Contacts of the helix formed by residues 1484 - 1494 (chain A) in PDB entry 5M64
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 LEU1484 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1483A LEU* 1.3 83.2 - - + +
1485A MET* 1.3 65.0 + - - +
1486A VAL* 5.9 2.2 - - + -
1487A ASN* 4.0 28.7 - - + +
1488A ILE* 3.2 25.9 - - + +
254B ASN 5.2 5.2 - - - +
255B ASP* 4.2 11.2 - - - +
256B GLY* 5.7 1.1 - - - -
304B ASP* 3.3 33.4 - - + +
305B ARG* 4.6 13.0 - - - -
308B LEU* 3.8 27.8 - - + -
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Residues in contact with MET1485 (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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1272A VAL* 3.9 26.7 - - + -
1274A GLU* 3.8 22.4 - - + +
1290A TYR* 3.5 42.2 - - + -
1292A ILE* 6.2 3.8 - - - -
1483A LEU* 3.7 21.7 + - + +
1484A LEU* 1.3 93.1 - - - +
1486A VAL* 1.3 67.6 + - - +
1487A ASN 3.1 1.6 - - - -
1488A ILE* 3.5 9.0 + - + +
1489A VAL* 3.1 34.6 + - + +
304B ASP* 5.7 0.4 + - - -
49I THR* 4.1 14.4 - - + +
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Residues in contact with VAL1486 (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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1270A VAL* 4.8 6.3 - - + +
1272A VAL* 5.0 3.8 - - + -
1484A LEU* 5.9 1.8 - - + -
1485A MET* 1.3 75.5 - - + +
1487A ASN* 1.3 62.0 + - + +
1489A VAL* 4.5 3.7 - - - +
1490A GLU* 3.1 28.0 + - - +
301B PHE* 5.5 13.2 - - + -
304B ASP* 5.6 5.6 - - - +
49I THR* 4.4 22.2 - - - +
50I THR 4.2 7.9 - - - +
51I THR* 3.6 40.9 + - + +
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Residues in contact with ASN1487 (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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1484A LEU* 4.0 23.9 - - + +
1485A MET 3.1 1.2 - - - +
1486A VAL* 1.3 82.4 - - + +
1488A ILE* 1.3 66.4 + - - +
1489A VAL 3.1 1.3 - - - -
1490A GLU* 3.2 14.8 + - - +
1491A GLU* 3.1 39.7 + - - +
254B ASN* 4.8 14.5 + - - +
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Residues in contact with ILE1488 (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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1325A LEU* 4.0 14.0 - - + +
1328A ALA* 3.8 34.5 - - + +
1329A ILE* 4.6 20.9 - - + -
1332A GLU* 4.7 11.7 - - + -
1484A LEU* 3.2 23.3 + - + +
1485A MET* 3.5 14.3 + - + +
1487A ASN* 1.3 78.7 - - - +
1489A VAL* 1.3 70.3 + - + +
1491A GLU* 3.7 22.5 + - - +
1492A ILE* 3.3 23.7 + - - +
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Residues in contact with VAL1489 (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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1270A VAL* 4.3 12.6 - - + -
1272A VAL* 5.8 3.6 - - + -
1292A ILE* 5.3 15.3 - - + -
1294A MET* 4.1 21.1 - - + -
1321A PHE* 4.3 10.5 - - + -
1325A LEU* 4.9 9.6 - - + -
1485A MET* 3.1 24.2 + - + +
1486A VAL* 4.5 3.8 - - - +
1488A ILE* 1.3 85.5 - - + +
1490A GLU* 1.3 60.1 + - - +
1491A GLU 3.3 0.2 - - - -
1492A ILE* 3.4 5.1 + - - +
1493A CYS* 2.8 43.4 + - - -
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Residues in contact with GLU1490 (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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1486A VAL 3.1 22.9 + - - +
1487A ASN* 3.2 21.1 + - - +
1489A VAL* 1.3 77.3 - - - +
1491A GLU* 1.3 78.2 + - - +
1493A CYS* 3.2 9.9 + - - +
1494A ARG* 2.5 70.4 + - - +
51I THR* 6.3 1.8 - - + -
55I ALA* 5.6 0.2 - - + -
56I PHE* 4.9 9.9 - - + -
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Residues in contact with GLU1491 (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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1328A ALA* 4.9 4.3 - - - +
1487A ASN* 3.1 33.6 + - - +
1488A ILE* 3.7 25.8 - - - +
1489A VAL 3.3 0.2 - - - -
1490A GLU* 1.3 89.6 + - - +
1492A ILE* 1.3 67.0 + - + +
1494A ARG* 3.2 5.9 + - - +
1495A LYS* 3.1 32.1 + - + +
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Residues in contact with ILE1492 (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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1321A PHE* 3.3 46.3 - - + +
1324A LEU* 3.2 40.6 - - + +
1325A LEU* 3.8 17.7 - - + -
1328A ALA* 3.6 15.9 - - + -
1488A ILE 3.3 17.2 + - - +
1489A VAL 3.4 5.9 + - - +
1491A GLU* 1.3 80.0 - - + +
1493A CYS* 1.3 62.3 + - - +
1495A LYS* 4.2 7.9 - - + -
1496A SER* 3.1 24.9 + - - -
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Residues in contact with CYS1493 (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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1262A LEU* 4.9 1.2 - - - +
1263A LEU* 4.3 10.3 + - - +
1264A SER* 3.3 49.3 + - - +
1267A ILE* 5.4 5.4 - - - -
1270A VAL* 5.4 5.8 - - - -
1294A MET* 5.0 10.5 - - - -
1321A PHE* 3.9 16.2 - - - -
1489A VAL* 2.8 40.1 + - - +
1490A GLU* 3.2 9.8 + - - +
1492A ILE* 1.3 79.8 - - - +
1494A ARG* 1.3 56.0 + - + +
1495A LYS 3.3 0.7 + - - -
1496A SER 4.2 5.2 + - - +
56I PHE* 5.1 4.0 - - + -
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Residues in contact with ARG1494 (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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1262A LEU* 4.6 27.1 - - + +
1264A SER* 4.8 9.4 - - - -
1265A GLU* 5.4 4.3 - - - +
1490A GLU* 2.5 50.5 + - - +
1491A GLU* 3.2 5.6 + - - +
1493A CYS* 1.3 76.6 - - - +
1495A LYS* 1.3 69.8 + - + +
1496A SER 3.9 0.2 - - - -
55I ALA* 2.7 49.2 + - - +
56I PHE* 3.2 21.7 - - - -
57I PRO* 6.1 0.7 - - - -
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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