Contacts of the helix formed by residues 3058 - 3068 (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 ASP3058 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3051C LEU* 4.8 23.2 - - + +
3056C GLU 3.8 5.5 - - - +
3057C ALA* 1.3 90.9 - - - +
3059C GLN* 1.3 71.0 + - + +
3060C SER 3.6 1.3 - - - +
3061C LEU* 3.1 21.3 - - + +
3062C LEU* 4.0 2.1 + - - +
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Residues in contact with GLN3059 (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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3021C SER* 3.6 34.1 + - - +
3023C ASN* 5.4 1.0 - - - +
3024C PRO* 4.0 13.2 - - + +
3044C MET* 4.8 14.1 - - + -
3058C ASP* 1.3 77.5 - - + +
3060C SER* 1.3 67.8 + - - +
3061C LEU 2.9 1.9 + - - -
3062C LEU* 3.6 0.5 + - - +
3063C THR* 2.3 66.5 + - - +
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Residues in contact with SER3060 (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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3044C MET* 3.8 25.0 + - - +
3045C ILE* 3.7 32.1 - - - +
3048C LYS* 4.9 15.0 - - - -
3058C ASP* 3.6 1.0 - - - +
3059C GLN* 1.3 81.4 - - - +
3061C LEU* 1.3 68.1 + - - +
3063C THR* 3.0 10.3 - - - -
3064C PHE* 2.9 25.1 + - - +
3065C ILE 3.4 0.3 + - - -
3067C LYS* 6.0 0.5 - - - -
3089C LEU* 4.9 5.1 - - - +
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Residues in contact with LEU3061 (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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3056C GLU* 4.9 4.9 - - + +
3057C ALA* 3.6 33.2 - - + +
3058C ASP* 3.1 17.8 + - + +
3059C GLN 2.9 2.0 + - - -
3060C SER* 1.3 82.2 - - - +
3062C LEU* 1.3 63.9 + - + +
3065C ILE* 2.8 30.7 + - + +
3089C LEU* 4.5 13.9 - - + +
3092C LEU* 6.0 0.2 - - + -
3093C GLN* 3.2 40.6 - - + +
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Residues in contact with LEU3062 (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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3058C ASP 4.0 1.7 + - - +
3059C GLN 3.6 2.5 + - - +
3061C LEU* 1.3 85.0 - - + +
3063C THR* 1.3 72.3 + - + +
3065C ILE* 3.0 10.1 - - + +
3066C ASP* 2.9 58.4 + - - +
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Residues in contact with THR3063 (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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3024C PRO* 5.6 0.8 - - - +
3025C PRO* 4.6 10.3 - - + +
3059C GLN* 2.3 65.7 + - - +
3060C SER* 3.0 4.2 - - - -
3062C LEU* 1.3 80.2 - - + +
3064C PHE* 1.3 63.0 + - - +
3066C ASP* 3.9 3.4 - - - +
3067C LYS* 2.9 39.7 + - - +
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Residues in contact with PHE3064 (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* 4.9 4.9 - - + -
3045C ILE* 3.7 35.2 - - + -
3060C SER* 2.9 21.6 + - - +
3063C THR* 1.3 75.2 + - - +
3065C ILE* 1.3 70.3 + - - +
3066C ASP 3.0 2.2 - - - -
3067C LYS* 3.3 38.1 - - + +
3068C ALA* 2.8 42.2 + - + +
3079C GLU* 5.9 4.9 - - + -
3083C SER* 3.3 35.0 - - - -
3085C GLU* 4.2 4.0 - - + -
3086C LEU* 4.4 14.1 - - + -
3089C LEU* 5.0 11.2 - - + -
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Residues in contact with ILE3065 (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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3060C SER 3.4 0.4 + - - -
3061C LEU* 2.8 26.8 + - + +
3062C LEU* 3.0 26.9 + - + +
3064C PHE* 1.3 82.1 - - - +
3066C ASP* 1.3 73.4 + - - +
3068C ALA* 4.0 4.1 + - - +
3069C MET* 2.9 44.7 + - + +
3086C LEU* 6.5 0.7 - - + -
3089C LEU* 4.8 19.0 - - + +
3090C TYR* 5.5 2.5 - - + -
3098C ARG* 4.2 30.1 - - - +
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Residues in contact with ASP3066 (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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3062C LEU* 2.9 40.2 + - - +
3063C THR* 3.9 3.0 - - - +
3065C ILE* 1.3 86.8 - - - +
3067C LYS* 1.3 54.7 + - - +
3068C ALA 2.9 4.7 - - - -
3069C MET* 2.2 51.1 + - - +
3070C HIS* 2.8 24.3 - - + +
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Residues in contact with LYS3067 (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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3024C PRO* 4.4 9.3 - - - +
3025C PRO* 3.3 31.8 - - + +
3028C ASN* 2.7 29.8 + - - +
3029C LYS* 3.2 21.9 + - - +
3041C LEU* 4.9 6.5 - - - +
3045C ILE* 5.2 4.3 - - - +
3060C SER* 6.0 0.2 - - - -
3063C THR* 2.9 25.2 + - - +
3064C PHE* 3.3 48.0 - - + +
3066C ASP* 1.3 75.5 - - - +
3068C ALA* 1.3 56.1 + - - +
3070C HIS* 3.4 13.2 - - + -
3071C GLY* 2.8 22.7 + - - -
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Residues in contact with ALA3068 (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* 2.8 40.5 + - + +
3065C ILE* 4.1 5.4 - - - +
3067C LYS* 1.3 76.8 - - - +
3069C MET* 1.3 48.6 + - - +
3070C HIS 3.1 5.2 - - - -
3072C GLU* 2.3 36.2 + - - +
3079C GLU* 3.0 19.2 - - + +
3086C LEU* 5.2 12.8 - - + -
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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