Contacts of the helix formed by residues 5232 - 5237 (chain a) 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 SER5232 (chain a).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5227a THR* 3.5 12.3 - - - +
5231a GLU* 1.3 76.6 - - - +
5233a ALA* 1.3 62.3 + - - +
5234a ASN 3.3 2.6 + - - -
5235a TYR* 2.6 45.2 + - - +
5002b GLY 4.7 2.0 + - - -
5004b PRO* 4.1 15.3 - - - +
5006b TYR* 5.1 0.4 - - - -
5007b ARG* 4.5 4.5 - - - +
5011l GLU* 4.7 3.6 + - - -
5210l MGE 2.9 38.8 - - - -
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Residues in contact with ALA5233 (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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5223a LEU* 4.4 14.8 - - + -
5227a THR* 4.0 12.2 - - - +
5231a GLU 3.6 0.8 + - - -
5232a SER* 1.3 74.5 - - - +
5234a ASN* 1.3 64.6 + - - +
5236a GLY 3.1 11.1 + - - -
5007b ARG* 4.8 1.0 - - - +
5479b PHE 5.5 1.1 - - - +
5480b SER* 5.6 5.2 - - - +
5139d ARG* 4.2 22.7 - - - +
5265d ARG* 3.3 22.1 + - - +
5360d MGE 4.3 21.2 + - - +
5210l MGE 4.1 2.2 + - - -
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Residues in contact with ASN5234 (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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5223a LEU* 5.8 0.7 - - - +
5232a SER* 4.3 1.1 - - - -
5233a ALA* 1.3 78.1 - - - +
5235a TYR* 1.3 67.9 + - + +
5236a GLY 3.0 3.1 + - - -
5237a TYR* 3.1 13.3 + - - +
5263d ASN* 3.2 24.3 + - - +
5265d ARG* 3.9 21.4 - - - +
5266d TRP* 3.2 36.9 - - - +
5269d PHE* 5.3 0.3 - - - +
5360d MGE 3.7 11.1 + - - +
5361d MGE 4.7 3.4 + - - -
5210l MGE 2.9 45.3 + - - +
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Residues in contact with TYR5235 (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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5227a THR* 4.3 5.8 - - + -
5231a GLU* 5.1 8.3 - - + +
5232a SER* 2.6 39.9 + - - +
5233a ALA 3.3 0.8 - - - -
5234a ASN* 1.3 79.6 - - + +
5236a GLY* 1.3 57.2 + - - +
5237a TYR 2.9 16.7 + - - +
5238a LYS* 5.0 4.5 - - - +
5263d ASN* 5.3 0.2 - - - +
5011l GLU* 2.5 38.0 + - - -
5013l ASN* 5.0 10.7 - - - +
5210l MGE 4.4 10.1 - - - -
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Residues in contact with GLY5236 (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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5226a GLU* 3.1 29.6 - - - +
5227a THR* 3.5 15.0 - - - +
5233a ALA 3.1 4.4 + - - -
5234a ASN 3.0 3.0 - - - -
5235a TYR* 1.3 77.0 - - - +
5237a TYR* 1.3 56.7 + - - +
5241a GLN* 4.1 6.9 + - - +
5245a THR* 4.2 1.4 + - - -
5265d ARG* 3.4 27.3 + - - -
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Residues in contact with TYR5237 (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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5234a ASN 3.1 13.9 + - - +
5235a TYR* 2.9 12.2 - - - +
5236a GLY* 1.3 80.2 - - - +
5238a LYS* 1.3 92.9 + - - +
5239a PHE* 3.6 8.3 - - - -
5240a GLY* 3.4 11.3 + - - -
5241a GLN* 3.4 33.1 + - + +
5245a THR* 3.5 21.8 - - + +
5242d GLU* 4.2 3.1 + - - -
5246d MET* 3.4 27.9 - - + +
5262d SER 4.6 0.7 - - - -
5263d ASN* 3.7 35.6 + - + +
5264d LYS* 3.5 32.5 - - + -
5265d ARG* 4.0 12.5 - - + +
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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