Contacts of the strand formed by residues 1362 - 1369 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1347H ILE* 6.3 0.4 - - + -
1350H LEU* 3.7 13.7 - - + +
1351H SER* 3.2 21.8 - - - -
1352H VAL* 3.5 18.7 + - + +
1360H PRO* 3.8 5.9 - - - +
1361H VAL* 1.3 84.0 - - - +
1363H LYS* 1.3 61.3 + - - +
1365H VAL* 3.7 29.2 - - + -
1383H SER 4.4 4.5 - - - +
1384H GLY* 4.9 5.6 - - - -
1387H SER* 3.7 37.7 - - - +
1388H PHE* 6.0 0.7 - - - -
1391H ALA* 5.9 3.8 - - + -
1552H LEU* 4.7 14.6 - - + -
1555H GLY* 3.3 8.1 - - - +
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Residues in contact with LYS1363 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1351H SER* 3.9 6.1 - - - +
1360H PRO* 4.7 13.0 - - + +
1362H LEU* 1.3 69.5 - - - +
1364H HIS* 1.3 70.8 + - + +
1365H VAL 3.2 1.5 + - - -
1554H ARG 4.8 4.9 - - - +
1555H GLY* 2.4 37.5 + - - +
1556H ALA* 3.3 16.9 - - + +
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Residues in contact with HIS1364 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1349H ASN* 3.7 26.8 - - + +
1350H LEU 3.3 7.5 + - - -
1351H SER* 3.7 6.6 + - - +
1363H LYS* 1.3 73.3 - - + +
1365H VAL* 1.3 66.0 + - - +
1366H ASN* 3.4 6.4 + - - +
1556H ALA* 5.2 2.9 - - + +
1557H ILE 5.4 1.9 + - - +
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Residues in contact with VAL1365 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1347H ILE* 3.3 29.3 - - + +
1349H ASN 2.9 21.1 + - - -
1350H LEU* 3.5 6.7 + - + +
1362H LEU* 3.7 34.8 - - + -
1363H LYS 4.2 0.9 - - - +
1364H HIS* 1.3 76.5 - - - +
1366H ASN* 1.3 65.2 + - - +
1367H THR* 5.1 2.9 - - - +
1552H LEU* 4.5 9.0 - - + -
1555H GLY 3.6 23.1 - - - +
1557H ILE* 4.2 26.7 - - + +
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Residues in contact with ASN1366 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1347H ILE 3.3 9.4 - - - +
1348H GLN* 4.9 1.6 - - - -
1349H ASN* 4.6 5.8 - - - +
1364H HIS 3.4 6.8 + - - +
1365H VAL* 1.3 79.7 - - - +
1367H THR* 1.3 63.9 + - - +
1557H ILE* 4.3 14.2 + - - +
1560H PHE* 3.9 13.2 - - - -
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Residues in contact with THR1367 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1346H GLN* 3.4 2.6 - - - +
1347H ILE* 2.9 35.9 + - - +
1365H VAL* 5.6 4.7 - - - -
1366H ASN* 1.3 76.0 - - - +
1368H LEU* 1.3 63.0 + - - +
1560H PHE* 4.4 27.4 - - - -
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Residues in contact with LEU1368 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1345H ILE 3.5 7.9 - - - +
1346H GLN* 4.1 11.0 - - + +
1367H THR* 1.3 77.9 - - - +
1369H ILE* 1.3 61.1 + - - +
1370H SER 4.2 0.7 + - - -
1560H PHE* 5.1 10.5 - - - -
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Residues in contact with ILE1369 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1343H GLY 4.3 1.2 - - - +
1344H LYS* 3.8 2.8 - - - +
1345H ILE* 2.7 44.8 + - + +
1368H LEU* 1.3 74.5 - - - +
1370H SER* 1.3 68.2 + - - +
1373H GLN* 4.9 9.6 - - + +
1375H ILE* 5.0 15.7 - - + -
1532H THR* 6.0 5.4 - - - -
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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