Contacts of the helix formed by residues 403 - 410 (chain E) in PDB entry 6C3P
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 SER 403 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401E HIS 3.5 1.0 + - - -
402E LEU* 1.3 85.9 - - - +
404E THR* 1.3 66.2 + - - +
405E SER* 4.4 6.4 - - - -
406E ASN* 3.2 26.5 + - - +
407E LEU 3.7 1.6 + - - -
617E ALA* 3.0 39.3 + - - +
618E GLU 4.2 1.1 - - - -
619E ILE* 3.5 22.9 - - - -
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Residues in contact with THR 404 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402E LEU* 3.7 1.8 + - - -
403E SER* 1.3 72.7 - - - +
405E SER* 1.3 57.0 + - - +
407E LEU* 2.7 33.9 + - + +
408E SER* 2.8 24.8 + - - +
619E ILE* 4.1 6.6 - - - +
688E TRP* 5.1 11.2 - - + -
724E LEU* 5.8 5.4 - - + -
729E GLU* 3.3 11.6 + - - -
1210E LEU* 5.3 2.9 - - - +
1211E THR* 4.0 13.7 - - + +
1214E ARG* 2.6 33.6 + - - -
2004E ATP 5.3 0.7 - - - +
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Residues in contact with SER 405 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403E SER* 3.3 5.7 - - - -
404E THR* 1.3 77.3 - - - +
406E ASN* 1.3 56.4 + - - +
408E SER* 4.2 8.7 - - - -
409E MET* 2.9 34.9 + - - +
410E GLY 4.2 0.3 + - - -
619E ILE* 5.9 0.4 - - - +
688E TRP* 2.8 54.5 + - - -
689E THR* 4.6 8.3 - - - -
729E GLU 5.4 4.8 + - - -
730E MET* 5.7 0.7 - - - -
731E GLN 5.6 1.4 + - - -
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Residues in contact with ASN 406 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402E LEU* 4.0 2.1 - - + +
403E SER* 3.2 25.0 + - - +
404E THR 3.0 0.2 - - - -
405E SER* 1.3 80.4 - - - +
407E LEU* 1.3 58.9 + - - +
410E GLY 3.8 11.9 + - - +
411E GLU* 2.9 37.8 + - - +
412E MET* 3.1 36.8 + - - +
616E SER* 3.4 18.4 - - - -
617E ALA* 3.9 9.9 - - + +
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Residues in contact with LEU 407 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402E LEU* 4.6 9.4 - - + -
403E SER 3.7 4.2 + - - +
404E THR* 2.7 22.4 + - + +
406E ASN* 1.3 75.4 - - - +
408E SER* 1.3 62.3 + - - +
410E GLY 4.4 2.9 - - - +
412E MET* 3.2 31.6 - - + +
413E THR* 3.6 2.8 - - - +
414E ALA* 3.4 28.5 - - + +
417E ILE* 3.6 15.5 - - + -
1207E VAL* 3.7 30.3 - - + +
1210E LEU* 6.0 3.1 - - + -
1475E THR* 5.4 1.2 - - - -
1476E GLU* 5.3 6.2 - - - +
1479E GLU* 4.9 7.9 - - + +
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Residues in contact with SER 408 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404E THR* 2.8 29.6 + - - +
405E SER* 3.3 5.1 + - - -
407E LEU* 1.3 79.6 - - - +
409E MET* 1.3 56.0 + - - +
1475E THR* 2.3 33.1 + - - +
1479E GLU* 3.5 27.3 + - - +
2004E ATP 3.1 38.0 + - - -
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Residues in contact with MET 409 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405E SER* 2.9 18.5 + - - +
408E SER* 1.3 79.0 - - - +
410E GLY* 1.3 58.9 + - - +
688E TRP* 5.0 0.9 - - + -
689E THR* 4.0 26.9 - - + +
1475E THR* 3.1 21.7 - - - +
1480E ASN* 3.0 46.2 - - - +
2004E ATP 3.3 26.7 - - + +
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Residues in contact with GLY 410 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405E SER 4.2 0.4 + - - -
406E ASN* 3.8 8.5 + - - +
407E LEU 4.4 1.6 - - - +
408E SER 3.6 1.0 - - - -
409E MET* 1.3 82.6 - - - +
411E GLU* 1.3 67.2 + - - +
412E MET 2.9 14.4 + - - +
413E THR* 4.8 5.2 - - - +
1475E THR* 4.9 5.1 - - - -
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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