Contacts of the strand formed by residues 5236 - 5246 (chain o) 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 GLU5236 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5047o THR 5.0 0.2 - - - +
5048o LEU* 3.0 39.3 - - + +
5230o VAL* 5.6 0.4 - - - +
5231o ASP* 3.3 22.8 + - + +
5234o THR* 2.8 38.1 + - - +
5235o GLY* 1.3 77.5 - - - +
5237o ILE* 1.3 63.3 + - - +
5266o TYR* 3.0 35.5 + - + +
5267o ALA 3.3 6.5 - - - +
5268o SER* 4.4 3.6 - - - -
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Residues in contact with ILE5237 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5048o LEU* 4.0 0.9 - - - -
5056o TYR* 5.4 1.8 - - + -
5066o ILE* 6.4 0.7 - - + -
5162o ILE* 3.9 22.9 - - + -
5168o PHE* 4.1 18.2 - - + -
5227o VAL* 3.7 26.9 - - + -
5229o LYS 3.2 9.6 - - - +
5230o VAL* 4.1 17.5 - - + -
5235o GLY 5.4 1.1 - - - -
5236o GLU* 1.3 78.8 - - - +
5238o ALA* 1.3 63.0 + - - +
5265o PHE* 4.1 8.7 - - + -
5266o TYR* 3.6 3.8 - - - -
5267o ALA* 3.0 52.1 + - + +
5269o ILE* 4.3 23.3 - - + -
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Residues in contact with ALA5238 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5046o PRO 5.2 4.0 - - - +
5047o THR* 5.7 0.7 - - - -
5048o LEU* 3.7 28.0 - - + +
5227o VAL* 3.5 5.2 - - - +
5228o ALA* 2.6 29.4 + - - -
5229o LYS* 2.9 19.0 + - + -
5237o ILE* 1.3 76.2 - - - +
5239o GLY* 1.3 53.4 + - - +
5264o VAL* 6.1 1.8 - - + -
5265o PHE* 3.3 18.8 - - - +
5266o TYR* 4.7 5.4 - - + -
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Residues in contact with GLY5239 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5226o ASN 3.5 10.3 - - - -
5228o ALA* 3.6 14.1 - - - -
5238o ALA* 1.3 78.2 - - - +
5240o THR* 1.3 63.7 + - - +
5264o VAL* 3.1 14.5 - - - +
5265o PHE* 3.0 33.9 + - - -
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Residues in contact with THR5240 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5224o SER 4.1 0.2 - - - +
5226o ASN* 3.0 38.8 + - - +
5228o ALA* 5.1 7.9 - - + -
5239o GLY* 1.3 78.5 - - - +
5241o PHE* 1.3 62.4 + - - +
5263o GLY 3.5 13.2 - - - +
5264o VAL* 5.4 4.5 - - + -
5265o PHE* 3.5 5.8 - - - -
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Residues in contact with PHE5241 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5071o LEU* 3.5 26.5 - - + -
5072o GLN 3.5 12.8 - - - -
5073o PRO* 4.2 0.9 - - + -
5146o PHE* 3.7 27.4 - + - -
5223o ILE* 4.2 9.0 - - + -
5224o SER 3.6 11.0 - - - +
5225o LEU* 4.2 13.2 - - + -
5240o THR* 1.3 78.4 - - - +
5242o GLU* 1.3 72.2 + - - +
5243o SER* 4.1 6.1 - - - -
5261o ILE* 3.5 28.5 - - + -
5262o GLN* 3.6 3.8 - - - +
5263o GLY* 3.2 41.5 + - - +
5264o VAL 3.4 35.4 - - - -
5265o PHE* 4.3 1.3 - - + -
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Residues in contact with GLU5242 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5223o ILE* 3.2 20.6 - - - -
5224o SER* 3.2 18.6 + - - +
5241o PHE* 1.3 76.6 - - - +
5243o SER* 1.3 63.1 + - - +
5260o LYS* 3.7 35.0 + - + +
5261o ILE 3.2 11.2 - - - +
5262o GLN* 3.3 26.6 - - + +
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Residues in contact with SER5243 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5146o PHE* 4.0 12.7 - - - -
5148o VAL* 5.9 1.3 - - - -
5172o PHE* 4.3 11.6 - - - -
5222o GLN 2.9 14.4 - - - -
5223o ILE* 3.2 21.3 - - - -
5241o PHE* 4.1 1.8 - - - -
5242o GLU* 1.3 72.5 - - - +
5244o GLU* 1.3 61.4 + - - +
5245o GLN* 4.8 2.3 + - - -
5260o LYS* 3.3 6.4 - - - +
5261o ILE* 2.8 52.4 + - - +
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Residues in contact with GLU5244 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5091o PHE* 3.5 20.2 - - + -
5172o PHE* 4.5 0.3 - - - -
5220o LYS 4.9 0.2 - - - +
5221o GLY* 3.6 2.3 - - - -
5222o GLN* 2.8 33.5 + - + +
5243o SER* 1.3 76.2 - - - +
5245o GLN* 1.3 65.8 + - - +
5258o GLU* 3.2 23.3 - - - +
5259o VAL 3.1 20.2 - - - +
5260o LYS* 3.6 20.3 + - + -
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Residues in contact with GLN5245 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5144o LEU* 4.5 3.1 - - + +
5145o LEU 3.0 35.7 + - - +
5146o PHE* 3.7 13.6 - - - +
5147o THR 3.5 25.5 + - - +
5172o PHE* 4.2 6.7 - - + -
5174o VAL* 3.9 27.6 - - + +
5220o LYS 5.0 2.7 - - - -
5221o GLY* 4.6 3.6 - - - -
5243o SER* 4.8 1.7 + - - -
5244o GLU* 1.3 78.2 - - - +
5246o LEU* 1.3 77.2 + - - +
5258o GLU* 3.8 4.5 - - - +
5259o VAL* 2.9 34.9 + - + +
5261o ILE* 4.2 16.8 - - + +
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Residues in contact with LEU5246 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5144o LEU* 4.3 2.8 - - - +
5145o LEU 4.7 1.2 + - - -
5174o VAL* 4.5 11.1 - - + +
5219o THR* 4.2 34.5 + - + +
5220o LYS 5.5 2.8 + - - +
5245o GLN* 1.3 97.5 + - - +
5247o SER* 1.3 67.1 + - - +
5256o PRO* 4.0 26.7 - - + +
5257o HIS 3.6 14.8 - - - +
5258o GLU* 3.9 22.4 - - + -
5259o VAL* 4.8 2.5 - - - -
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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