Contacts of the helix formed by residues 251 - 255 (chain G) in PDB entry 4OR5
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 ARG 251 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ARG* 2.4 45.0 - - - +
26C TYR* 3.3 22.6 + - - -
40C THR* 4.9 3.0 + - - -
44C GLY* 5.7 1.4 - - - -
46C SER* 5.7 5.7 + - - -
249G PRO 3.3 12.1 + - - +
250G ASN* 1.3 73.3 - - - +
252G LEU* 1.3 66.9 + - - +
253G LYS 3.4 1.6 - - - -
254G ARG* 3.2 31.3 + - - +
255G ILE* 3.5 14.8 - - + +
26H TYR* 4.1 14.4 - - - -
40H THR 4.2 8.5 + - - -
41H LYS 3.4 25.1 - - - +
42H ALA 3.1 7.2 + - - +
44H GLY* 4.2 9.8 - - - -
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Residues in contact with LEU 252 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250G ASN* 3.9 3.1 - - - +
251G ARG* 1.3 70.9 - - - +
253G LYS* 1.3 52.2 - - - +
254G ARG 2.2 22.4 + - - -
255G ILE* 2.7 23.4 + - + +
256G TRP* 3.0 39.5 + - + +
28H LYS* 4.8 15.7 - - + +
31H CYS* 4.7 8.5 - - + -
32H PHE* 4.8 13.5 - - + -
38H PHE* 5.3 0.4 - - + -
42H ALA* 3.3 33.8 + - + +
43H LEU* 6.5 0.4 - - + -
55J MET 3.7 18.2 - - - +
56J LEU* 3.6 29.6 - - + +
62J MET* 6.1 0.9 - - - -
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Residues in contact with LYS 253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B PRO* 4.3 4.2 - - - +
115B GLN* 3.1 41.2 - - + +
246G GLU* 5.2 9.7 + - - +
250G ASN* 3.2 33.8 - - + +
251G ARG 3.3 2.5 + - - +
252G LEU* 1.3 74.0 - - - +
254G ARG* 1.3 64.0 + - + +
256G TRP* 3.7 15.7 - - + +
257G ASN* 5.4 0.7 + - - -
54J SER* 3.9 27.6 - - - +
55J MET* 3.9 20.3 - - - +
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Residues in contact with ARG 254 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B LEU 5.6 2.2 + - - -
114B PRO* 4.0 34.4 - - + +
46C SER* 6.3 1.4 - - - -
48C GLY* 3.8 34.4 + - - -
249G PRO 5.0 2.0 + - - -
250G ASN 3.5 19.7 + - - -
251G ARG* 3.4 21.7 - - - +
252G LEU 2.2 17.1 + - - -
253G LYS* 1.3 75.7 - - - +
255G ILE* 1.3 61.8 + - + +
256G TRP* 3.5 1.6 - - - -
257G ASN* 5.0 6.8 - - - +
258G TRP* 4.8 11.4 - - - -
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Residues in contact with ILE 255 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ASN* 3.0 29.4 - - - +
26C TYR* 6.0 1.3 - - - +
251G ARG* 3.5 37.0 - - + +
252G LEU* 2.7 10.6 + - + -
254G ARG* 1.3 77.0 - - + +
256G TRP* 1.3 55.0 + - - +
257G ASN* 2.6 19.1 + - - -
258G TRP* 3.5 21.5 + - + +
259G ARG 4.8 0.2 + - - -
26H TYR* 2.6 40.4 - - + +
27H CYS* 3.3 18.2 - - + -
28H LYS* 4.3 6.1 - - - +
31H CYS* 5.2 5.6 - - - -
41H LYS 5.3 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