Contacts of the helix formed by residues 5278 - 5294 (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 SER5278 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5274b GLN 3.5 3.8 + - - -
5275b TRP* 3.0 15.8 + - - +
5276b ASP 3.3 2.5 + - - -
5277b SER* 1.3 78.9 - - - +
5279b TYR* 1.3 65.7 + - - +
5280b PHE 3.4 2.5 - - - -
5281b GLN* 3.5 36.5 + - - +
5282b GLN* 2.9 24.6 + - - +
5313b ASP* 5.5 0.4 - - - -
5358b ARG* 4.5 11.7 + - - +
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Residues in contact with TYR5279 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5171b PRO* 2.6 30.5 + - - +
5172b TYR* 3.2 40.6 + + - -
5274b GLN* 2.7 58.9 + - + +
5277b SER* 2.9 11.7 + - - +
5278b SER* 1.3 75.3 - - - +
5280b PHE* 1.3 73.6 + + - +
5282b GLN* 3.3 19.4 + - - +
5283b GLU* 3.5 7.6 + - - +
5062h TRP* 3.4 17.7 - + + +
5063h LYS* 4.2 13.1 - - + +
5208h DGD 4.4 21.1 - - - -
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Residues in contact with PHE5280 (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* 3.9 30.5 - + + -
5265b ILE* 4.0 10.1 - - + -
5270b PRO* 4.4 6.1 - - + -
5274b GLN* 3.6 51.2 + - + +
5275b TRP* 6.0 0.7 - - - -
5278b SER 3.4 0.2 - - - -
5279b TYR* 1.3 82.9 - + - +
5281b GLN* 1.3 63.6 + - - +
5282b GLN 3.2 0.2 + - - -
5283b GLU* 3.4 6.4 + - - +
5284b ILE* 3.1 28.5 + - - +
5309b LEU* 4.1 12.9 - - + +
5312b TYR* 3.3 61.0 - + + -
5313b ASP* 4.0 20.0 - - + +
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Residues in contact with GLN5281 (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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5278b SER* 3.2 32.1 + - - +
5280b PHE* 1.3 78.6 - - - +
5282b GLN* 1.3 70.7 + - - +
5284b ILE* 3.3 7.1 + - - +
5285b ASN* 3.1 35.8 + - - +
5313b ASP* 3.7 25.4 + - - +
5358b ARG* 3.0 33.3 + - - +
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Residues in contact with GLN5282 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5277b SER* 2.7 31.7 + - - -
5278b SER* 2.9 15.8 + - - +
5279b TYR* 3.5 11.9 - - - +
5280b PHE 3.2 0.2 - - - -
5281b GLN* 1.3 79.6 - - - +
5283b GLU* 1.3 54.9 + - - +
5285b ASN* 2.9 9.4 + - - +
5286b ARG* 2.8 34.8 + - - +
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Residues in contact with GLU5283 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5172b TYR* 3.5 59.8 + - + +
5279b TYR 3.5 1.8 + - - +
5280b PHE 3.4 7.3 + - - +
5282b GLN* 1.3 78.7 - - - +
5284b ILE* 1.3 62.1 + - - +
5286b ARG* 3.0 45.5 + - - +
5287b ARG* 3.1 35.0 + - - +
5309b LEU* 4.3 17.3 - - + -
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Residues in contact with ILE5284 (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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5280b PHE 3.1 14.6 + - - +
5281b GLN* 3.4 8.1 - - - +
5282b GLN 3.0 0.8 + - - -
5283b GLU* 1.3 73.4 - - - +
5285b ASN* 1.3 68.6 + - - +
5287b ARG* 2.9 15.1 + - - +
5288b VAL* 2.9 12.4 + - + +
5302b TRP* 3.4 35.2 - - + -
5305b ILE* 3.6 20.8 - - + +
5309b LEU* 3.5 29.6 - - + -
5310b ALA* 4.1 13.5 - - + -
5313b ASP* 3.8 31.2 - - + +
5428b GLU* 4.8 6.7 - - + +
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Residues in contact with ASN5285 (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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5281b GLN* 3.1 35.2 + - - +
5282b GLN* 2.9 12.6 + - - +
5284b ILE* 1.3 76.3 - - - +
5286b ARG* 1.3 59.9 + - - +
5287b ARG 2.8 0.9 + - - -
5288b VAL* 2.9 8.3 + - - +
5289b GLN* 2.6 45.6 + - + +
5302b TRP* 4.8 15.3 - - - -
