRO 2.8 21.2 + - - +
1343A ASP* 4.0 5.6 - - - +
1344A ALA 3.3 0.2 - - - -
1345A TYR* 1.3 80.7 - - - +
1347A ASN* 1.3 66.3 + - - +
1348A GLN 3.2 0.5 + - - -
1349A ILE* 3.3 35.2 + - - +
1350A GLU* 3.4 9.5 + - - +
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Residues in contact with ASN1347 (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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1150A HIS* 4.1 7.7 - - - +
1343A ASP* 3.0 24.3 + - - +
1344A ALA* 3.4 8.2 - - - +
1345A TYR 3.2 0.2 - - - -
1346A ASN* 1.3 79.0 - - - +
1348A GLN* 1.3 61.2 + - - +
1349A ILE 3.5 0.3 + - - -
1350A GLU* 3.6 20.3 + - - +
1351A TYR* 5.7 0.9 - - - -
1388A MET* 3.7 17.6 - - + +
1390A ASN* 2.8 42.8 + - + +
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Residues in contact with GLN1348 (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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1337A TYR* 2.6 34.8 + - - -
1344A ALA 3.1 8.0 + - - +
1345A TYR 2.8 9.5 + - - +
1347A ASN* 1.3 78.2 - - - +
1349A ILE* 1.3 60.9 + - - +
1350A GLU 3.4 0.4 + - - -
1351A TYR 4.7 1.9 + - - -
1359A ARG* 4.3 7.6 + - - -
1366A ARG 4.4 0.2 - - - +
1367A PRO* 2.7 43.2 + - + +
1368A PHE* 4.2 6.3 - - - -
1388A MET* 3.6 23.6 - - - -
1391A GLY* 3.6 6.2 - - - -
1392A SER 3.1 25.6 + - - +
1902A TYR* 4.6 0.4 - - - +
1903A GLN* 3.1 38.8 + - - +
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Residues in contact with ILE1349 (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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1338A LYS* 6.1 0.4 - - - +
1345A TYR* 3.4 44.6 - - + +
1346A ASN* 3.4 29.4 - - - +
1348A GLN* 1.3 77.6 - - - +
1350A GLU* 1.3 63.6 + - - +
1351A TYR 3.1 4.6 + - - -
1352A GLU* 3.2 38.4 + - - +
1365A GLY* 5.3 1.6 - - - -
1366A ARG 3.8 4.9 - - - +
1367A PRO* 3.7 25.6 - - + -
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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