Contacts of the helix formed by residues 403 - 409 (chain A) in PDB entry 3C6G
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 ASN 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A HIS* 3.2 27.5 + - - +
66A MET* 3.6 20.9 - - + +
67A ARG 3.7 2.8 - - - +
89A LEU 3.0 22.7 + - - +
90A ASN* 3.0 21.9 + - - +
95A VAL* 4.7 1.2 - - - +
377A LEU* 3.7 14.2 - - - +
401A ILE 3.6 1.4 + - - -
402A THR* 1.3 68.9 - - - +
404A LEU* 1.3 57.2 + - - +
405A TYR* 3.3 13.7 + - - +
406A SER* 2.7 52.5 + - - +
407A VAL* 3.4 7.0 + - - +
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Residues in contact with LEU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A VAL* 4.6 12.3 - - + -
99A LEU* 5.6 0.2 - - + -
373A ASN* 4.2 0.7 - - - +
375A VAL 3.6 19.1 - - - +
376A PRO 3.1 8.1 + - - +
378A GLY* 3.9 15.9 - - - +
402A THR* 3.0 34.4 + - - +
403A ASN* 1.3 69.4 - - - +
405A TYR* 1.3 64.9 + - - +
407A VAL* 3.0 17.5 + - - +
408A HIS* 3.1 26.5 + - + -
439A VAL* 3.8 36.3 - - + +
440A PRO* 4.6 3.1 - - + +
442A SER* 4.4 14.8 - - - +
601A HEM 3.9 15.9 - - + -
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Residues in contact with TYR 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A HIS* 3.4 53.6 - + + -
64A VAL* 4.1 19.6 - - + +
67A ARG* 3.4 31.3 + - + -
373A ASN* 3.5 32.1 + - + +
376A PRO* 3.0 14.0 + - + +
403A ASN* 3.3 7.9 - - - +
404A LEU* 1.3 76.3 - - - +
406A SER* 1.3 59.4 + - - +
408A HIS* 3.2 2.8 + - - -
409A PHE* 3.0 64.1 + + - +
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Residues in contact with SER 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ARG* 4.1 23.2 + - - +
90A ASN* 3.2 11.8 - - - -
91A GLY* 2.8 26.5 + - - -
403A ASN* 2.7 37.7 + - - +
405A TYR* 1.3 83.4 - - - +
407A VAL* 1.3 57.2 + - - +
409A PHE 3.7 2.2 - - - +
410A ASP* 3.2 25.1 + - - +
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Residues in contact with VAL 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLY* 3.7 21.8 - - - +
92A TYR* 3.6 32.3 - - + +
95A VAL* 4.0 17.3 - - + -
403A ASN 3.9 11.2 - - - +
404A LEU* 3.0 12.9 + - - +
406A SER* 1.3 75.7 + - - +
408A HIS* 1.3 62.7 + - - +
409A PHE 3.2 0.2 - - - -
410A ASP* 3.2 18.5 + - - +
414A TRP* 3.2 11.6 + - - -
437A ALA* 3.4 19.1 - - - +
439A VAL* 3.8 19.1 - - + -
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Residues in contact with HIS 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369A LEU 4.4 3.4 - - - -
370A ARG* 2.7 56.0 + - + +
373A ASN* 2.6 25.0 + - - +
404A LEU* 3.1 15.3 + - + -
405A TYR 3.7 6.1 - - - +
407A VAL* 1.3 76.9 - - - +
409A PHE* 1.3 57.2 + - + +
410A ASP 3.5 0.4 - - - -
414A TRP* 3.4 15.2 + - - +
437A ALA 3.6 15.0 - - - -
438A LEU* 3.5 20.3 - - + +
439A VAL* 3.0 28.4 + - + +
440A PRO* 3.5 28.4 - - + -
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Residues in contact with PHE 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ARG* 2.9 46.5 + - - +
370A ARG* 3.8 11.0 - - - -
371A PHE* 4.1 22.2 - + - -
373A ASN* 3.6 22.9 - - - -
405A TYR* 3.0 46.0 + + - +
406A SER 3.7 3.1 - - - +
408A HIS* 1.3 85.9 - - + +
410A ASP* 1.3 61.4 + - - +
411A GLU 3.2 1.7 + - - -
417A PRO* 3.2 47.1 - - + +
418A GLU* 3.8 13.5 - - + -
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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