Contacts of the helix formed by residues 5268 - 5272 (chain b) in PDB entry 3A0B
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 THR5268 (chain b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5253b MET 5.9 0.2 - - - -
5254b TRP 4.2 8.4 + - - -
5255b TYR 5.2 0.4 - - - -
5256b GLY 4.7 5.6 + - - -
5262b ILE* 4.5 0.6 - - - +
5267b PRO* 1.3 74.6 - - - +
5269b ARG* 1.3 67.6 + - - +
5270b TYR* 2.9 29.3 + - - +
5271b GLN* 2.8 59.2 + - + +
5315b ASN* 3.5 6.9 + - - -
5445b ARG* 4.1 8.1 - - - +
5062h TRP* 3.3 30.9 - - + +
6058h DGD 4.3 3.3 + - - +
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Residues in contact with ARG5269 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5254b TRP* 3.8 34.8 + - + +
5267b PRO 3.7 3.0 + - - -
5268b THR* 1.3 71.2 + - - +
5270b TYR* 1.3 72.7 + - + +
5271b GLN 2.8 7.3 + - - -
5272b TRP* 3.3 4.0 + - - +
5273b ASP* 2.5 56.9 + - - +
5315b ASN* 3.1 22.1 + - - +
5316b PRO* 3.8 10.8 - - + +
5317b ALA* 3.7 20.5 - - + +
5358b ALA* 3.0 34.8 - - - +
5359b PHE* 3.9 12.5 - - - -
5163d GLY 3.8 3.2 + - - -
5164d GLN* 2.9 43.6 - - - +
5165d SER* 4.0 10.7 + - - -
5292d ASN* 4.4 3.6 - - - +
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Residues in contact with TYR5270 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5254b TRP* 2.8 45.4 + + - -
5255b TYR* 3.3 27.8 - + - -
5268b THR* 2.9 11.3 + - - +
5269b ARG* 1.3 97.5 - - - +
5271b GLN* 1.3 52.5 + - - -
5272b TRP 3.4 0.9 - - - -
5273b ASP* 2.7 20.0 - - + -
5274b SER* 3.1 16.3 - - - +
5087d HIS* 4.2 2.2 + - - -
5162d LEU 3.1 12.1 + - - -
5164d GLN 2.5 30.2 + - - -
5165d SER* 4.2 9.2 - - - -
6058h DGD 2.6 59.0 + - - +
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Residues in contact with GLN5271 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5168b PRO 5.0 1.0 + - - -
5262b ILE* 3.6 20.4 - - - +
5267b PRO* 4.8 0.4 - - + -
5268b THR* 2.8 40.6 + - + +
5270b TYR* 1.3 73.9 - - - +
5272b TRP* 1.3 59.9 + - - +
5274b SER 4.0 1.1 - - - -
5275b SER 3.9 0.7 - - - -
5276b TYR* 3.1 72.5 + - + +
5277b PHE* 3.4 42.2 + - + -
5310b ASP* 5.6 0.3 - - - +
5062h TRP* 3.0 32.6 - - - +
6058h DGD 3.8 3.0 + - - -
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Residues in contact with TRP5272 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5268b THR 4.0 0.2 + - - -
5269b ARG 3.7 0.4 - - - +
5271b GLN* 1.3 78.3 - - - +
5273b ASP* 1.3 66.5 + - - +
5274b SER 3.2 1.1 - - - -
5275b SER* 2.9 22.3 + - - +
5277b PHE* 5.3 3.6 - + + -
5309b TYR 5.4 1.3 - - - +
5310b ASP* 3.4 35.9 - - - -
5311b TYR 4.7 4.9 - - - +
5312b ILE* 3.5 28.7 - - + +
5315b ASN* 3.3 40.6 - - + +
5355b ARG* 3.6 33.0 - - + -
5356b MET 3.3 26.9 + - - -
5357b PRO* 4.5 4.7 - - + +
5358b ALA 4.6 7.2 - - - +
5422b ILE 4.1 8.1 - - - -
5423b PHE 3.7 17.5 - - - -
5424b GLY* 3.8 9.9 - - - -
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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