Contacts of the strand formed by residues 1371 - 1377 (chain B) in PDB entry 6XAF
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 ILE1371 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1373A VAL* 3.8 34.0 + - + +
1391A ASN* 5.4 1.3 - - - +
1393A TRP* 4.0 14.8 - - + -
1369B VAL* 3.8 14.3 - - - +
1370B GLY* 1.3 82.9 - - - +
1372B ASP* 1.3 61.9 + - - +
1373B VAL* 3.9 10.8 + - + -
1393B TRP* 3.8 26.5 - - + -
1394B ASP 3.5 7.0 - - - +
1395B PHE* 3.9 15.0 - - + -
1400B GLU* 3.8 15.9 - - + +
1403B SER* 4.1 5.6 - - - +
1404B THR* 3.5 32.3 - - + -
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Residues in contact with ASP1372 (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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1348A THR* 5.8 2.6 - - - +
1351A LEU* 5.5 0.2 - - - +
1369B VAL* 3.7 21.1 - - + +
1371B ILE* 1.3 72.8 - - - +
1373B VAL* 1.3 68.5 + - - +
1374B LYS* 3.2 32.1 + - - +
1392B VAL 3.5 2.8 - - - +
1393B TRP* 3.6 1.7 - - - -
1394B ASP* 2.8 53.6 + - + +
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Residues in contact with VAL1373 (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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1369A VAL* 4.4 11.4 - - - +
1370A GLY 5.5 0.5 + - - -
1371A ILE* 3.8 44.4 + - + +
1373A VAL* 4.8 3.4 - - + -
1371B ILE* 3.9 9.1 + - + -
1372B ASP* 1.3 81.8 + - - +
1374B LYS* 1.3 65.9 + - - +
1391B ASN* 3.9 27.4 - - - +
1392B VAL 3.2 8.5 - - - +
1393B TRP* 3.7 44.4 - - + +
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Residues in contact with LYS1374 (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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1351A LEU* 4.2 18.2 - - + -
1355A MET* 3.5 40.2 - - + -
1372B ASP* 3.2 27.5 + - - +
1373B VAL* 1.3 75.6 - - - +
1375B ASP* 1.3 63.4 + - - +
1391B ASN* 3.6 2.9 - - - +
1392B VAL* 2.7 44.9 + - + +
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Residues in contact with ASP1375 (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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1355A MET* 3.5 14.9 - - - +
1365A GLN 5.4 9.8 + - - +
1366A SER* 5.4 3.6 + - - -
1370A GLY* 5.6 5.2 + - - -
1374B LYS* 1.3 76.1 - - - +
1376B TRP* 1.3 60.0 + - - +
1377B PRO* 3.5 9.4 - - + +
1389B VAL* 4.2 21.0 - - + +
1390B LEU 3.4 2.0 - - - -
1391B ASN* 2.7 35.6 + - - +
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Residues in contact with TRP1376 (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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1337A LEU* 3.9 24.5 - - + -
1351A LEU* 4.5 2.2 - - + -
1354A LEU* 3.5 45.0 + - + -
1355A MET* 3.7 39.3 - - + +
1356A LYS* 4.5 7.8 - - - +
1501A ARG* 4.1 21.1 - - + -
1504A ILE* 4.2 12.1 - - + -
1505A ILE* 5.2 0.9 - - + -
1375B ASP* 1.3 73.6 - - - +
1377B PRO* 1.3 76.3 + - + +
1378B ILE* 3.5 29.2 + - + +
1389B VAL* 3.6 2.0 - - - +
1390B LEU* 2.7 56.8 + - + +
1392B VAL* 3.9 13.5 - - + -
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Residues in contact with PRO1377 (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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1355A MET* 5.1 2.7 - - + -
1375B ASP* 3.5 12.1 - - + +
1376B TRP* 1.3 100.5 + - + +
1378B ILE* 1.3 59.3 + - - +
1379B GLN* 5.4 6.9 - - - +
1389B VAL* 3.9 23.5 - - + -
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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