Contacts of the strand formed by residues 129 - 135 (chain 3) in PDB entry 3EPD
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 LYS 129 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1283 GLY* 1.3 72.2 - - - +
1303 ILE* 1.3 66.5 + - - +
1553 ILE* 4.7 8.3 - - + -
1563 TRP 3.2 9.9 - - - +
1573 ASP* 2.9 43.6 + - + +
1943 TYR* 3.9 3.1 - - - +
1953 GLN* 2.8 37.1 + - + -
1963 THR* 3.3 37.1 + - + +
1973 ARG 4.3 1.1 + - - -
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Residues in contact with ILE 130 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723 LEU* 4.1 30.7 - - + -
823 ILE* 4.5 2.9 - - + -
1283 GLY 5.2 0.2 - - - -
1293 LYS* 1.3 77.5 - - - +
1313 LEU* 1.3 63.4 + - - +
1323 VAL* 4.0 1.3 + - + +
1543 VAL 3.7 0.5 - - - +
1553 ILE* 3.4 2.4 - - - +
1563 TRP* 2.8 65.1 + - + +
1583 LEU* 4.4 13.0 - - + -
1923 MET* 3.6 34.8 - - + -
1933 PHE 3.7 7.4 - - - +
1943 TYR* 4.4 15.5 - - + -
1953 GLN* 4.0 4.0 - - - +
1983 ILE* 4.7 8.3 - - + -
2103 MET* 5.1 1.6 - - - -
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Residues in contact with LEU 131 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1303 ILE* 1.3 72.1 - - - +
1323 VAL* 1.3 60.4 + - - +
1333 ALA* 4.0 23.3 - - + -
1453 ARG* 4.0 16.4 - - + -
1483 ALA* 4.2 16.2 - - + -
1493 MET* 3.9 20.0 - - + +
1533 HIS* 3.9 30.3 - - + +
1543 VAL 3.5 3.6 - - - -
1553 ILE* 4.1 10.3 - - + +
1923 MET* 3.3 5.2 - - - +
1933 PHE* 2.9 37.2 + - + +
1953 GLN* 3.4 28.8 - - + +
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Residues in contact with VAL 132 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1183 PHE* 3.7 31.6 - - + -
1303 ILE* 5.1 4.0 - - + +
1313 LEU* 1.3 74.1 - - - +
1333 ALA* 1.3 60.3 + - - +
1533 HIS* 3.2 3.3 - - - +
1543 VAL* 2.9 50.4 + - + +
1563 TRP* 5.3 9.4 - - + -
1643 CYS* 5.3 4.7 - - + -
1663 MET* 3.7 28.4 - - + +
1903 ILE* 4.9 4.0 - - + -
1913 SER 3.7 8.3 - - - +
1923 MET* 3.9 20.6 - - + +
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Residues in contact with ALA 133 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313 LEU* 4.0 10.1 - - + -
1323 VAL* 1.3 75.0 - - - +
1343 TYR* 1.3 62.3 + - - +
1353 ALA 4.3 0.2 - - - -
1423 PRO* 6.4 0.2 - - + -
1483 ALA* 3.6 23.6 - - + +
1523 THR 3.2 11.0 - - - +
1533 HIS* 3.9 5.8 - - + -
1663 MET* 3.9 5.5 - - - +
1893 TYR 4.4 0.2 - - - -
1903 ILE* 3.3 11.3 - - - +
1913 SER* 2.9 44.6 + - - +
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Residues in contact with TYR 134 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873 LEU* 3.8 10.3 - - + +
1333 ALA* 1.3 74.9 - - - +
1353 ALA* 1.3 67.1 + - - +
1363 PRO* 3.5 31.2 - - + +
1373 PRO* 4.4 0.2 - - - +
1513 GLY* 3.7 1.4 - - - -
1523 THR* 2.8 46.7 + - + +
1663 MET* 4.1 6.7 - - + -
1683 VAL* 3.7 43.1 - - + -
1693 PRO* 4.1 25.4 + - + -
1713 ILE* 4.2 20.3 + - + -
1773 ARG* 4.6 1.9 + - - -
1873 GLY 2.7 29.2 + - - -
1883 GLY 4.4 0.2 - - - -
1893 TYR 3.3 12.6 - - - -
1903 ILE* 4.2 8.7 - - + -
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Residues in contact with ALA 135 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2632 ARG* 4.2 13.9 - - + -
2642 ASN* 4.4 5.4 - - - +
1343 TYR* 1.3 73.7 - - - +
1363 PRO* 1.3 72.9 - - - +
1403 GLN 5.9 0.2 - - - +
1423 PRO* 4.1 25.4 - - + -
1483 ALA* 6.2 0.4 - - - +
1513 GLY* 5.0 2.2 - - - -
1883 GLY* 3.2 2.3 - - - -
1893 TYR* 2.8 45.9 + - + +
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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