Contacts of the helix formed by residues 5054 - 5059 (chain b) 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 PRO5054 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5045b PHE* 6.0 0.4 - - + -
5049b ASP 3.6 3.3 - - - +
5050b PRO* 4.1 19.1 - - + +
5051b VAL 4.0 8.7 - - - +
5052b LEU 3.3 8.3 - - - +
5053b ASN* 1.3 96.0 - - - +
5055b MET* 1.3 68.9 + - + +
5056b TRP* 3.1 45.1 - - + +
5057b ARG* 2.9 25.8 + - + +
5058b GLN* 3.8 3.4 + - - -
5266b GLU* 4.9 4.5 - - - +
5308b LYS* 6.0 2.5 - - - -
5311b PHE* 4.5 2.2 - - + -
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Residues in contact with MET5055 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5045b PHE* 3.7 26.9 - - + -
5053b ASN 3.9 0.2 + - - -
5054b PRO* 1.3 71.1 - - + +
5056b TRP* 1.3 63.4 + - - +
5058b GLN* 3.1 12.3 + - - +
5060b MET* 3.2 32.0 + - + +
5063b LEU* 3.7 23.1 - - + +
5064b PRO* 3.8 21.8 - - + -
5067b ALA* 4.3 7.9 - - + -
5080b ILE* 3.2 43.1 - - + -
5093b PHE* 5.2 0.2 - - + -
5266b GLU 4.1 10.8 - - - +
5267b LEU* 3.6 31.6 - - + +
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Residues in contact with TRP5056 (chain b).
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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5054b PRO* 3.1 31.8 - - + +
5055b MET* 1.3 76.2 - - - +
5057b ARG* 1.3 68.7 + - + +
5058b GLN 3.2 0.4 - - - -
5059b GLY 3.8 4.9 + - - -
5060b MET 5.0 0.9 - - - -
5265b ILE 3.9 8.4 + - - -
5266b GLU* 3.6 24.3 + - - +
5267b LEU 4.0 9.2 - - - +
5268b PHE 3.8 8.3 - - - -
5269b GLY* 3.7 29.8 - - - +
5270b PRO* 3.6 17.5 - - + -
5311b PHE* 4.4 9.2 - + - -
5312b TYR* 3.9 22.8 + + - -
5317b ASN* 3.0 43.7 - - + -
5330b MET* 4.0 19.1 - - - +
5446b SER* 4.7 1.1 - - - -
5447b PRO* 3.5 30.7 - - + +
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Residues in contact with ARG5057 (chain b).
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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5052b LEU 4.3 5.9 + - - +
5053b ASN* 4.0 5.4 - - - +
5054b PRO* 2.9 35.5 + - + +
5056b TRP* 1.3 86.5 - - + +
5058b GLN* 1.3 57.5 - - - +
5059b GLY 3.3 1.1 - - - -
5311b PHE* 4.0 17.8 - - + -
5314b TYR* 4.4 1.8 - - - -
5316b GLY 3.7 15.4 + - - -
5317b ASN* 2.8 40.0 + - - +
5329b PRO* 3.3 0.7 - - - +
5330b MET* 2.9 43.8 + - - +
5331b ASN* 3.2 30.3 + - - +
5334b ASP* 2.7 32.9 + - - -
5335b GLY 3.0 18.0 + - - -
5337b ALA* 4.6 1.8 - - - +
5432b PHE* 4.2 6.4 - - - -
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Residues in contact with GLN5058 (chain b).
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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5044b THR 4.0 3.6 - - - +
5045b PHE* 3.4 20.9 - - - -
5046b ASP* 2.8 48.9 + - - +
5053b ASN* 3.1 39.5 + - - +
5054b PRO 3.8 5.7 + - - +
5055b MET 3.1 6.6 + - - +
5057b ARG* 1.3 79.0 - - - +
5059b GLY* 1.3 63.1 + - - +
5060b MET* 3.0 17.4 - - + +
5329b PRO* 3.2 11.9 - - - -
5331b ASN* 3.9 9.4 - - - +
5517b CLA 2.9 13.7 - - - +
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Residues in contact with GLY5059 (chain b).
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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5041b GLU* 4.3 1.2 - - - +
5056b TRP 3.8 7.6 + - - -
5057b ARG 3.3 3.6 + - - -
5058b GLN* 1.3 77.3 - - - +
5060b MET* 1.3 63.2 + - - +
5061b PHE* 3.6 1.6 + - - +
5329b PRO* 3.2 14.0 - - - +
5330b MET 5.0 0.2 - - - -
5447b PRO* 4.7 2.5 - - - -
5517b CLA 3.1 55.2 - - - +
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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