Contacts of the helix formed by residues 1443 - 1450 (chain B) in PDB entry 6V65
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 PHE1443 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1321B VAL* 3.8 35.7 - - + -
1336B GLN* 4.2 30.7 - - + -
1339B LEU* 4.2 9.6 - - + -
1340B LEU* 3.5 35.0 - - + -
1424B ILE* 4.2 13.9 - - + -
1434B PHE* 4.5 6.7 - - + -
1439B HIS 3.6 20.0 - - - -
1440B MET* 3.4 39.9 - - + +
1441B ARG 2.8 1.4 + - - -
1442B PRO* 1.3 82.0 - - + +
1444B ASN* 1.3 64.5 + - - +
1445B ASP 3.2 2.7 - - - -
1446B PHE* 3.0 17.9 + - + +
1447B VAL* 3.0 18.2 + - + +
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Residues in contact with ASN1444 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1433B LEU* 3.7 17.8 - - + +
1434B PHE* 2.8 49.7 + - - +
1440B MET 4.1 0.2 + - - -
1441B ARG* 2.8 26.0 + - - +
1442B PRO 3.4 0.2 - - - -
1443B PHE* 1.3 77.0 - - - +
1445B ASP* 1.3 61.1 + - - +
1447B VAL* 3.3 6.6 - - - +
1448B LYS* 2.8 33.2 + - - +
1601B FMT 3.1 35.3 + - - -
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Residues in contact with ASP1445 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1442B PRO 4.5 6.6 + - - +
1443B PHE* 3.2 1.0 - - - +
1444B ASN* 1.3 78.8 - - - +
1446B PHE* 1.3 62.6 + - - +
1448B LYS* 4.0 10.7 - - - +
1449B SER* 3.4 22.3 + - - -
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Residues in contact with PHE1446 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1340B LEU* 3.8 50.3 - - + -
1343B THR* 3.9 22.4 - - + -
1344B GLU* 4.1 42.2 - - + -
1347B PHE* 5.6 1.3 - - + -
1424B ILE* 4.2 12.6 - - + -
1428B ILE* 4.2 7.4 - - + -
1442B PRO 5.3 0.2 + - - -
1443B PHE* 3.0 11.6 + - - +
1445B ASP* 1.3 80.5 - - - +
1447B VAL* 1.3 62.4 + - + +
1449B SER* 2.9 21.9 + - - -
1450B ASN* 3.5 33.5 + - - -
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Residues in contact with VAL1447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1424B ILE* 3.6 32.5 - - + +
1427B SER* 4.6 2.5 - - - -
1428B ILE* 3.7 24.5 - - + +
1432B VAL 4.7 3.4 - - - +
1433B LEU* 3.9 20.0 - - + -
1434B PHE* 4.1 13.5 - - + -
1443B PHE 3.0 12.9 + - - +
1444B ASN* 3.3 22.0 - - - +
1446B PHE* 1.3 76.3 - - + +
1448B LYS* 1.3 68.4 + - - +
1450B ASN 3.5 1.4 + - - -
1451B PHE* 3.1 35.0 + - + -
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Residues in contact with LYS1448 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1433B LEU* 4.1 23.5 - - + +
1444B ASN 2.8 18.8 + - - +
1445B ASP* 4.0 11.4 - - - +
1447B VAL* 1.3 78.0 - - - +
1449B SER* 1.3 61.9 + - - +
1450B ASN 3.7 0.2 + - - -
1451B PHE* 3.6 36.0 + - + +
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Residues in contact with SER1449 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1445B ASP 3.4 11.1 + - - -
1446B PHE* 2.9 23.6 + - - -
1448B LYS* 1.3 81.7 - - - +
1450B ASN* 1.3 67.6 + - - +
1451B PHE 3.3 1.4 + - - -
1452B ASP* 4.7 4.0 + - - +
1453B ALA* 5.1 2.8 + - - +
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Residues in contact with ASN1450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1347B PHE* 3.6 31.8 - - + -
1428B ILE* 3.2 27.8 - - + +
1446B PHE* 3.5 45.6 + - - +
1447B VAL 3.5 2.2 + - - -
1448B LYS 3.4 0.2 - - - -
1449B SER* 1.3 84.8 + - - +
1451B PHE* 1.3 66.7 + - - +
1452B ASP 3.5 1.3 - - - -
1453B ALA* 4.0 9.5 - - - +
1454B ALA 3.5 11.1 + - - -
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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