Contacts of the helix formed by residues 3622 - 3629 (chain C) in PDB entry 5Y3R
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 ALA3622 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3619C ASP* 2.9 38.2 + - + +
3621C LYS* 1.3 72.9 - - - +
3623C PRO* 1.3 60.8 - - + +
3624C GLY 3.3 0.9 - - - +
3625C LEU* 2.8 19.5 + - + +
3626C GLY 2.2 35.9 + - - -
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Residues in contact with PRO3623 (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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3621C LYS 3.0 8.9 - - - +
3622C ALA* 1.3 82.8 - - + +
3624C GLY* 1.3 60.6 + - - +
3626C GLY* 2.8 16.6 + - - +
3627C ALA* 2.9 17.0 + - - +
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Residues in contact with GLY3624 (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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3622C ALA* 3.3 0.6 - - - +
3623C PRO* 1.3 82.1 - - - +
3625C LEU* 1.3 65.6 + - - +
3627C ALA* 3.8 4.8 + - - +
3628C PHE* 3.8 23.0 + - - -
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Residues in contact with LEU3625 (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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3614C TYR 3.0 31.2 - - - +
3615C ALA* 3.0 30.5 - - - +
3616C ALA 3.9 11.0 - - - +
3619C ASP* 2.9 35.9 - - + +
3620C PRO* 4.0 2.9 - - + +
3622C ALA* 2.8 26.3 + - + +
3624C GLY* 1.3 72.8 - - - +
3626C GLY* 1.3 51.0 + - - +
3628C PHE* 2.9 8.3 + - - -
3629C ARG* 2.2 40.1 + - + -
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Residues in contact with GLY3626 (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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3620C PRO 3.6 1.6 - - - -
3622C ALA 2.2 25.0 + - - -
3623C PRO* 2.8 10.7 + - - -
3625C LEU* 1.3 65.1 - - - +
3627C ALA* 1.3 55.4 + - - -
3629C ARG* 2.8 64.9 + - - +
3686C TRP* 4.0 1.6 + - - -
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Residues in contact with ALA3627 (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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3623C PRO 2.9 15.3 + - - +
3624C GLY* 4.1 5.8 - - - +
3625C LEU 3.1 0.2 + - - -
3626C GLY* 1.3 68.5 - - - +
3628C PHE* 1.3 70.8 + - + +
3686C TRP* 2.6 35.9 + - - -
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Residues in contact with PHE3628 (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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3571C PHE* 5.8 10.1 - + - -
3574C ALA* 3.4 38.6 - - + +
3575C LEU* 5.3 1.3 - - - -
3577C GLN* 2.6 26.3 - - + +
3615C ALA 6.2 0.2 - - - +
3624C GLY 3.8 12.3 + - - +
3625C LEU* 2.9 9.6 + - - +
3627C ALA* 1.3 81.2 - - + +
3629C ARG* 1.3 56.7 + - - +
3630C ARG* 3.7 0.5 + - - +
3686C TRP* 2.9 23.2 - + - -
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Residues in contact with ARG3629 (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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3577C GLN* 3.4 8.9 + - - +
3616C ALA 5.6 0.4 - - - -
3620C PRO* 3.0 17.1 + - + +
3621C LYS* 3.2 14.8 + - - +
3625C LEU* 2.2 34.3 + - + +
3626C GLY* 2.8 39.3 + - - +
3627C ALA 2.8 0.7 - - - +
3628C PHE* 1.3 68.4 - - - +
3630C ARG* 1.3 58.0 + - - +
3633C ILE* 3.3 23.1 - - + -
3634C GLN* 2.5 38.9 + - - +
3638C LYS* 2.8 48.7 - - - +
3686C TRP* 2.1 30.7 + - - -
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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