Contacts of the helix formed by residues 5353 - 5359 (chain c) in PDB entry 2AXT
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 GLY5353 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5336a ALA 4.5 6.3 - - - -
5338a ASN* 3.8 27.1 - - - +
5339a PHE* 4.9 3.4 - - - -
5342c MET* 3.2 11.2 - - - +
5352c GLY* 1.3 70.7 - - - -
5354c GLU* 1.3 64.1 + - - -
5355c THR* 2.8 8.5 + - - -
5356c MET* 2.9 26.4 + - - +
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Residues in contact with GLU5354 (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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5087a ASN* 3.4 13.8 + - - +
5333a GLU* 3.3 3.4 - - - +
5336a ALA* 3.7 28.0 + - + +
5337a HIS* 3.1 19.8 + - + +
5342a ASP* 3.1 5.9 - - - +
5343a LEU 5.4 0.2 + - - -
5344a ALA* 2.3 23.8 + - + +
5565a OEC 2.1 54.8 + - - -
5353c GLY* 1.3 70.2 - - - -
5355c THR* 1.3 58.2 + - - +
5356c MET* 2.8 10.9 + - - -
5357c ARG* 3.2 28.2 + - - +
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Residues in contact with THR5355 (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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5339a PHE* 5.1 4.5 - - - -
5310c SER* 3.2 46.3 + - - +
5311c GLN* 2.8 34.4 - - - +
5314c ALA* 4.6 5.1 - - + +
5351c PHE* 4.2 10.1 - - + +
5352c GLY 3.4 17.5 + - - -
5353c GLY* 2.8 1.8 + - - -
5354c GLU* 1.3 72.5 + - - +
5356c MET* 1.3 55.4 + - - +
5357c ARG 2.9 6.3 - - - -
5358c PHE* 2.8 29.8 + - + -
5359c TRP* 3.7 4.7 + - - -
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Residues in contact with MET5356 (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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5062a GLY* 3.3 44.0 - - - +
5063a ILE* 4.2 3.8 - - + +
5087a ASN* 3.2 22.2 - - - +
5088a ALA* 4.1 21.8 - - - +
5337c LEU* 3.8 10.1 - - + -
5342c MET* 3.5 43.1 - - + +
5350c ILE* 3.8 17.0 - - + +
5351c PHE 4.0 2.8 + - - -
5353c GLY 2.9 17.0 + - - +
5354c GLU* 2.8 1.8 + - - -
5355c THR* 1.3 76.9 - - - +
5357c ARG* 1.3 56.8 + - - +
5359c TRP* 3.3 25.8 - - - -
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Residues in contact with ARG5357 (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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5087a ASN* 2.5 47.0 + - - +
5088a ALA 5.6 0.4 - - - -
5089a ILE 5.9 0.2 - - - -
5090a GLY* 4.5 5.7 - - - -
5091a LEU 5.4 0.9 + - - -
5092a HIS* 5.6 1.7 - - - -
5165a GLN* 2.8 23.7 + - - +
5166a GLY 4.1 17.7 - - - +
5167a SER* 3.9 7.9 - - - +
5169a SER* 3.5 7.7 + - - -
5170a ASP* 3.1 31.1 + - - -
5344a ALA* 3.5 19.2 + - - -
5565a OEC 4.4 0.8 + - - -
5354c GLU* 3.2 28.8 + - - +
5355c THR 2.9 0.4 - - - -
5356c MET* 1.3 80.8 - - - +
5358c PHE* 1.3 93.5 + - + +
5359c TRP* 3.3 8.2 + - - -
5360c ASP* 3.9 12.1 - - - +
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Residues in contact with PHE5358 (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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5164a GLY 5.4 1.3 - - - -
5165a GLN 3.4 28.0 - - - -
5166a GLY* 3.8 11.2 - - - -
5343a LEU 3.8 3.6 - - - -
5344a ALA* 3.5 18.8 - - + -
5292c PHE* 6.2 0.2 - + - -
5306c GLY 4.9 1.8 - - - -
5307c PRO* 3.4 45.3 - - + +
5310c SER* 3.3 40.2 - - - -
5311c GLN* 3.6 13.2 - - - +
5355c THR* 2.8 13.3 + - + +
5357c ARG* 1.3 99.5 - - + +
5359c TRP* 1.3 55.3 + - - +
5360c ASP* 2.7 14.3 + - - +
5361c PHE* 3.0 17.5 + - - +
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Residues in contact with TRP5359 (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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5088a ALA 4.6 5.7 + - - -
5092a HIS* 3.6 36.4 + + - -
5311c GLN* 4.6 8.1 - - - +
5344c SER* 3.6 20.0 - - - -
5345c PRO* 4.4 10.8 - - + +
5346c THR* 3.6 15.3 - - + -
5348c GLU* 3.2 31.2 - - + -
5350c ILE* 3.5 43.9 - - + +
5351c PHE 5.8 0.4 - - - +
5355c THR 3.7 3.2 + - - +
5356c MET 3.3 18.6 - - - +
5357c ARG* 3.3 5.7 - - - -
5358c PHE* 1.3 74.9 - - - +
5360c ASP* 1.3 68.0 + - - +
5361c PHE 3.5 3.2 - - - +
5362c ARG* 5.5 1.7 - - - -
5370c ARG* 5.3 3.5 + - - -
5033o TYR* 3.3 27.2 + - - -
5037o VAL* 4.3 13.2 - - + -
5038o GLY* 4.8 0.9 - - - -
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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