Contacts of the helix formed by residues 5298 - 5308 (chain d) 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 PHE5298 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5076a ASN* 3.7 16.8 - - - -
5078a ILE* 3.8 23.6 - - + -
5079a THR* 3.5 33.0 - - + -
5193d LEU* 4.0 14.6 - - + -
5297d ASP* 1.3 79.3 - - - +
5299d ILE* 1.3 67.0 + - - +
5300d SER* 3.2 0.9 - - - +
5301d GLN* 3.1 26.2 + - + +
5302d GLU* 3.3 11.1 + - - +
5315d TYR* 2.9 22.2 + + - +
5033l SER* 3.9 15.0 - - - -
5034l TYR* 3.6 40.2 - + - -
5037l ASN* 3.4 19.1 - - - +
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Residues in contact with ILE5299 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5326b ARG* 4.5 9.9 - - + -
5440b ASP* 3.3 23.8 - - - +
5442b ILE* 3.5 28.9 - - + -
5444b ARG* 3.9 19.1 - - - +
5297d ASP* 3.9 10.7 - - - +
5298d PHE* 1.3 71.9 - - - +
5300d SER* 1.3 65.7 - - - +
5302d GLU* 2.8 19.7 + - + +
5303d ILE* 3.0 34.7 + - + +
5037l ASN* 2.9 24.0 + - + +
5002m GLU 5.5 2.2 - - - +
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Residues in contact with SER5300 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5298d PHE* 4.6 0.2 - - - +
5299d ILE* 1.3 76.2 - - - +
5301d GLN* 1.3 69.5 + - - +
5303d ILE* 4.0 1.9 + - - +
5304d ARG* 3.5 20.1 + - - +
5037l ASN* 3.0 31.8 + - - -
5001m MET* 4.0 21.0 - - - +
5002m GLU* 3.6 37.4 + - - +
5003m VAL* 4.3 10.6 - - - +
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Residues in contact with GLN5301 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5074a GLY 2.8 25.0 + - - -
5075a ASN* 4.3 8.3 - - - +
5076a ASN* 4.9 4.2 - - - +
5079a THR* 4.4 9.6 + - - +
5298d PHE* 3.4 30.5 - - + +
5299d ILE 3.0 0.8 - - - -
5300d SER* 1.3 83.5 + - - +
5302d GLU* 1.3 60.0 + - - +
5304d ARG* 3.3 5.8 + - - +
5305d ALA* 3.0 30.2 + - - +
5311d PHE* 3.4 23.4 - - + -
5313d THR* 3.4 20.3 + - - +
5315d TYR* 3.5 22.3 - - + -
5316d THR* 5.5 1.6 - - + -
5001m MET* 3.3 15.5 - - - +
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Residues in contact with GLU5302 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5442b ILE* 5.6 0.9 - - + -
5297d ASP* 4.2 14.6 - - + +
5298d PHE 3.6 11.0 - - - +
5299d ILE* 2.8 11.6 + - + +
5301d GLN* 1.3 73.6 - - - +
5303d ILE* 1.3 65.6 + - - +
5305d ALA* 3.2 3.3 + - - +
5306d ALA* 2.8 26.1 + - - +
5315d TYR* 2.8 27.0 + - - +
5316d THR* 6.2 0.4 - - - -
5319d LEU* 3.0 19.1 - - - +
5186o LYS* 2.7 29.7 - - - +
5199o ALA* 3.1 21.4 - - + +
5200o LEU* 4.1 19.9 - - + +
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Residues in contact with ILE5303 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5440b ASP* 4.6 14.1 - - + -
5299d ILE* 3.0 32.7 + - + +
5300d SER 4.2 4.0 - - - +
5302d GLU* 1.3 75.5 - - - +
5304d ARG* 1.3 64.8 + - - +
5306d ALA* 3.4 5.4 + - - +
5307d GLU* 3.3 38.7 + - - +
5002m GLU* 3.6 44.0 - - + +
5200o LEU* 4.6 15.2 - - + +
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Residues in contact with ARG5304 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5073a TYR 4.1 8.7 + - - -
5074a GLY* 4.6 2.2 - - - -
5568a LMT 3.1 26.9 + - - -
5300d SER 3.5 12.7 + - - +
5301d GLN 3.3 8.7 + - - +
5302d GLU 3.2 0.6 - - - -
5303d ILE* 1.3 80.4 - - - +
5305d ALA* 1.3 57.0 + - - +
5307d GLU* 3.2 7.8 + - - +
5308d ASP* 2.7 58.8 + - - +
5311d PHE* 3.5 46.3 - - + -
5001m MET* 3.9 25.4 - - - +
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Residues in contact with ALA5305 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5301d GLN 3.0 17.1 + - - +
5302d GLU* 3.9 2.5 - - - +
5304d ARG* 1.3 74.1 - - - +
5306d ALA* 1.3 64.0 + - - +
5308d ASP 3.5 14.9 - - - +
5309d PRO* 4.5 0.9 - - - +
5311d PHE* 4.2 22.0 - - + +
5316d THR* 4.8 7.9 - - + -
5185o PRO* 5.8 2.0 - - + +
5186o LYS* 3.8 30.8 - - + +
5188o ARG* 3.3 17.7 + - - -
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Residues in contact with ALA5306 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5302d GLU 2.8 15.9 + - - +
5303d ILE 3.7 4.7 - - - +
5304d ARG 3.1 0.2 - - - -
5305d ALA* 1.3 77.0 - - - +
5307d GLU* 1.3 64.7 + - + +
5186o LYS* 5.4 3.8 - - - -
5188o ARG* 2.9 29.1 + - - +
5197o ALA* 4.2 7.2 - - + -
5200o LEU* 3.6 26.7 - - + -
5208o LEU* 4.1 21.3 - - + +
5211o ALA* 3.9 5.4 - - - +
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Residues in contact with GLU5307 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5303d ILE* 3.3 26.8 + - + +
5304d ARG* 3.2 7.8 + - - +
5306d ALA* 1.3 84.3 - - + +
5308d ASP* 1.3 59.4 + - + +
5309d PRO* 3.2 12.0 - - - +
5207o GLU* 5.9 4.3 - - + +
5208o LEU* 4.0 20.9 - - + +
5211o ALA* 3.8 8.7 - - - +
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Residues in contact with ASP5308 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5304d ARG* 2.7 46.7 + - + +
5305d ALA* 3.5 13.4 - - - +
5307d GLU* 1.3 72.0 - - + +
5309d PRO* 1.3 63.3 - - - +
5310d GLU* 2.8 29.4 + - - +
5311d PHE* 3.4 19.9 + - + +
5185o PRO* 5.2 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