Contacts of the helix formed by residues 1487 - 1496 (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 ASN1487 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1241C ASN* 5.0 8.3 - - - +
1429C MET* 4.3 18.7 - - + +
1430C ASP* 2.8 33.0 + - + +
1431C ASP* 3.8 19.8 + - - +
1432C PRO* 5.2 0.8 - - - +
1485C TYR* 3.2 16.8 - - - -
1486C ALA* 1.3 74.1 - - - +
1488C HIS* 1.3 82.0 + - - +
1489C LYS 3.2 0.2 - - - -
1490C THR* 2.3 37.9 + - + +
1491C LEU* 3.5 7.8 - - - +
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Residues in contact with HIS1488 (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* 4.2 29.3 + + - -
1386C ALA* 3.9 16.5 - - + -
1387C LEU* 3.1 56.2 + - + +
1429C MET* 5.9 0.4 - - + -
1484C LEU* 3.9 15.6 - - + +
1485C TYR* 3.6 25.0 + + + +
1486C ALA 3.2 1.0 - - - -
1487C ASN* 1.3 105.5 + - - +
1489C LYS* 1.3 61.7 + - - +
1491C LEU* 3.1 23.5 + - + +
1492C LEU* 3.3 14.7 + - - +
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Residues in contact with LYS1489 (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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445C ASP* 5.8 3.4 - - - +
1479C ASP 5.0 0.9 - - - -
1480C ARG* 2.5 32.1 + - - +
1481C ARG* 4.3 3.2 - - - +
1482C ILE* 3.4 26.2 + - + +
1484C LEU* 4.1 16.4 - - + +
1485C TYR 3.4 19.7 - - - +
1486C ALA* 3.7 11.7 - - - +
1487C ASN 3.2 0.4 - - - -
1488C HIS* 1.3 75.5 - - - +
1490C THR* 1.3 60.4 + - + +
1492C LEU* 3.3 8.8 + - - +
1493C GLN* 2.9 30.0 + - - +
1503C TYR* 5.6 8.6 + - + +
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Residues in contact with THR1490 (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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1429C MET* 5.9 1.0 - - - +
1486C ALA 4.7 2.7 - - - +
1487C ASN* 2.3 40.7 + - + +
1489C LYS* 1.3 78.4 - - + +
1491C LEU* 1.3 66.3 + - - +
1493C GLN* 4.1 6.7 - - - +
1494C LYS* 3.4 20.4 + - - +
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Residues in contact with LEU1491 (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* 4.1 30.5 - - + -
1351C MET* 3.9 26.8 - - + +
1387C LEU* 4.4 7.6 - - + -
1424C VAL* 4.9 2.4 - - - +
1425C TYR* 5.5 12.6 - - + -
1429C MET* 4.3 21.8 - - + -
1442C THR* 5.4 4.5 - - + -
1444C ALA* 4.2 15.3 - - + -
1487C ASN 3.5 17.7 - - - +
1488C HIS* 3.1 15.0 + - + +
1490C THR* 1.3 86.9 + - - +
1492C LEU* 1.3 58.6 + - + +
1494C LYS* 3.2 7.9 + - - +
1495C ALA* 2.8 27.8 + - - +
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Residues in contact with LEU1492 (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* 4.6 10.8 - - + -
1374C VAL* 4.4 26.7 - - + -
1387C LEU* 4.2 27.1 - - + -
1478C VAL* 4.6 23.7 - - + +
1484C LEU* 4.7 11.9 - - + -
1488C HIS 3.5 14.6 - - - +
1489C LYS* 3.3 10.8 + - - +
1491C LEU* 1.3 79.1 - - + +
1493C GLN* 1.3 60.8 + - - +
1495C ALA* 3.5 13.4 - - + +
1496C ALA* 2.9 32.1 + - + +
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Residues in contact with GLN1493 (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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1489C LYS 2.9 17.4 + - - +
1490C THR* 4.1 7.6 - - - +
1492C LEU* 1.3 75.6 - - - +
1494C LYS* 1.3 59.9 + - - +
1496C ALA* 4.3 3.8 + - - +
1497C ALA* 4.3 13.0 + - - +
1503C TYR* 4.5 30.0 - - + +
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Residues in contact with LYS1494 (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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1424C VAL* 3.5 21.8 - - + +
1425C TYR* 5.4 8.3 - - + -
1490C THR 3.4 11.1 + - - +
1491C LEU* 3.2 10.6 + - - +
1492C LEU 3.2 0.6 - - - -
1493C GLN* 1.3 76.9 - - - +
1495C ALA* 1.3 62.6 + - - +
1497C ALA* 3.9 14.3 + - - +
1498C GLU* 4.2 3.8 + - - +
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Residues in contact with ALA1495 (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* 3.7 27.1 - - + -
1424C VAL* 4.2 13.2 - - + -
1446C SER* 5.9 0.4 - - - -
1491C LEU 2.8 16.1 + - - +
1492C LEU* 3.0 17.2 + - + +
1494C LYS* 1.3 76.2 - - - +
1496C ALA* 1.3 63.6 + - - +
1497C ALA 3.2 2.2 - - - -
1498C GLU* 3.2 18.6 + - - +
1499C PHE* 3.8 12.9 - - + -
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Residues in contact with ALA1496 (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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1372C LEU* 6.2 1.8 - - - -
1478C VAL* 5.7 7.6 - - + -
1492C LEU* 2.9 14.8 + - - +
1493C GLN* 4.3 4.7 + - - +
1495C ALA* 1.3 74.4 - - - +
1497C ALA* 1.3 56.4 + - - +
1498C GLU 3.2 0.2 - - - -
1499C PHE* 3.2 4.4 + - - +
1500C GLY* 2.7 33.4 + - - -
1501C ALA* 3.2 33.0 + - + +
1502C HIS 4.9 5.8 - - - +
1503C TYR* 6.2 4.0 - - + -
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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