Contacts of the helix formed by residues 403 - 410 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401G HIS 3.5 0.8 + - - -
402G LEU* 1.3 82.8 - - - +
404G THR* 1.3 65.6 + - - +
405G SER* 4.4 6.8 - - - -
406G ASN* 3.2 30.0 + - - +
407G LEU 3.7 1.9 + - - -
617G ALA* 3.0 39.9 + - - +
618G GLU 4.2 0.9 - - - -
619G ILE* 3.5 22.7 - - - -
1210G LEU* 6.0 0.2 - - - -
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Residues in contact with THR 404 (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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402G LEU* 3.7 1.8 + - - -
403G SER* 1.3 71.6 - - - +
405G SER* 1.3 55.8 + - - +
407G LEU* 2.7 34.9 + - + +
408G SER* 2.8 25.5 + - - +
619G ILE* 4.1 6.0 - - - +
688G TRP* 5.1 10.8 - - + -
724G LEU* 5.8 4.9 - - + -
729G GLU* 3.3 11.6 + - - -
1210G LEU* 5.3 3.5 - - - +
1211G THR* 4.0 13.6 - - + +
1214G ARG* 2.6 34.5 + - - +
2004G ATP 5.3 0.7 - - - +
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Residues in contact with SER 405 (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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403G SER* 3.3 5.7 - - - -
404G THR* 1.3 77.6 - - - +
406G ASN* 1.3 56.8 + - - +
408G SER* 4.2 8.1 - - - -
409G MET* 2.9 35.9 + - - +
619G ILE* 5.9 0.4 - - - +
688G TRP* 2.8 54.2 + - - -
689G THR* 4.6 8.5 - - - -
729G GLU 5.4 4.2 + - - -
730G MET* 5.7 0.9 - - - -
731G GLN 5.6 1.2 + - - -
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Residues in contact with ASN 406 (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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402G LEU* 4.0 1.9 - - + +
403G SER* 3.2 24.6 + - - +
404G THR 3.0 0.6 - - - -
405G SER* 1.3 80.9 - - - +
407G LEU* 1.3 60.0 + - - +
410G GLY 3.8 11.9 + - - +
411G GLU* 2.9 38.9 + - - +
412G MET* 3.1 38.4 + - - +
616G SER* 3.4 18.0 - - - -
617G ALA* 3.9 9.9 - - + +
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Residues in contact with LEU 407 (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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402G LEU* 4.6 9.0 - - + -
403G SER 3.7 4.4 + - - +
404G THR* 2.7 22.4 + - + +
406G ASN* 1.3 74.5 - - - +
408G SER* 1.3 64.5 + - - +
410G GLY 4.4 3.0 - - - +
412G MET* 3.2 30.6 - - + +
413G THR* 3.6 3.1 - - - +
414G ALA* 3.4 28.7 - - + +
417G ILE* 3.6 15.3 - - + -
1207G VAL* 3.8 29.4 - - + +
1210G LEU* 6.0 3.6 - - + -
1475G THR* 5.4 0.9 - - - -
1476G GLU* 5.3 6.2 - - - +
1479G GLU* 4.9 8.1 - - + +
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Residues in contact with SER 408 (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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404G THR* 2.8 29.0 + - - +
405G SER* 3.9 5.6 - - - -
407G LEU* 1.3 79.6 - - - +
409G MET* 1.3 54.9 + - - +
1475G THR* 2.3 33.3 + - - -
1479G GLU* 3.5 28.4 + - - +
2004G ATP 3.1 38.5 + - - -
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Residues in contact with MET 409 (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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405G SER* 2.9 18.1 + - - +
408G SER* 1.3 78.1 - - - +
410G GLY* 1.3 59.6 + - - +
688G TRP* 6.1 0.2 - - + -
689G THR* 4.0 27.8 - - + +
1475G THR* 3.1 21.6 - - - +
1480G ASN* 3.0 46.0 - - - +
2004G ATP 3.3 26.9 - - + +
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Residues in contact with GLY 410 (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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405G SER 4.2 0.4 + - - -
406G ASN* 3.8 8.3 + - - -
407G LEU 4.4 1.7 - - - +
408G SER 3.6 1.0 - - - -
409G MET* 1.3 83.9 - - - +
411G GLU* 1.3 66.5 + - - +
412G MET 2.9 14.6 + - - +
413G THR* 4.8 4.5 - - - +
1475G THR* 4.9 5.7 - - - +
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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