Contacts of the helix formed by residues 1430 - 1440 (chain C) in PDB entry 4QY4
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 ASP1430 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1409C PHE 3.2 12.3 - - - +
1410C ILE 3.2 17.9 - - - +
1411C GLN* 3.6 5.1 - - - +
1412C LEU* 2.9 38.9 + - + +
1429C VAL* 1.3 77.3 - - - +
1431C PHE* 1.3 59.6 + - - +
1432C LYS* 3.8 3.0 - - - +
1433C LYS* 2.8 36.3 + - - +
1434C ILE* 3.1 26.7 + - - +
1456C LEU* 3.7 8.3 - - - -
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Residues in contact with PHE1431 (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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1391C ILE* 4.2 23.6 - - + -
1394C VAL* 3.7 27.8 - - + -
1395C ILE* 4.2 12.8 - - + -
1406C SER* 4.2 14.1 - - - -
1409C PHE* 2.9 49.0 + + + +
1410C ILE* 4.0 24.2 - - + -
1430C ASP* 1.3 68.7 - - - +
1432C LYS* 1.3 60.6 + - - +
1434C ILE* 3.7 19.2 - - + +
1435C LYS* 2.9 36.2 + - - +
1453C VAL* 4.6 13.0 - - + -
1456C LEU* 4.0 22.7 - - + -
1457C CYS* 5.9 0.2 - - - -
1477C LEU* 4.5 8.3 - - + -
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Residues in contact with LYS1432 (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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1410C ILE* 2.9 26.1 + - + +
1411C GLN* 3.5 33.2 - - + +
1430C ASP* 3.8 4.9 - - - +
1431C PHE* 1.3 77.3 - - - +
1433C LYS* 1.3 61.3 + - - +
1435C LYS* 3.4 8.7 + - + +
1436C GLU* 3.1 21.9 + - - +
1439C ARG* 5.2 1.0 + - - -
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Residues in contact with LYS1433 (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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1428C PRO 5.5 0.7 - - - +
1429C VAL* 4.3 6.1 - - + -
1430C ASP* 2.8 28.9 + - - +
1432C LYS* 1.3 77.2 - - - +
1434C ILE* 1.3 58.1 + - - +
1436C GLU* 2.7 42.1 + - - +
1437C ARG* 2.9 70.2 + - + +
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Residues in contact with ILE1434 (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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1391C ILE* 3.9 22.2 - - + -
1429C VAL* 3.9 14.8 - - + -
1430C ASP 3.1 10.8 + - - +
1431C PHE* 3.7 17.7 - - + +
1432C LYS 3.3 0.2 - - - -
1433C LYS* 1.3 74.2 - - - +
1435C LYS* 1.3 64.7 + - - +
1437C ARG* 3.0 13.7 + - - +
1438C ILE* 3.0 13.9 + - + +
1443C TYR* 3.4 22.4 - - - +
1449C LEU* 3.9 22.0 - - + -
1452C ASP* 4.2 9.6 - - + +
1453C VAL* 4.1 17.9 - - + -
1456C LEU* 3.8 28.9 - - + -
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Residues in contact with LYS1435 (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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1388C ASN* 4.3 16.8 - - - +
1391C ILE* 4.0 11.4 - - + -
1392C ASP* 3.4 20.9 + - - -
1395C ILE* 3.3 32.9 - - + +
1431C PHE 2.9 21.6 + - - +
1432C LYS* 3.5 11.0 - - + +
1434C ILE* 1.3 75.7 - - - +
1436C GLU* 1.3 56.2 + - - +
1438C ILE* 3.3 9.7 + - + +
1439C ARG* 3.0 42.3 + - - +
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Residues in contact with GLU1436 (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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1432C LYS 3.1 9.8 + - - +
1433C LYS* 2.7 46.6 + - + +
1435C LYS* 1.3 79.3 - - - +
1437C ARG* 1.3 58.0 + - + +
1439C ARG* 3.4 29.3 - - - +
1440C ASN* 2.9 44.6 + - + +
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Residues in contact with ARG1437 (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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1428C PRO 5.0 6.5 + - - -
1429C VAL* 3.8 12.3 - - - +
1433C LYS* 2.9 54.2 + - + +
1434C ILE 3.0 1.8 + - - +
1436C GLU* 1.3 73.7 - - + +
1438C ILE* 1.3 63.9 + - - +
1441C HIS 3.3 1.2 + - - -
1442C LYS* 2.8 53.8 + - + +
1443C TYR* 3.5 29.3 + - + +
1452C ASP* 2.9 35.1 + - - -
1455C LEU* 5.9 0.8 - - - +
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Residues in contact with ILE1438 (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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1384C THR* 4.1 11.4 + - + +
1387C MET* 4.0 37.7 - - + +
1388C ASN* 3.3 38.8 - - - +
1391C ILE* 3.7 32.3 - - + -
1434C ILE* 3.0 23.2 + - + +
1435C LYS* 3.5 10.1 - - + +
1437C ARG* 1.3 74.1 - - - +
1439C ARG* 1.3 61.3 + - - +
1441C HIS* 2.9 27.5 + - - -
1443C TYR* 3.9 17.9 - - + -
1449C LEU* 4.4 1.6 - - + -
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Residues in contact with ARG1439 (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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1384C THR* 5.6 2.7 - - - -
1388C ASN* 5.8 1.1 - - - +
1432C LYS 5.2 1.0 + - - -
1435C LYS* 3.0 25.5 + - - +
1436C GLU* 3.4 48.5 + - - +
1438C ILE* 1.3 78.9 - - + +
1440C ASN* 1.3 69.2 + - - +
1441C HIS* 3.4 22.5 + - - -
1501C ZN 3.7 6.8 - - - -
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Residues in contact with ASN1440 (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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1436C GLU* 2.9 37.6 + - - +
1437C ARG 3.8 0.2 - - - -
1439C ARG* 1.3 93.1 + - - +
1441C HIS* 1.3 73.6 + - - +
1442C LYS* 3.2 30.6 + - + +
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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