Contacts of the helix formed by residues 463 - 471 (chain C) in PDB entry 5Y9F
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 PHE 463 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C HIS* 3.3 57.7 - + + +
455C ARG 5.8 1.3 - - - -
457C SER* 3.5 32.3 - - - -
459C ASP 3.2 23.6 - - - -
460C LEU 3.2 5.0 + - - +
461C ASP 3.3 0.6 - - - -
462C GLN* 1.3 94.4 - - + +
464C PRO* 1.3 75.3 - - + +
466C GLY 3.2 1.4 + - - +
467C ARG* 2.9 29.3 + - - +
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Residues in contact with PRO 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C HIS* 5.4 0.7 - - - +
106C GLU* 5.9 0.2 - - - +
374C GLN* 3.7 17.3 - - - +
462C GLN 4.7 0.9 - - - +
463C PHE* 1.3 88.6 - - + +
465C LEU* 1.3 59.0 + - - +
467C ARG* 3.1 27.4 + - - +
468C LYS* 2.9 50.5 + - - +
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Residues in contact with LEU 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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36C HIS* 4.2 7.2 - - + -
104C GLY 4.3 3.6 - - - +
105C VAL 4.5 1.1 - - - -
106C GLU* 3.5 32.5 - - + +
310C PRO* 3.8 9.4 - - + -
312C TRP* 3.5 26.7 - - + -
374C GLN* 3.5 29.3 + - + +
375C PHE* 3.5 43.3 - - - +
376C ILE* 3.8 10.3 - - + +
463C PHE* 4.6 0.4 - - - +
464C PRO* 1.3 81.4 - - - +
466C GLY* 1.3 57.3 + - - +
468C LYS* 4.4 3.5 - - + +
469C PHE* 2.9 27.9 + - - +
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Residues in contact with GLY 466 (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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36C HIS* 4.0 7.6 - - - -
376C ILE* 3.9 17.7 - - - -
460C LEU* 3.2 28.5 - - - +
463C PHE 3.2 4.6 + - - -
464C PRO 3.1 1.2 - - - -
465C LEU* 1.3 79.3 - - - +
467C ARG* 1.3 56.2 + - - +
469C PHE* 3.2 4.5 + - - +
470C LEU* 2.9 31.2 + - - +
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Residues in contact with ARG 467 (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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460C LEU 4.4 0.2 - - - -
461C ASP* 3.0 38.9 + - + +
462C GLN* 3.6 5.9 + - - +
463C PHE 2.9 34.0 + - - +
464C PRO* 3.1 32.3 + - - +
466C GLY* 1.3 73.6 - - - +
468C LYS* 1.3 66.9 + - + +
470C LEU* 3.0 21.8 + - + +
471C LEU* 3.3 17.1 + - + +
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Residues in contact with LYS 468 (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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106C GLU* 3.1 32.5 + - - +
310C PRO* 3.8 25.2 - - + +
312C TRP* 3.6 20.5 + - + -
464C PRO* 2.9 37.0 + - - +
465C LEU* 3.9 5.2 - - - +
467C ARG* 1.3 75.9 - - + +
469C PHE* 1.3 60.8 + - - +
471C LEU* 3.4 25.8 + - - +
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Residues in contact with PHE 469 (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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34C PHE* 3.6 52.7 - + - -
103C VAL* 3.5 21.8 - - + -
312C TRP* 3.5 31.1 - + + -
376C ILE* 3.7 22.9 - - + -
460C LEU* 3.7 21.3 - - + -
465C LEU 2.9 19.6 + - - +
466C GLY 3.5 3.6 - - - +
467C ARG 3.1 0.4 - - - -
468C LYS* 1.3 73.2 - - - +
470C LEU* 1.3 68.1 + - + +
471C LEU 3.1 4.1 + - - -
472C GLN* 3.9 8.5 + - - -
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Residues in contact with LEU 470 (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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460C LEU* 3.8 26.2 - - + -
461C ASP* 4.3 31.2 - - + +
466C GLY 2.9 17.4 + - - +
467C ARG* 3.0 11.6 + - - +
469C PHE* 1.3 80.2 - - + +
471C LEU* 1.3 61.3 + - + +
472C GLN 3.0 7.1 + - - -
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Residues in contact with LEU 471 (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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312C TRP* 5.8 1.6 + - - -
467C ARG* 3.3 16.1 + - + +
468C LYS* 3.6 18.2 - - - +
469C PHE 3.1 4.0 - - - +
470C LEU* 1.3 77.4 - - + +
472C GLN* 1.3 56.1 + - - +
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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