Contacts of the helix formed by residues 5167 - 5171 (chain a) 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 SER5167 (chain a).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5085a SER* 4.1 1.6 + - - -
5087a ASN 4.4 0.4 - - - -
5089a ILE 3.4 5.9 + - - -
5090a GLY* 2.7 28.8 - - - -
5091a LEU* 2.3 33.0 + - - -
5162a PRO* 4.4 7.4 - - - +
5165a GLN* 3.7 2.3 - - - +
5166a GLY* 1.3 75.1 + - - +
5168a PHE* 1.3 62.2 + - - +
5169a SER* 2.4 24.8 + - - -
5170a ASP* 3.3 11.8 + - - +
5357c ARG* 3.4 20.8 - - - +
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Residues in contact with PHE5168 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5084a PRO* 4.0 8.3 - - - +
5085a SER* 2.7 22.1 + - - +
5089a ILE 5.3 0.7 - - - -
5091a LEU* 3.3 38.4 - - + +
5092a HIS 3.8 0.9 - - - -
5112a TYR* 5.1 15.6 + + + -
5113a GLN* 3.6 24.9 - - + -
5116a ILE* 5.5 0.2 - - + -
5117a PHE* 3.3 40.4 - + - -
5158a PHE 4.4 11.7 - - - -
5159a LEU* 4.7 9.4 - - + -
5162a PRO* 4.0 26.5 - - + -
5167a SER* 1.3 77.1 + - - +
5169a SER* 1.3 55.2 + - - -
5170a ASP 2.8 9.3 + - - -
5171a GLY* 3.0 15.4 + - - -
5218c PHE* 4.4 16.4 - + - -
6055c DGD 5.5 0.9 - - - -
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Residues in contact with SER5169 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5060a ILE* 4.7 9.2 - - - +
5061a ASP* 4.8 3.0 - - - +
5084a PRO* 4.1 12.4 - - - +
5085a SER* 3.3 16.6 + - - -
5086a SER 3.6 0.7 - - - -
5087a ASN* 2.8 51.9 + - - -
5167a SER* 2.4 15.9 + - - -
5168a PHE* 1.3 67.3 - - - +
5170a ASP* 1.3 70.1 + - - +
5171a GLY 3.6 0.7 + - - -
6001a OEC 4.4 6.2 + - - -
5357c ARG* 3.4 11.3 - - - -
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Residues in contact with ASP5170 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5161a TYR* 3.4 36.2 - - + +
5162a PRO* 4.7 4.6 - - + +
5165a GLN* 5.4 4.8 - - + +
5167a SER 3.3 5.4 + - - +
5168a PHE 3.0 2.8 - - - -
5169a SER* 1.3 82.6 - - - +
5171a GLY* 1.3 56.7 + - - +
5172a MET 3.8 3.0 + - - -
5173a PRO* 6.0 0.2 - - - -
5182a PHE* 4.1 8.6 - - + -
5185a VAL* 4.4 11.5 - - + +
5333a GLU* 3.9 1.0 - - - +
6001a OEC 2.5 55.4 + - - -
5357c ARG* 3.2 20.7 + - - -
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Residues in contact with GLY5171 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5084a PRO* 4.4 3.1 - - - +
5112a TYR* 2.5 26.7 + - - -
5157a VAL 3.9 10.8 - - - -
5158a PHE* 5.4 0.7 - - - -
5161a TYR* 5.6 0.2 - - - -
5162a PRO* 4.4 13.9 - - - -
5168a PHE* 3.0 13.3 + - - -
5169a SER 3.6 1.4 + - - -
5170a ASP* 1.3 77.0 - - - +
5172a MET* 1.3 69.8 + - - -
5173a PRO* 2.9 5.7 - - - +
5182a PHE* 5.0 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