Contacts of the helix formed by residues 3070 - 3075 (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 HIS3070 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3025C PRO* 6.1 0.9 - - + -
3029C LYS* 4.1 9.6 - - + +
3066C ASP* 2.8 42.9 + - + +
3067C LYS* 3.4 10.1 - - + +
3068C ALA 3.1 0.6 - - - -
3069C MET* 1.3 91.7 + - + +
3071C GLY* 1.3 59.2 + - - +
3072C GLU 2.9 0.4 - - - -
3073C LEU* 2.4 42.8 + - + +
3074C GLN* 2.9 11.8 + - - +
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Residues in contact with GLY3071 (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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3029C LYS* 3.2 7.6 - - - +
3067C LYS 2.8 19.8 + - - -
3070C HIS* 1.3 70.5 - - - +
3072C GLU* 1.3 57.6 + - - +
3074C GLN* 3.0 42.4 + - - +
3075C LYS 3.3 5.0 - - - +
3079C GLU* 2.7 23.7 - - - +
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Residues in contact with GLU3072 (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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14C ARG* 3.1 32.7 + - - +
3068C ALA 2.3 30.9 + - - +
3069C MET* 3.0 31.7 - - - +
3071C GLY* 1.3 75.9 - - - +
3073C LEU* 1.3 61.3 + - + +
3074C GLN 3.0 5.0 + - - -
3075C LYS* 3.8 12.3 + - - -
3076C ALA* 4.2 10.8 + - + +
3079C GLU* 2.6 19.0 + - - +
3102C TYR* 4.3 19.6 + - - -
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Residues in contact with LEU3073 (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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14C ARG* 3.8 36.1 - - - +
3069C MET 3.2 24.2 - - - +
3070C HIS* 2.4 36.8 + - + +
3072C GLU* 1.3 72.0 - - + +
3074C GLN* 1.3 60.0 + - - +
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Residues in contact with GLN3074 (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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3029C LYS* 3.1 42.4 + - + +
3031C TRP 5.5 1.4 + - - -
3070C HIS 2.9 6.5 + - - +
3071C GLY* 3.0 29.6 + - - +
3073C LEU* 1.3 82.5 - - - +
3075C LYS* 1.3 66.6 + - + +
3079C GLU* 6.0 0.2 - - - +
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Residues in contact with LYS3075 (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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2550C ILE* 4.6 9.3 + - - +
2848C PHE* 3.7 13.6 + - + +
2850C PHE* 3.7 28.7 - - - -
3071C GLY 3.3 2.0 - - - +
3072C GLU 4.0 3.4 - - - -
3074C GLN* 1.3 83.4 - - + +
3076C ALA* 1.3 63.6 + - - +
3077C ILE* 3.5 29.7 - - + +
3078C LEU* 5.1 17.3 - - + +
3079C GLU* 2.9 23.5 + - - +
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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