Contacts of the strand formed by residues 1362 - 1369 (chain B) in PDB entry 5TWV
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1347B ILE* 6.3 1.1 - - + -
1350B LEU* 3.7 12.8 - - + +
1351B SER* 3.2 21.8 - - - -
1352B VAL* 3.5 17.8 + - + +
1360B PRO* 3.8 5.9 - - - +
1361B VAL* 1.3 84.7 - - - +
1363B LYS* 1.3 61.1 + - - +
1365B VAL* 3.7 28.3 - - + -
1383B SER* 4.4 4.5 - - - +
1384B GLY* 4.9 5.6 - - - -
1387B SER* 3.7 37.9 - - - +
1388B PHE 5.3 0.4 - - - +
1391B ALA* 5.9 3.4 - - + -
1552B LEU* 4.7 13.9 - - + -
1555B GLY* 3.3 8.5 - - - +
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Residues in contact with LYS1363 (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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1351B SER* 3.9 6.1 - - - +
1360B PRO* 4.7 13.0 - - + +
1362B LEU* 1.3 69.1 - - - +
1364B HIS* 1.3 71.8 + - + +
1365B VAL 3.2 2.3 + - - -
1554B ARG 4.8 4.7 - - - +
1555B GLY* 2.4 36.9 + - - +
1556B ALA* 3.3 17.1 - - + +
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Residues in contact with HIS1364 (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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1349B ASN* 3.7 26.3 - - + +
1350B LEU 3.3 7.5 + - - -
1351B SER* 3.7 7.1 + - - +
1363B LYS* 1.3 73.5 - - + +
1365B VAL* 1.3 65.7 + - - +
1366B ASN* 3.4 6.2 + - - +
1556B ALA* 5.2 3.4 - - + +
1557B ILE 5.4 1.9 + - - +
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Residues in contact with VAL1365 (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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1347B ILE* 3.3 29.7 - - + +
1349B ASN 2.9 21.5 + - - -
1350B LEU 3.5 6.4 + - - +
1362B LEU* 3.7 34.1 - - + -
1363B LYS 4.1 1.1 - - - +
1364B HIS* 1.3 75.7 - - - +
1366B ASN* 1.3 64.5 + - - +
1367B THR* 5.1 3.1 - - - +
1552B LEU* 4.5 8.3 - - + -
1555B GLY 3.6 23.1 - - - +
1557B ILE* 4.2 26.9 - - + +
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Residues in contact with ASN1366 (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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1347B ILE 3.3 10.3 - - - +
1348B GLN* 4.9 1.3 - - - -
1349B ASN 4.6 5.6 - - - +
1364B HIS 3.4 6.7 + - - +
1365B VAL* 1.3 79.4 - - - +
1367B THR* 1.3 63.6 + - - +
1557B ILE* 4.3 14.1 + - - +
1560B PHE* 3.9 13.7 - - - -
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Residues in contact with THR1367 (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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1346B GLN* 3.4 2.6 - - - +
1347B ILE* 2.9 35.8 + - - +
1365B VAL* 5.6 4.0 - - - -
1366B ASN* 1.3 75.8 - - - +
1368B LEU* 1.3 62.7 + - - +
1560B PHE* 4.4 27.4 - - - -
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Residues in contact with LEU1368 (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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1345B ILE 3.5 7.6 - - - +
1346B GLN* 4.1 10.8 - - + +
1367B THR* 1.3 78.1 - - - +
1369B ILE* 1.3 59.9 + - - +
1370B SER 4.1 1.3 + - - -
1560B PHE* 5.1 10.9 - - - -
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Residues in contact with ILE1369 (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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1343B GLY 4.3 1.0 - - - +
1344B LYS* 3.8 3.5 - - - +
1345B ILE* 2.7 46.1 + - + +
1368B LEU* 1.3 73.6 - - - +
1370B SER* 1.3 67.7 + - - +
1373B GLN* 4.9 9.2 - - + +
1375B ILE* 5.0 15.0 - - + -
1532B THR* 6.0 5.6 - - - -
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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