Contacts of the helix formed by residues 1400 - 1411 (chain G) in PDB entry 4Z94
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 THR1400 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1373G ASP* 2.9 30.0 + - - +
1398G HIS 4.4 4.4 + - - -
1399G ILE* 1.3 75.7 + - - +
1401G GLY* 1.3 62.3 + - - +
1402G LYS* 3.2 18.2 - - + +
1403G GLY 3.1 1.2 + - - -
1404G ILE* 2.9 34.5 + - - +
1427G HIS* 5.2 13.6 + - - +
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Residues in contact with GLY1401 (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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1400G THR* 1.3 80.4 + - - +
1402G LYS* 1.3 56.2 + - - -
1404G ILE* 4.2 3.7 - - - +
1405G LEU* 2.8 39.1 + - - +
1429G CYS* 4.2 14.2 - - - +
1433G THR* 3.6 23.3 - - - -
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Residues in contact with LYS1402 (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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1373G ASP* 4.9 1.3 - - - +
1377G PHE* 3.6 41.5 - - + -
1400G THR* 3.2 12.8 - - + +
1401G GLY* 1.3 75.7 - - - +
1403G GLY* 1.3 60.6 + - - +
1405G LEU* 4.4 4.5 - - + -
1406G ALA* 3.0 31.2 + - - +
1409G ARG* 4.5 24.1 - - - +
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Residues in contact with GLY1403 (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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1373G ASP* 2.9 27.8 + - - -
1376G ALA* 3.5 22.9 - - - +
1377G PHE* 4.2 6.5 - - - -
1399G ILE* 3.8 0.9 - - - -
1400G THR 3.1 0.4 + - - -
1402G LYS* 1.3 75.3 - - - +
1404G ILE* 1.3 65.9 + - - +
1406G ALA* 3.3 3.5 + - - +
1407G ILE* 3.1 25.2 + - - +
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Residues in contact with ILE1404 (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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1399G ILE* 3.7 11.5 - - + +
1400G THR* 2.9 28.8 + - - +
1401G GLY* 3.8 4.3 - - - +
1403G GLY* 1.3 74.3 - - - +
1405G LEU* 1.3 67.9 + - + +
1407G ILE* 3.1 20.9 + - + +
1408G PHE* 3.1 35.4 + - + -
1422G PHE* 4.0 30.7 - - + -
1425G GLN* 4.6 14.8 - - + -
1427G HIS 6.1 0.9 - - - +
1429G CYS* 3.9 24.7 - - - +
1433G THR* 4.9 2.2 - - + -
1437G ILE* 3.9 18.2 - - + -
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Residues in contact with LEU1405 (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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1401G GLY 2.8 29.7 + - - +
1402G LYS* 4.2 4.0 - - + +
1404G ILE* 1.3 75.4 - - - +
1406G ALA* 1.3 53.9 + - - +
1408G PHE* 2.8 23.7 + - + +
1409G ARG* 2.8 40.0 + - - +
1432G LYS 5.3 0.2 - - - +
1433G THR* 3.8 25.1 - - + +
1436G GLU* 3.5 38.1 - - + -
1437G ILE* 3.9 19.3 - - + +
1440G LEU* 4.0 12.0 - - + +
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Residues in contact with ALA1406 (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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1377G PHE* 3.9 21.5 - - + -
1380G ALA* 3.5 13.4 - - + +
1384G LYS* 5.8 0.2 + - - -
1402G LYS* 3.0 23.7 + - - +
1403G GLY 3.6 4.7 - - - +
1404G ILE 3.3 0.2 - - - -
1405G LEU* 1.3 74.7 - - - +
1407G ILE* 1.3 62.2 + - - +
1409G ARG* 3.4 22.0 + - - +
1410G ALA* 3.0 22.9 + - - +
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Residues in contact with ILE1407 (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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1376G ALA* 3.6 30.5 - - + +
1379G ILE* 4.3 11.0 - - + -
1380G ALA* 3.9 9.0 - - + +
1383G LEU* 4.0 17.0 - - + -
1394G LEU* 3.8 27.1 - - + -
1399G ILE* 5.4 0.9 - - + -
1403G GLY 3.1 17.2 + - - +
1404G ILE* 3.1 12.0 + - - +
1406G ALA* 1.3 78.1 - - - +
1408G PHE* 1.3 58.2 + - + +
1410G ALA* 3.1 5.0 + - - +
1411G LEU* 3.0 30.1 + - + +
1417G LEU* 6.1 0.2 - - + -
1420G LEU* 4.3 28.5 - - + -
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Residues in contact with PHE1408 (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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1404G ILE* 3.1 28.1 + - + -
1405G LEU* 2.8 14.5 + - + +
1407G ILE* 1.3 71.1 - - + +
1409G ARG* 1.3 63.7 + - - +
1411G LEU* 3.4 27.3 + - + +
1412G LEU* 3.9 7.4 + - - +
1420G LEU* 3.8 24.2 - - + -
1422G PHE* 3.6 32.1 - + - -
1437G ILE* 3.9 41.7 - - + -
1440G LEU* 3.8 27.8 - - + +
1441G LEU* 4.9 22.4 - - + -
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Residues in contact with ARG1409 (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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1402G LYS* 4.5 24.0 - - - +
1405G LEU* 2.8 36.4 + - - +
1406G ALA* 3.5 34.5 - - - +
1408G PHE* 1.3 69.2 - - - +
1410G ALA* 1.3 68.5 + - - +
1412G LEU* 2.9 38.9 + - + +
1413G GLN* 5.0 1.4 - - - +
1436G GLU* 5.6 3.8 + - - +
1440G LEU* 3.9 22.0 - - + +
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Residues in contact with ALA1410 (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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1380G ALA* 3.3 35.2 - - + +
1383G LEU* 4.3 8.7 - - + -
1384G LYS* 4.3 21.7 - - + +
1406G ALA 3.0 14.2 + - - +
1407G ILE 3.1 10.3 + - - +
1409G ARG* 1.3 76.8 - - - +
1411G LEU* 1.3 51.5 + - - +
1413G GLN* 2.7 36.1 + - - +
1414G ASN* 3.7 4.2 + - - +
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Residues in contact with LEU1411 (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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1383G LEU* 4.6 10.1 - - + -
1407G ILE* 3.0 22.2 + - + +
1408G PHE* 3.7 26.2 - - + +
1409G ARG 3.0 0.8 + - - -
1410G ALA* 1.3 75.0 - - - +
1412G LEU* 1.3 60.9 + - - +
1413G GLN 3.2 0.7 - - - -
1414G ASN* 3.2 39.4 - - + +
1417G LEU* 3.8 37.0 - - + +
1420G LEU* 4.0 26.7 - - + -
1441G LEU* 6.3 1.3 - - + -
1444G ASN* 3.3 27.5 + - + +
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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