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Residues in contact with ARG5286 (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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5282b GLN 2.8 20.9 + - - +
5283b GLU* 3.0 40.3 + - - +
5285b ASN* 1.3 73.1 - - - +
5287b ARG* 1.3 80.0 + - - +
5289b GLN* 4.4 4.7 - - - +
5290b ALA* 3.4 19.4 + - - +
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Residues in contact with ARG5287 (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* 5.8 1.4 - - - -
5174b LEU* 3.6 26.3 - - - +
5283b GLU* 3.1 37.0 + - - +
5284b ILE 2.9 7.6 + - - +
5285b ASN 2.8 0.6 + - - -
5286b ARG* 1.3 96.3 - - - +
5288b VAL* 1.3 55.4 + - - +
5290b ALA* 2.9 8.7 + - - +
5291b SER* 2.8 39.4 + - - +
5304b ALA 5.1 2.2 + - - -
5305b ILE* 4.1 18.6 - - + +
5306b PRO* 3.6 23.0 - - - +
5309b LEU* 4.0 13.5 - - - +
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Residues in contact with VAL5288 (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 2.9 16.1 + - - +
5285b ASN* 3.5 10.5 - - - +
5287b ARG* 1.3 77.4 - - - +
5289b GLN* 1.3 66.3 + - - +
5291b SER* 3.2 9.6 + - - -
5292b LEU* 3.1 35.3 + - + +
5298b LEU* 5.0 1.8 - - + -
5301b ALA* 4.1 12.2 - - + +
5302b TRP* 3.7 61.5 - - + +
5305b ILE* 3.9 12.8 - - + -
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Residues in contact with GLN5289 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5285b ASN* 2.6 31.0 + - + +
5286b ARG* 4.4 4.5 - - - +
5288b VAL* 1.3 76.9 - - - +
5290b ALA* 1.3 58.9 + - - +
5292b LEU* 3.3 34.2 - - - +
5293b ALA* 3.3 18.2 + - - +
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Residues in contact with ALA5290 (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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5286b ARG* 3.4 16.8 + - - +
5287b ARG* 2.9 11.8 + - - +
5289b GLN* 1.3 74.9 - - - +
5291b SER* 1.3 58.3 + - - +
5292b LEU 3.0 1.6 - - - -
5293b ALA* 2.6 31.7 + - - +
5294b SER* 3.0 14.4 + - - +
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Residues in contact with SER5291 (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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5287b ARG* 2.8 22.1 + - - +
5288b VAL* 3.5 9.0 - - - -
5290b ALA* 1.3 72.7 - - - +
5292b LEU* 1.3 60.6 + - - +
5294b SER* 3.2 19.9 + - - -
5296b ALA* 3.1 24.5 + - - +
5301b ALA* 3.8 28.9 + - - -
5304b ALA* 4.7 7.6 - - - +
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Residues in contact with LEU5292 (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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5288b VAL* 3.1 22.2 + - + +
5289b GLN* 3.3 38.6 - - - +
5290b ALA 3.0 0.6 - - - -
5291b SER* 1.3 72.6 - - - +
5293b ALA* 1.3 57.1 + - - +
5294b SER 3.0 1.3 - - - -
5295b GLY* 2.7 25.6 + - - -
5296b ALA 3.4 22.7 + - - +
5298b LEU* 4.2 21.8 - - + +
5301b ALA* 4.0 14.1 - - + -
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Residues in contact with ALA5293 (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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5289b GLN 3.3 8.1 + - - +
5290b ALA* 2.6 18.0 + - - +
5292b LEU* 1.3 75.5 - - - +
5294b SER* 1.3 57.0 + - - +
5295b GLY 3.0 4.0 + - - -
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Residues in contact with SER5294 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5290b ALA* 3.0 13.0 + - - +
5291b SER* 3.3 16.4 + - - -
5292b LEU 3.0 0.6 - - - -
5293b ALA* 1.3 76.4 - - - +
5295b GLY* 1.3 63.8 + - - +
5296b ALA* 5.1 1.3 - - - +
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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