Contacts of the helix formed by residues 1364 - 1373 (chain A) in PDB entry 5LUQ
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 CYS1364 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1293A ALA* 3.9 17.9 - - - -
1296A PHE* 3.4 40.3 - - + -
1299A GLU* 4.5 1.6 - - - +
1362A ASP* 3.5 9.4 - - - -
1363A LEU* 1.3 74.5 - - - +
1365A ASN* 1.3 51.7 + - - +
1366A THR* 2.7 17.7 + - - +
1367A HIS* 3.0 45.6 + - + +
1368A LEU* 3.8 11.9 + - - +
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Residues in contact with ASN1365 (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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1359A LEU* 3.1 34.5 - - - +
1362A ASP* 2.6 23.6 + - - +
1363A LEU* 2.8 11.1 - - + +
1364A CYS* 1.3 69.1 - - - +
1366A THR* 1.3 57.7 + - - +
1368A LEU* 3.4 23.6 - - - +
1369A MSE 2.9 40.9 - - - +
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Residues in contact with THR1366 (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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1363A LEU 4.1 8.6 + - - -
1364A CYS* 2.7 4.1 + - - -
1365A ASN* 1.3 79.3 + - - +
1367A HIS* 1.3 76.3 + - + +
1369A MSE 3.0 9.0 + - - +
1370A ARG* 3.0 44.7 + - + +
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Residues in contact with HIS1367 (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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1293A ALA 5.6 0.2 - - - -
1296A PHE* 4.0 13.5 + - - +
1297A PHE* 4.1 29.4 - + + -
1299A GLU* 4.1 10.5 - - + +
1300A SER* 3.9 28.2 - - - +
1303A MSE 5.5 0.7 - - - +
1364A CYS* 3.0 34.0 + - + +
1366A THR* 1.3 86.4 - - + +
1368A LEU* 1.3 65.9 + - - +
1370A ARG* 3.0 15.1 + - - +
1371A VAL* 3.0 15.9 + - - +
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Residues in contact with LEU1368 (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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1296A PHE* 4.2 10.1 - - + -
1299A GLU* 3.8 17.5 + - - +
1345A THR* 3.6 33.0 - - + +
1349A LEU* 5.2 4.9 - - + -
1359A LEU* 5.9 0.4 - - + -
1362A ASP* 3.7 19.5 - - - +
1364A CYS 3.8 6.0 + - - +
1365A ASN* 3.4 37.0 - - - +
1367A HIS* 1.3 76.9 - - - +
1369A MSE 1.3 88.3 + - + +
1371A VAL* 3.0 12.1 - - - +
1372A LEU* 2.8 38.2 + - + +
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Residues in contact with MSE1369 (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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1365A ASN* 2.9 41.3 - - - +
1366A THR* 3.0 7.8 + - - +
1368A LEU* 1.3 87.5 - - + +
1370A ARG* 1.3 68.1 + - + +
1371A VAL 2.6 14.7 + - - -
1372A LEU* 3.0 20.1 + - - -
1373A VAL* 3.1 20.6 + - + +
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Residues in contact with ARG1370 (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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1303A MSE 3.6 16.3 - - + +
1366A THR* 3.5 31.8 - - + +
1367A HIS* 3.0 9.5 + - - +
1369A MSE 1.3 90.5 - - - +
1371A VAL* 1.3 56.2 + - - +
1373A VAL* 4.2 10.6 - - - +
1374A GLN* 3.4 23.2 + - - +
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Residues in contact with VAL1371 (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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1299A GLU* 4.5 20.2 - - + +
1300A SER* 5.8 0.9 - - - -
1303A MSE 3.5 41.4 - - + +
1338A VAL* 4.8 14.8 - - + -
1342A MSE 5.2 3.5 - - + +
1367A HIS 3.0 11.8 + - - +
1368A LEU* 3.0 28.9 - - - +
1369A MSE 2.6 6.7 + - - -
1370A ARG* 1.3 75.0 - - - +
1372A LEU* 1.3 67.1 + - + +
1373A VAL 3.3 1.5 + - - -
1374A GLN* 3.5 16.0 + - - +
1378A GLU* 4.5 15.5 - - - +
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Residues in contact with LEU1372 (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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1342A MSE 3.3 52.2 - - + +
1345A THR* 5.7 3.6 - - + -
1368A LEU* 2.8 46.9 + - + +
1369A MSE 3.9 13.7 - - - +
1371A VAL* 1.3 75.6 - - + +
1373A VAL* 1.3 72.1 + - + +
1374A GLN 3.2 0.7 + - - -
1375A THR* 3.3 19.8 + - - -
1378A GLU* 5.5 0.7 - - - +
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Residues in contact with VAL1373 (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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1369A MSE 3.1 22.6 + - + +
1370A ARG* 4.2 12.1 - - - +
1372A LEU* 1.3 83.9 - - + +
1374A GLN* 1.3 62.4 + - + +
1375A THR* 2.4 31.0 + - - +
1376A LEU* 3.9 7.9 - - + +
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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