Contacts of the helix formed by residues 403 - 410 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401H HIS 3.5 1.0 + - - -
402H LEU* 1.3 81.1 - - - +
404H THR* 1.3 66.4 + - - +
405H SER* 4.4 6.2 - - - -
406H ASN* 3.2 31.4 + - - +
407H LEU 3.7 1.4 + - - -
617H ALA* 3.0 39.6 + - - +
618H GLU 4.3 1.1 - - - -
619H ILE* 3.5 24.0 - - - -
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Residues in contact with THR 404 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402H LEU* 3.7 2.0 + - - -
403H SER* 1.3 72.2 - - - +
405H SER* 1.3 56.7 + - - +
407H LEU* 2.7 34.9 + - + +
408H SER* 2.8 24.8 + - - +
619H ILE* 4.1 5.8 - - - +
688H TRP* 5.1 11.0 - - + -
724H LEU* 5.8 5.2 - - + -
729H GLU* 3.3 12.3 + - - -
1210H LEU* 5.3 3.5 - - - +
1211H THR* 4.0 13.7 - - + +
1214H ARG* 2.6 33.8 + - - -
2004H ATP 5.3 0.4 - - - +
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Residues in contact with SER 405 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403H SER* 3.3 5.0 - - - -
404H THR* 1.3 78.1 - - - +
406H ASN* 1.3 57.4 + - - +
408H SER* 4.2 8.1 - - - -
409H MET* 2.9 35.2 + - - +
410H GLY 4.2 0.3 + - - -
688H TRP* 2.8 54.3 + - - -
689H THR* 4.6 7.6 - - - -
729H GLU 5.4 4.6 + - - -
730H MET* 5.7 0.7 - - - -
731H GLN 5.6 1.6 + - - -
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Residues in contact with ASN 406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402H LEU* 4.0 2.1 - - + +
403H SER* 3.2 25.1 + - - +
404H THR 3.0 0.4 + - - -
405H SER* 1.3 80.6 - - - +
407H LEU* 1.3 58.6 + - - +
410H GLY* 3.8 11.9 + - - +
411H GLU* 2.9 39.0 + - - +
412H MET* 3.1 38.4 + - - +
616H SER* 3.4 17.4 - - - -
617H ALA* 3.9 10.7 - - + +
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Residues in contact with LEU 407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402H LEU* 4.6 9.0 - - + -
403H SER 3.7 3.3 + - - +
404H THR* 2.7 23.1 + - + +
406H ASN* 1.3 75.6 - - - +
408H SER* 1.3 64.0 + - - +
410H GLY 4.4 2.5 - - - +
412H MET* 3.2 31.4 - - + +
413H THR* 3.6 2.6 - - - +
414H ALA* 3.4 27.4 - - + +
417H ILE* 3.6 16.6 - - + -
1207H VAL* 3.8 29.6 - - + +
1208H GLU* 6.3 0.2 - - - -
1210H LEU* 6.0 3.8 - - + -
1475H THR* 5.4 1.0 - - - -
1476H GLU* 5.3 6.1 - - - +
1479H GLU* 4.9 8.7 - - + +
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Residues in contact with SER 408 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404H THR* 2.8 29.7 + - - +
405H SER* 3.9 5.4 - - - -
407H LEU* 1.3 79.2 - - - +
409H MET* 1.3 56.0 + - - +
1475H THR* 2.3 32.9 + - - -
1479H GLU* 3.5 27.2 + - - +
2004H ATP 3.1 38.1 + - - -
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Residues in contact with MET 409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405H SER* 2.9 17.9 + - - +
408H SER* 1.3 77.7 - - - +
410H GLY* 1.3 58.9 + - - +
688H TRP* 5.0 0.4 - - + -
689H THR* 4.0 27.8 - - + +
1475H THR* 3.1 22.0 - - - +
1480H ASN* 3.0 45.5 - - - +
2004H ATP 3.3 26.7 - - + +
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Residues in contact with GLY 410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405H SER 4.2 0.2 + - - -
406H ASN* 3.8 8.7 + - - +
407H LEU 4.4 1.7 - - - +
408H SER 3.6 0.8 - - - -
409H MET* 1.3 82.6 - - - +
411H GLU* 1.3 66.5 + - - +
412H MET 2.9 14.3 + - - +
413H THR* 4.8 5.0 - - - +
1475H THR* 4.9 5.8 - - - +
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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