Contacts of the helix formed by residues 5100 - 5108 (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 ASP5100 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5092d LEU* 4.1 1.6 - - - -
5097d ALA 3.3 8.9 + - - +
5098d GLN 3.2 5.3 + - - -
5099d GLY* 1.3 71.1 - - - +
5101d PHE* 1.3 62.5 + - - +
5102d THR* 2.9 16.8 + - - +
5103d ARG* 2.8 32.8 + - + +
5104d TRP* 2.9 18.7 + - - +
5073e LYS* 3.3 33.9 + - - +
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Residues in contact with PHE5101 (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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5050d THR* 6.1 0.4 - - + -
5092d LEU* 3.4 21.1 - - + -
5099d GLY 3.0 7.2 + - - +
5100d ASP* 1.3 70.3 + - - +
5102d THR* 1.3 69.7 + - - +
5104d TRP* 3.0 20.3 - + - +
5105d CYS* 3.0 45.4 + - - -
5357d BCR 3.7 31.2 - - + -
5046e VAL* 4.0 18.6 - - + -
5047e PHE* 3.6 27.6 - + - -
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Residues in contact with THR5102 (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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5100d ASP* 2.9 25.3 + - - +
5101d PHE* 1.3 76.4 - - - +
5103d ARG* 1.3 83.8 + - + +
5105d CYS* 2.7 31.8 + - - +
5106d GLN* 3.1 11.5 + - - +
5045e ASP 3.6 6.4 + - - +
5046e VAL 2.4 30.6 + - - -
5047e PHE 5.0 0.2 - - - -
5048e GLY* 3.2 17.8 + - - -
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Residues in contact with ARG5103 (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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5097d ALA* 4.8 4.7 - - - +
5100d ASP* 2.8 20.7 + - + +
5102d THR* 1.3 84.7 - - - +
5104d TRP* 1.3 59.3 + - - +
5106d GLN* 2.5 55.8 + - - +
5107d LEU* 2.8 22.3 + - + +
5073e LYS* 3.5 37.1 + - + +
5076e VAL* 4.1 13.7 - - - +
5077e GLU* 3.0 42.6 + - - +
5080e LEU* 3.8 22.4 - - - +
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Residues in contact with TRP5104 (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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5090d LEU* 2.8 28.1 + - + -
5092d LEU* 3.2 35.4 - - + +
5097d ALA* 3.6 17.4 - - + +
5100d ASP 2.9 14.7 + - - +
5101d PHE* 3.0 36.6 - + - +
5103d ARG* 1.3 76.2 - - - +
5105d CYS* 1.3 62.9 + - - +
5107d LEU* 3.6 4.5 + - - +
5108d GLY 3.4 2.3 + - - -
5109d GLY* 2.8 54.1 + - - -
5110d LEU* 4.6 10.8 - - + -
5113d PHE* 3.3 40.2 - + + -
5355d CLA 3.7 22.7 - + + -
5357d BCR 4.0 24.9 - - + -
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Residues in contact with CYS5105 (chain d).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5055d VAL* 3.4 46.6 - - + +
5056d THR 4.4 3.1 - - - +
5101d PHE* 3.0 49.1 + - - -
5102d THR* 2.7 15.2 + - - +
5104d TRP* 1.3 85.7 - - - +
5106d GLN* 1.3 56.6 + - - -
5108d GLY* 3.6 9.4 + - - -
5109d GLY 4.5 1.1 + - - +
5110d LEU* 4.2 15.7 + - - +
5047e PHE* 3.9 8.7 - - + +
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Residues in contact with GLN5106 (chain d).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5055d VAL* 5.2 1.1 - - - -
5056d THR* 5.1 9.5 - - + +
5059d TYR* 3.8 46.4 + - + +
5060d THR* 4.1 10.9 + - - +
5102d THR* 3.5 13.0 - - - +
5103d ARG* 2.5 52.7 + - - +
5105d CYS* 1.3 70.9 - - - +
5107d LEU* 1.3 65.0 + - + +
5108d GLY 3.1 5.2 + - - -
5047e PHE 4.6 2.5 - - - +
5048e GLY* 2.8 46.2 + - - +
5076e VAL* 3.5 11.2 - - + +
5080e LEU* 4.8 7.9 - - - +
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Residues in contact with LEU5107 (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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5060d THR* 4.8 3.8 - - - +
5081d PRO* 3.3 14.3 - - - +
5082d ALA 3.8 1.0 + - - -
5085d MET* 3.1 30.8 - - + +
5090d LEU* 3.9 8.1 - - + +
5096d GLU* 4.2 28.9 - - + +
5097d ALA* 4.7 3.4 - - - +
5103d ARG* 2.8 29.5 + - + +
5104d TRP* 4.4 4.9 - - + +
5106d GLN* 1.3 76.6 - - + +
5108d GLY* 1.3 59.0 + - - +
5066e VAL* 4.1 13.9 - - + -
5072e ALA* 3.5 28.7 - - + +
5073e LYS* 4.5 4.3 - - + +
5076e VAL* 3.6 31.4 - - + -
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Residues in contact with GLY5108 (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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5060d THR* 4.9 3.8 - - - -
5079d SER 4.7 8.3 - - - -
5081d PRO* 3.9 14.0 - - - +
5090d LEU* 3.4 11.9 - - - +
5104d TRP 3.4 1.2 + - - -
5105d CYS 3.6 6.7 + - - -
5106d GLN 3.1 6.0 + - - -
5107d LEU* 1.3 80.2 - - - +
5109d GLY* 1.3 66.0 + - - +
5110d LEU* 3.2 3.4 - - - -
5111d TRP* 3.1 20.8 + - - +
5112d THR 4.1 0.7 + - - -
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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