Contacts of the strand formed by residues 1362 - 1369 (chain D) in PDB entry 5YWB
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 LEU1362 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1350D LEU* 4.3 19.1 - - + -
1351D SER* 2.7 28.7 + - - -
1352D VAL* 3.4 29.6 - - + +
1360D PRO* 3.8 8.4 - - - +
1361D VAL* 1.3 82.0 - - - +
1363D LYS* 1.3 62.1 + - - +
1365D VAL* 3.7 25.4 - - + -
1383D SER 4.5 6.5 - - - +
1384D GLY 4.5 1.8 - - - +
1387D SER* 4.0 16.4 - - - +
1388D PHE* 4.5 21.5 - - + -
1391D ALA* 5.5 0.4 - - + -
1552D LEU* 4.1 20.2 - - + -
1555D GLY 3.7 14.8 - - - +
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Residues in contact with LYS1363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1350D LEU 4.3 0.9 - - - -
1351D SER* 4.5 6.5 - - - +
1360D PRO* 5.4 13.9 - - + -
1362D LEU* 1.3 80.6 - - - +
1364D HIS* 1.3 104.7 + - + +
1365D VAL* 3.5 0.9 + - - +
1555D GLY* 3.5 16.5 + - - +
1556D ALA* 3.9 17.9 - - + +
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Residues in contact with HIS1364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1349D ASN* 4.1 29.4 + - - +
1350D LEU 3.5 6.0 + - - -
1351D SER* 5.0 1.4 - - - -
1363D LYS* 1.3 114.3 - - + +
1365D VAL* 1.3 63.8 + - - +
1366D ASN* 3.7 4.8 + - - +
1556D ALA* 4.8 7.9 - - + +
1557D ILE 5.6 0.5 + - - -
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Residues in contact with VAL1365 (chain D).
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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1347D ILE* 3.7 7.8 - - + +
1348D GLN 3.6 1.4 - - - -
1349D ASN 2.8 14.7 + - - -
1350D LEU* 2.8 61.5 + - + +
1362D LEU* 3.7 37.5 - - + -
1363D LYS 4.2 5.2 - - - +
1364D HIS* 1.3 77.8 - - - +
1366D ASN* 1.3 60.9 + - - +
1367D ALA* 5.3 1.6 - - + -
1388D PHE* 4.6 10.8 - - + -
1555D GLY 4.8 1.1 - - - +
1556D ALA* 5.4 0.4 - - - -
1557D ILE* 3.6 32.3 - - + -
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Residues in contact with ASN1366 (chain D).
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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1347D ILE 3.2 9.0 - - - +
1348D GLN* 4.3 14.7 - - - +
1349D ASN* 4.4 4.9 - - - +
1364D HIS 3.7 6.2 + - - +
1365D VAL* 1.3 76.7 - - - +
1367D ALA* 1.3 71.6 + - - +
1368D LEU* 5.9 1.9 - - - +
1557D ILE* 5.1 6.6 - - - +
1559D GLU* 4.7 5.0 - - - +
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Residues in contact with ALA1367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1346D GLN* 3.4 3.3 - - - +
1347D ILE* 2.9 44.3 + - + +
1365D VAL* 5.3 2.5 - - + -
1366D ASN* 1.3 82.1 + - - +
1368D LEU* 1.3 59.9 + - - +
1369D ILE* 5.8 1.6 - - + -
1388D PHE* 5.5 2.0 - - + -
1550D MET* 4.0 20.9 - - + -
1557D ILE* 5.2 7.2 - - + -
1559D GLU* 3.1 21.5 - - + +
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Residues in contact with LEU1368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1345D ILE 3.5 9.4 - - - +
1346D GLN* 4.2 12.6 - - + +
1366D ASN* 5.9 1.8 - - - +
1367D ALA* 1.3 76.2 - - - +
1369D ILE* 1.3 71.8 + - - +
1370D SER* 4.5 15.7 - - - +
1548D LEU* 4.4 12.2 - - + +
1559D GLU* 3.3 22.0 + - - +
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Residues in contact with ILE1369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1343D GLY 4.2 2.0 - - - +
1344D LYS* 3.2 9.8 - - - +
1345D ILE* 2.9 65.3 + - + +
1347D ILE* 6.6 0.2 - - + -
1367D ALA* 5.7 1.6 - - + -
1368D LEU* 1.3 83.8 - - - +
1370D SER* 1.3 72.3 + - - +
1375D ILE* 3.6 53.8 - - + -
1388D PHE* 6.0 3.4 - - + -
1392D PHE* 6.0 0.4 - - + -
1532D THR* 3.8 14.1 - - + -
1534D VAL* 4.0 10.8 - - + -
1548D LEU* 5.1 1.3 - - - -
1550D MET* 4.4 13.5 - - + -
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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