Contacts of the helix formed by residues 3076 - 3083 (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 ALA3076 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3072C GLU* 4.2 13.1 + - + +
3075C LYS* 1.3 77.0 - - - +
3077C ILE* 1.3 72.7 + - + +
3079C GLU* 3.1 12.1 - - - +
3080C LEU* 2.9 33.3 + - + +
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Residues in contact with ILE3077 (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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2849C SER* 3.4 26.7 - - - +
2850C PHE* 5.1 5.2 - - + -
3075C LYS* 3.5 37.0 - - + +
3076C ALA* 1.3 73.8 - - + +
3078C LEU* 1.3 68.1 + - + +
3080C LEU* 2.8 22.4 + - + +
3081C HIS* 2.7 39.0 - - + +
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Residues in contact with LEU3078 (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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2848C PHE* 3.5 33.7 - - + +
2849C SER* 3.1 20.2 - - - +
3038C GLU* 5.4 0.2 - - - +
3075C LYS* 5.1 16.6 - - + +
3077C ILE* 1.3 84.1 - - + +
3079C GLU* 1.3 67.6 - - + +
3081C HIS* 2.8 16.0 + - - +
3082C TYR* 2.8 72.0 + - + +
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Residues in contact with GLU3079 (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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3064C PHE* 5.9 4.5 - - + -
3068C ALA* 3.0 27.7 - - + +
3071C GLY* 2.7 22.8 - - - +
3072C GLU* 2.6 34.0 + - - -
3075C LYS 2.9 14.3 - - - +
3076C ALA* 3.1 13.1 - - - +
3078C LEU* 1.3 82.0 - - + +
3080C LEU* 1.3 69.7 + - + +
3082C TYR* 2.8 21.6 + - - +
3083C SER* 2.9 13.3 + - - +
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Residues in contact with LEU3080 (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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3076C ALA* 2.9 33.8 + - + +
3077C ILE* 2.8 21.5 + - + +
3079C GLU* 1.3 74.5 - - + +
3081C HIS* 1.3 68.0 + - + +
3083C SER 2.7 35.5 + - - +
3084C GLN* 3.4 13.7 + - - +
3086C LEU* 3.6 16.8 - - + -
3101C TYR* 5.7 1.8 - - + +
3102C TYR* 4.5 3.4 - - + -
3105C ASN* 3.4 48.9 - - + +
3108C GLN* 6.4 1.3 - - + -
3109C SER* 6.0 0.7 - - - -
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Residues in contact with HIS3081 (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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2849C SER* 3.7 12.6 + - - -
2881C LEU* 6.0 6.7 - - + +
3077C ILE* 2.7 47.2 + - + +
3078C LEU* 2.8 24.0 + - - +
3080C LEU* 1.3 84.9 - - + +
3082C TYR* 1.3 71.4 + - + +
3084C GLN 5.3 0.3 + - - -
3109C SER* 4.4 30.3 - - - +
3112C GLN* 5.1 18.8 - - + +
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Residues in contact with TYR3082 (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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2879C GLY* 4.6 7.5 - - - -
2880C CYS* 3.8 44.5 + - + -
2881C LEU* 5.2 5.3 + - + -
3038C GLU* 3.1 26.9 - - - -
3041C LEU* 4.3 19.6 - - + +
3042C PRO* 5.8 0.5 - - - +
3078C LEU* 2.8 56.5 + - + +
3079C GLU* 3.4 8.1 - - - +
3081C HIS* 1.3 91.7 - - + +
3083C SER* 1.3 63.4 + - - +
3084C GLN 4.2 0.6 + - - -
3085C GLU* 3.6 13.7 - - - +
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Residues in contact with SER3083 (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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3041C LEU* 5.6 1.7 - - - +
3045C ILE* 4.0 2.6 - - - +
3064C PHE* 3.3 27.0 - - - -
3079C GLU* 2.9 8.1 + - - -
3080C LEU* 2.7 18.1 + - - +
3082C TYR* 1.3 78.2 + - - +
3084C GLN* 1.3 58.3 + - - +
3085C GLU* 2.0 43.8 + - - +
3086C LEU* 3.0 24.9 - - - +
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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