Contacts of the helix formed by residues 459 - 465 (chain C) in PDB entry 3ZXR
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 GLU 459 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C PRO* 5.7 0.5 - - - +
322C PRO 3.4 9.2 - - - +
323C THR* 3.7 19.1 - - - +
324C VAL* 4.2 11.9 + - + -
423C LEU* 3.9 3.2 - - + +
454C PHE* 3.3 19.6 - - + -
455C LYS* 2.9 48.4 + - - +
458C ASN* 1.3 88.3 - - + +
460C ILE* 1.3 69.5 + - - +
461C GLU 3.5 1.1 - - - -
462C PRO* 3.5 3.0 - - - +
463C VAL* 3.2 28.8 + - - +
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Residues in contact with ILE 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C VAL* 4.3 7.0 - - + -
423C LEU* 4.0 17.3 - - + -
424C SER* 3.8 29.4 - - - +
427C ILE* 4.0 17.5 - - + -
455C LYS 2.9 24.8 + - - +
456C ARG* 3.9 26.7 - - + +
459C GLU* 1.3 73.4 - - - +
461C GLU* 1.3 59.4 + - + +
463C VAL* 3.4 2.1 + - - +
464C ASN* 2.9 49.3 + - - +
507C CL 4.1 19.3 - - + -
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Residues in contact with GLU 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456C ARG 3.0 17.3 + - - +
457C GLU* 4.6 14.1 - - - +
460C ILE* 1.3 83.0 - - + +
462C PRO* 1.4 66.4 - - + +
464C ASN* 3.1 8.5 + - + +
465C ILE* 3.1 46.3 + - + +
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Residues in contact with PRO 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457C GLU 3.4 23.3 - - - +
458C ASN* 3.5 17.3 - - - +
459C GLU 3.5 13.7 - - - +
461C GLU* 1.4 93.5 - - + +
463C VAL* 1.3 61.0 + - + +
465C ILE* 3.6 11.0 - - + +
466C ARG* 2.7 44.3 + - - +
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Residues in contact with VAL 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324C VAL* 4.1 33.7 - - + -
328C LYS* 5.5 4.0 - - - +
459C GLU* 3.2 19.5 + - + +
460C ILE 3.8 2.7 - - - +
462C PRO* 1.3 75.2 - - + +
464C ASN* 1.3 71.1 + - - +
466C ARG* 3.2 25.3 + - - +
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Residues in contact with ASN 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424C SER* 5.8 1.6 - - - -
460C ILE* 2.9 39.5 + - - +
461C GLU* 3.1 9.6 + - + +
463C VAL* 1.3 82.8 - - - +
465C ILE* 1.3 62.7 + - + +
466C ARG 3.5 2.9 + - - +
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Residues in contact with ILE 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461C GLU* 3.1 38.1 + - + +
462C PRO* 3.6 13.0 - - + +
464C ASN* 1.3 79.4 - - + +
466C ARG* 1.3 74.8 + - + +
467C PRO* 3.3 12.0 - - - +
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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