Contacts of the helix formed by residues 3947 - 3952 (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 GLY3947 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3946C PHE* 1.3 78.4 - - - +
3948C SER* 1.3 54.9 + - - +
3949C ALA 3.5 0.9 - - - -
3950C THR* 3.5 9.8 - - - +
3951C GLN* 2.5 47.7 + - - +
4038C TRP* 5.3 0.2 - - - -
4044C ILE* 4.7 0.8 - - - +
4048C LYS* 4.0 1.6 - - - +
4061C CYS* 5.2 4.7 - - - -
4064C LEU* 3.5 30.9 - - - +
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Residues in contact with SER3948 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3945C ALA 4.5 4.3 - - - -
3946C PHE* 3.5 3.7 - - - +
3947C GLY* 1.3 76.0 - - - +
3949C ALA* 1.3 57.7 + - - +
3951C GLN* 2.7 30.7 + - - +
3952C PHE* 2.9 30.5 + - - -
4016C PHE* 5.9 5.2 - - - -
4020C MET* 6.0 1.1 - - - -
4035C GLU* 5.3 7.1 + - - +
4038C TRP* 2.9 35.8 - - - -
4040C PRO* 4.8 2.9 - - - +
4044C ILE* 4.6 3.8 - - - +
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Residues in contact with ALA3949 (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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3919C GLY* 6.5 0.4 - - - -
3920C ILE 5.9 1.1 - - - +
3944C HIS* 3.6 40.4 - - + +
3945C ALA 3.7 12.8 + - - +
3946C PHE 5.2 0.4 - - - +
3947C GLY 3.5 0.4 - - - -
3948C SER* 1.3 76.4 - - - +
3950C THR* 1.3 64.6 + - - +
3952C PHE* 2.8 41.8 + - + +
3955C VAL* 3.2 8.9 - - + +
4016C PHE* 5.8 1.6 - - + -
4020C MET* 5.4 1.1 - - - -
4027C TRP* 5.2 0.7 - - - +
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Residues in contact with THR3950 (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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3946C PHE 3.9 6.7 + - - +
3947C GLY* 3.5 23.8 - - - +
3949C ALA* 1.3 78.5 - - - +
3951C GLN* 1.3 62.0 - - - +
3952C PHE 2.8 3.6 + - - -
3955C VAL* 2.6 22.0 - - - +
3956C PRO* 2.9 16.3 - - - +
3957C GLU* 2.3 53.7 + - - +
4061C CYS* 5.3 13.0 - - + -
4064C LEU* 6.4 0.2 - - + -
4065C LEU* 5.4 8.6 - - + +
4074C PHE* 4.5 1.3 - - - -
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Residues in contact with GLN3951 (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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3947C GLY 2.5 30.0 + - - +
3948C SER* 2.7 15.1 + - - +
3950C THR* 1.3 73.9 - - + +
3952C PHE* 1.3 59.1 + - + +
4030C GLU* 4.1 0.2 - - - +
4038C TRP* 4.5 12.9 - - - +
4064C LEU* 2.4 52.3 + - - +
4065C LEU* 3.6 14.1 - - - +
4067C GLY* 4.3 1.4 - - - -
4068C HIS* 2.7 64.8 + - + +
4074C PHE* 4.6 0.4 - - - -
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Residues in contact with PHE3952 (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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3948C SER* 2.9 29.4 - - - -
3949C ALA* 2.8 34.7 + - - +
3950C THR 2.8 3.4 + - - +
3951C GLN* 1.3 76.9 - - + +
3953C LEU* 1.3 57.5 + - - +
3954C PRO* 3.9 3.4 - - + -
3955C VAL* 2.7 45.5 + - + +
3956C PRO* 2.9 3.8 - - - +
4020C MET* 3.4 26.9 - - + -
4027C TRP* 3.3 40.2 - + - -
4030C GLU* 3.0 37.7 - - + +
4031C ILE* 5.5 1.3 - - + -
4034C ALA* 4.8 11.2 - - + -
4035C GLU* 6.5 0.9 - - + -
4068C HIS* 4.5 0.2 - - - -
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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