Contacts of the strand formed by residues 1440 - 1449 (chain C) in PDB entry 6PUO
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 ILE1440 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1339C LEU* 4.9 9.6 - - + -
1345C ASN* 3.7 29.2 - - + +
1347C THR* 4.0 15.0 - - + -
1428C TYR* 3.6 2.9 - - - -
1429C MET* 2.9 58.1 + - + +
1431C ASP* 4.5 12.6 - - + +
1433C ARG* 5.1 17.5 - - + +
1434C ASN* 4.0 17.6 - - - +
1439C TRP* 1.3 85.9 - - - +
1441C GLU* 1.3 68.5 + - - +
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Residues in contact with GLU1441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1312C SER* 2.6 25.8 + - - -
1313C PHE* 2.6 36.1 + - + -
1314C HIS* 3.9 8.5 + - - +
1327C PRO* 5.1 1.2 - - - +
1344C PRO* 3.7 15.3 - - + -
1345C ASN 3.1 10.5 + - - +
1346C HIS* 3.2 24.8 - - + +
1347C THR* 3.0 25.8 + - - +
1427C GLY 3.3 16.6 - - - +
1428C TYR* 3.8 9.8 + - - +
1429C MET 4.5 0.4 - - - +
1439C TRP* 3.4 13.3 + - + -
1440C ILE* 1.3 78.6 - - - +
1442C THR* 1.3 62.0 + - - +
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Residues in contact with THR1442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313C PHE* 5.3 3.4 - - - -
1346C HIS* 5.5 0.2 - - - +
1347C THR* 3.3 22.4 + - - +
1349C TYR* 3.4 21.7 + - + -
1425C TYR* 4.8 14.4 - - + -
1426C LYS* 3.4 6.9 - - - +
1427C GLY 3.2 31.3 + - - +
1429C MET* 3.8 28.5 - - + -
1441C GLU* 1.3 77.1 - - - +
1443C VAL* 1.3 82.4 + - - +
1444C ALA* 5.2 0.7 - - + +
1491C LEU* 5.4 5.4 - - + -
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Residues in contact with VAL1443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313C PHE* 4.2 24.0 - - + -
1346C HIS* 6.3 1.1 - - + -
1347C THR 3.2 10.0 + - - +
1348C LEU* 3.6 20.9 - - + +
1349C TYR* 2.8 28.8 + - - +
1423C GLU* 3.8 13.9 - - - +
1425C TYR 3.9 2.0 - - - -
1426C LYS* 3.7 28.5 - - + -
1442C THR* 1.3 85.1 + - - +
1444C ALA* 1.3 62.6 + - - +
1445C VAL* 3.8 0.7 - - + -
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Residues in contact with ALA1444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1349C TYR* 3.4 7.0 - - - +
1351C MET* 4.5 6.7 - - + -
1423C GLU* 3.4 4.9 - - - +
1424C VAL* 2.7 41.1 + - + +
1425C TYR* 2.9 33.4 + - + +
1442C THR* 5.7 1.3 - - + +
1443C VAL* 1.3 73.3 - - - +
1445C VAL* 1.3 59.5 + - - +
1491C LEU* 4.2 24.9 - - + -
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Residues in contact with VAL1445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1348C LEU* 4.5 14.4 - - + -
1349C TYR 3.4 4.2 + - - +
1350C PRO* 3.6 26.8 - - + +
1351C MET* 3.1 29.0 + - - +
1419C LYS* 3.8 25.6 - - + +
1421C GLY* 4.1 2.5 - - - +
1422C MET 3.4 14.6 - - - +
1423C GLU* 3.3 32.1 - - - +
1443C VAL* 3.8 2.6 - - + -
1444C ALA* 1.3 74.1 - - - +
1446C SER* 1.3 61.9 + - - +
1447C VAL* 5.0 4.5 - - + +
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Residues in contact with SER1446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1351C MET* 3.6 18.2 - - - -
1353C THR* 5.1 6.5 - - - -
1422C MET* 2.5 40.9 + - - +
1423C GLU 4.8 0.3 + - - -
1424C VAL* 3.7 23.9 - - - +
1445C VAL* 1.3 75.7 - - - +
1447C VAL* 1.3 62.8 + - - +
1448C HIS* 3.7 4.5 + - - +
1495C ALA* 5.9 0.9 - - - -
1499C PHE* 4.8 14.7 - - - -
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Residues in contact with VAL1447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1350C PRO* 6.1 3.6 - - + -
1351C MET 3.2 7.4 + - - +
1352C VAL* 3.6 27.7 - - + -
1353C THR* 3.2 23.4 + - - +
1418C LEU* 3.9 27.1 - - + +
1419C LYS* 5.7 4.0 - - - +
1421C GLY* 5.0 12.3 - - - -
1445C VAL* 4.1 6.1 - - + +
1446C SER* 1.3 73.8 - - - +
1448C HIS* 1.3 66.9 + - - +
1449C PHE* 4.7 16.2 - - + -
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Residues in contact with HIS1448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1353C THR* 2.4 31.9 + - - +
1355C TRP* 3.1 31.6 + + - -
1372C LEU* 4.0 18.4 - - + -
1446C SER 3.7 3.3 + - - +
1447C VAL* 1.3 78.8 - - - +
1449C PHE* 1.3 93.5 + - - +
1450C GLN* 3.1 23.4 + - - -
1499C PHE* 3.3 41.5 - + + -
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Residues in contact with PHE1449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1352C VAL* 6.0 7.0 - - + -
1353C THR 2.9 14.3 + - - +
1354C ARG* 3.9 12.4 - - + -
1355C TRP* 3.7 0.9 - - - -
1418C LEU* 6.6 0.2 - - + -
1447C VAL* 4.7 18.2 - - + -
1448C HIS* 1.3 95.4 + - - +
1450C GLN* 1.3 57.8 + - - +
1451C ASP 4.3 7.4 - - - +
1452C GLN* 2.7 32.5 + - - +
1456C GLU* 3.1 38.1 - - + -
1457C LEU* 3.6 29.6 - - + -
1460C LEU* 4.4 13.5 - - + -
1475C TRP* 5.0 16.2 - + - -
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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