Contacts of the helix formed by residues 1437 - 1447 (chain G) in PDB entry 2VKZ
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 THR1437 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1435G ILE* 4.1 1.7 - - - +
1436G LYS* 1.3 89.8 - - + +
1438G SER* 1.3 61.8 + - - +
1439G LYS* 3.1 13.4 + - + +
1440G ASP* 3.0 42.2 + - - +
1441G ILE* 3.1 17.5 - - - +
1460G LEU* 3.6 10.4 - - - +
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Residues in contact with SER1438 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949A GLU* 3.9 18.5 + - - -
1437G THR* 1.3 74.3 + - - +
1439G LYS* 1.3 62.2 + - - +
1440G ASP 3.2 1.6 - - - -
1441G ILE* 3.0 22.2 - - - +
1442G ALA* 3.2 11.4 + - - +
1460G LEU* 4.4 8.0 - - - +
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Residues in contact with LYS1439 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949A GLU* 3.8 16.2 + - - +
952A GLU* 4.7 29.7 + - + +
953A VAL* 4.6 16.1 - - + +
956A ALA* 4.7 15.5 - - + +
1437G THR* 3.1 11.7 + - - +
1438G SER* 1.3 77.1 - - - +
1440G ASP* 1.3 80.4 + - - +
1442G ALA* 3.1 8.5 + - - +
1443G VAL* 2.9 28.9 + - + +
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Residues in contact with ASP1440 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1433G MET* 5.6 5.6 - - + +
1434G HIS 4.2 3.8 - - - +
1435G ILE* 4.4 8.9 - - + -
1436G LYS* 3.3 16.5 + - - +
1437G THR* 3.0 44.7 + - - +
1439G LYS* 1.3 92.5 - - - +
1441G ILE* 1.3 63.8 + - - +
1443G VAL* 3.2 8.1 + - - +
1444G LEU* 3.2 24.9 + - - +
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Residues in contact with ILE1441 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1435G ILE* 4.4 9.5 - - + +
1437G THR 3.1 16.8 - - - +
1438G SER* 3.0 23.3 - - - +
1440G ASP* 1.3 74.2 - - - +
1442G ALA* 1.3 60.9 - - - +
1444G LEU* 3.5 7.6 + - - +
1445G ARG* 3.0 69.9 + - + +
1459G LEU* 3.5 37.9 - - + +
1460G LEU* 4.9 9.9 - - + +
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Residues in contact with ALA1442 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953A VAL* 4.6 22.0 - - + -
957A VAL* 4.9 2.8 - - + +
1438G SER 3.2 14.6 + - - +
1439G LYS* 3.1 14.1 + - - +
1441G ILE* 1.3 79.5 - - - +
1443G VAL* 1.3 63.6 + - - +
1445G ARG* 3.2 10.5 + - - +
1446G SER* 3.1 20.3 + - - -
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Residues in contact with VAL1443 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953A VAL* 6.3 0.9 - - - -
956A ALA* 4.5 14.6 - - + +
957A VAL* 4.1 28.9 - - + +
960A GLU* 5.0 11.0 - - + -
1433G MET* 5.6 1.8 - - + -
1439G LYS* 2.9 19.0 + - + +
1440G ASP* 3.6 10.3 - - - +
1442G ALA* 1.3 71.3 - - + +
1444G LEU* 1.3 61.3 + - + +
1446G SER* 2.9 32.2 + - - +
1447G LYS* 3.6 6.3 + - + +
1519G PHE* 3.8 31.2 - - + -
1523G ASN* 5.9 1.3 - - - +
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Residues in contact with LEU1444 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1433G MET* 3.9 21.5 - - + -
1435G ILE* 3.7 36.8 - - + -
1440G ASP 3.2 10.3 + - - +
1441G ILE* 3.8 8.3 - - - +
1443G VAL* 1.3 76.5 - - - +
1445G ARG* 1.3 61.6 + - - +
1446G SER 2.9 5.8 + - - -
1447G LYS* 3.2 10.8 + - + +
1449G TRP* 4.7 4.5 - - + -
1450G PHE* 3.2 69.7 - - + +
1459G LEU* 4.6 4.0 - - + -
1464G LEU* 4.2 1.6 - - + -
1466G PHE* 4.4 2.9 - - + -
1519G PHE* 3.8 26.9 - - + -
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Residues in contact with ARG1445 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1441G ILE* 3.0 57.4 + - + +
1442G ALA* 3.2 8.2 + - - +
1444G LEU* 1.3 75.5 - - - +
1446G SER* 1.3 60.9 + - - +
1447G LYS 3.3 6.9 + - - +
1450G PHE* 4.6 14.5 - - + +
1452G LEU* 5.4 7.7 - - + +
1455G GLU* 3.9 20.5 + - - +
1456G ASP* 5.5 1.0 - - - +
1457G PHE 3.9 17.8 + - - -
1458G ASP* 5.9 0.2 - - - +
1459G LEU* 5.3 2.4 - - - +
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Residues in contact with SER1446 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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957A VAL* 4.0 28.9 - - - +
960A GLU* 6.0 1.6 - - - +
961A THR* 5.1 6.9 - - - +
1442G ALA 3.1 11.4 + - - -
1443G VAL* 2.9 18.2 + - - +
1444G LEU 2.9 1.0 - - - -
1445G ARG* 1.3 79.1 - - - +
1447G LYS* 1.3 70.4 + - - +
1448G GLU* 3.8 6.4 + - - +
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Residues in contact with LYS1447 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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960A GLU* 4.5 18.7 + - + +
961A THR* 5.5 4.2 - - + +
964A GLU* 3.0 44.1 + - - +
1443G VAL* 3.7 12.8 - - + +
1444G LEU* 3.2 10.4 + - - +
1445G ARG 3.9 5.3 - - - +
1446G SER* 1.3 87.9 - - - +
1448G GLU* 1.3 64.4 + - - +
1449G TRP* 3.2 46.9 + - + +
1450G PHE* 3.3 19.8 + - + +
1515G PRO 5.3 2.7 + - - -
1519G PHE* 4.1 28.5 - - + +
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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