Contacts of the helix formed by residues 5306 - 5313 (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 PRO5306 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5174b LEU* 4.6 9.6 - - + -
5287b ARG* 3.6 27.1 - - - +
5304b ALA 3.1 10.0 - - - +
5305b ILE* 1.3 91.5 - - + +
5307b GLU* 1.3 66.7 + - - +
5308b LYS* 4.4 6.1 - - + +
5309b LEU* 3.2 34.5 + - + +
5310b ALA 3.3 8.5 + - - -
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Residues in contact with GLU5307 (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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85O LYS* 3.1 29.4 - - - +
5051b VAL* 4.3 13.3 - - + +
5052b LEU* 4.0 18.6 - - + +
5305b ILE 3.5 1.9 + - - +
5306b PRO* 1.3 71.6 - - - +
5308b LYS* 1.3 66.3 + - - +
5310b ALA* 3.0 9.7 + - - +
5311b PHE* 2.9 23.4 + - - +
5339b ALA* 3.8 1.6 - - - +
5340b TRP* 2.8 51.3 + - + +
5404b GLY* 5.3 1.4 - - - -
5430b PHE* 4.5 1.4 - - - -
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Residues in contact with LYS5308 (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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5050b PRO* 3.5 26.4 + - - +
5051b VAL* 3.9 29.2 - - + +
5054b PRO* 6.0 2.5 - - - -
5173b GLY 3.7 20.0 - - - +
5174b LEU* 3.9 28.3 + - + +
5266b GLU* 3.3 21.7 + - - +
5306b PRO* 3.2 4.5 - - + -
5307b GLU* 1.3 80.8 - - - +
5309b LEU* 1.3 62.4 + - - +
5311b PHE* 3.3 18.6 + - - +
5312b TYR* 3.4 22.7 + - + -
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Residues in contact with LEU5309 (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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5172b TYR* 5.2 2.5 - - + -
5174b LEU* 3.7 19.5 - - + +
5280b PHE* 4.1 25.8 - - + +
5283b GLU* 4.3 13.7 - - + -
5284b ILE* 3.5 31.9 - - + -
5287b ARG* 4.0 30.5 - - - +
5305b ILE* 4.5 3.4 - - + -
5306b PRO* 3.2 30.2 + - + +
5307b GLU 3.1 0.4 - - - -
5308b LYS* 1.3 76.6 - - - +
5310b ALA* 1.3 66.6 + - - +
5312b TYR* 3.1 15.3 + - - +
5313b ASP* 3.5 6.2 + - - +
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Residues in contact with ALA5310 (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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5284b ILE* 4.1 13.0 - - + -
5305b ILE* 4.4 5.0 - - + +
5306b PRO 3.3 7.4 + - - +
5307b GLU 3.0 8.3 + - - +
5309b LEU* 1.3 79.0 - - - +
5311b PHE* 1.3 58.0 + - - +
5313b ASP* 2.8 28.9 + - - +
5340b TRP* 3.9 33.9 - - + -
5428b GLU* 3.7 14.2 - - + +
5430b PHE* 3.6 10.3 - - + -
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Residues in contact with PHE5311 (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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5051b VAL 4.0 7.6 - - - -
5052b LEU* 3.3 40.8 - - + -
5054b PRO* 4.5 1.1 - - + -
5056b TRP* 4.4 11.2 - + - -
5057b ARG* 4.0 27.6 - - + -
5307b GLU 2.9 6.7 + - - +
5308b LYS* 3.3 11.9 - - + +
5309b LEU 3.1 0.2 - - - -
5310b ALA* 1.3 77.1 - - - +
5312b TYR* 1.3 63.0 + + + +
5313b ASP 3.1 0.9 + - - -
5314b TYR* 3.2 23.1 - + - +
5317b ASN* 3.1 41.0 + - - -
5337b ALA* 3.4 30.7 - - + -
5430b PHE* 3.2 30.9 - + - -
5432b PHE* 4.5 3.6 - + - -
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Residues in contact with TYR5312 (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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5056b TRP* 3.9 22.4 + + - -
5172b TYR 3.2 13.2 - - - -
5173b GLY* 2.6 31.7 + - - -
5174b LEU* 4.4 1.1 - - + -
5265b ILE* 3.8 14.3 + - + -
5266b GLU* 3.3 18.2 - - - +
5270b PRO* 3.3 35.4 - - + +
5275b TRP* 5.3 4.2 - - - +
5280b PHE* 3.3 52.5 - + + -
5308b LYS* 3.4 29.8 + - + -
5309b LEU* 3.1 9.6 + - - +
5311b PHE* 1.3 77.3 - + + +
5313b ASP* 1.3 57.2 + - - +
5314b TYR 3.1 9.4 + - - +
5317b ASN* 4.8 3.2 - - - +
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Residues in contact with ASP5313 (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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5275b TRP* 4.3 7.4 - - - -
5278b SER* 5.5 0.9 - - - -
5280b PHE* 4.0 10.6 - - + +
5281b GLN* 3.7 21.0 + - - +
5284b ILE* 3.8 22.6 - - + +
5309b LEU 3.5 0.6 + - - +
5310b ALA 2.8 13.8 + - - +
5312b TYR* 1.3 76.9 - - - +
5314b TYR* 1.3 56.9 + - - +
5358b ARG* 2.9 42.7 + - - -
5427b GLY* 3.7 3.6 - - - -
5428b GLU* 3.0 32.6 + - + +
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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