Contacts of the helix formed by residues 2873 - 2878 (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 PRO2873 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2870C SER 3.6 5.8 - - - +
2871C LEU 2.9 21.8 - - - +
2872C ASP* 1.3 106.2 - - - +
2874C ALA* 1.3 62.2 + - - +
2876C VAL* 3.4 28.9 - - + -
2877C SER* 2.7 8.5 + - - -
2913C LYS* 6.3 2.9 - - + -
2917C PRO* 4.6 14.6 - - + -
2920C VAL* 6.1 0.7 - - + -
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Residues in contact with ALA2874 (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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2873C PRO* 1.3 72.7 - - - +
2875C ALA* 1.3 58.5 + - - +
2876C VAL 2.8 2.9 - - - -
2877C SER* 2.4 37.7 + - - -
2878C ALA 3.2 4.2 + - - +
2917C PRO* 3.2 31.3 - - - +
2920C VAL* 3.4 21.3 - - + +
2921C LEU* 3.5 26.0 - - + +
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Residues in contact with ALA2875 (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* 5.2 6.4 - - - -
2874C ALA* 1.3 79.3 - - - +
2876C VAL* 1.3 60.3 + - + +
2878C ALA* 2.8 33.6 - - - +
2879C GLY* 3.4 15.7 + - - -
2920C VAL* 4.3 11.6 - - + +
3034C PRO* 5.9 8.5 - - + -
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Residues in contact with VAL2876 (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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2841C ASN 4.6 4.0 - - - +
2844C LEU* 3.1 45.0 - - + +
2845C ASN* 5.2 4.9 - - + +
2848C PHE* 5.4 5.2 - - - -
2871C LEU 4.3 1.8 - - - +
2872C ASP* 2.8 13.2 - - - +
2873C PRO* 3.0 47.8 - - + +
2874C ALA 2.8 0.8 - - - -
2875C ALA* 1.3 76.2 - - + +
2877C SER* 1.3 65.2 + - - +
2878C ALA* 4.3 0.3 - - - -
3033C GLU* 6.5 1.3 - - + -
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Residues in contact with SER2877 (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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2844C LEU* 3.7 5.5 - - - +
2854C PHE* 5.2 1.0 - - - -
2857C CYS* 3.4 33.4 - - - +
2872C ASP* 2.5 28.5 + - - -
2873C PRO 3.9 1.1 - - - -
2874C ALA* 2.4 22.8 + - - -
2876C VAL* 1.3 73.7 - - - +
2878C ALA* 1.3 64.1 + - - +
2882C ALA* 4.4 9.9 - - - +
2885C GLN* 4.8 10.0 + - - +
2886C GLN* 5.6 6.3 - - - -
2921C LEU* 6.5 0.4 - - - -
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Residues in contact with ALA2878 (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* 6.0 5.4 - - + -
2854C PHE* 3.6 17.5 - - + -
2874C ALA 3.3 2.4 - - - +
2875C ALA* 2.8 25.0 - - - -
2876C VAL 4.3 0.2 - - - -
2877C SER* 1.3 82.5 + - - +
2879C GLY* 1.3 69.4 + - - +
2881C LEU 3.4 11.0 - - - +
2882C ALA* 3.3 25.9 - - + +
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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