Contacts of the strand formed by residues 1382 - 1392 (chain A) in PDB entry 4YKN
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 ARG1382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1339A LEU 4.0 4.9 - - - +
1340A CYS* 4.1 7.6 - - + -
1376A VAL* 3.7 18.2 - - - +
1380A ASN* 3.1 28.9 + - - +
1381A PRO* 1.3 74.1 - - - +
1383A TRP* 1.3 68.0 + - - +
1384A ASN* 5.2 4.5 - - - +
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Residues in contact with TRP1383 (chain A).
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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1338A ILE* 3.6 15.7 - - + +
1339A LEU 2.9 8.5 + - - -
1340A CYS* 3.9 10.1 - - - -
1341A ALA* 4.0 16.4 - - + -
1354A ILE* 4.2 18.6 - - + -
1355A TYR* 3.9 16.7 - - - +
1356A VAL* 3.6 28.7 - - + -
1373A THR* 3.1 25.7 + - + -
1374A GLN* 2.9 32.9 + - + -
1376A VAL* 3.2 18.0 - - + +
1381A PRO* 3.6 36.8 - - + -
1382A ARG* 1.3 76.3 - - - +
1384A ASN* 1.3 71.7 + - - +
1385A GLU* 3.2 14.6 + - + +
1406A ILE* 5.0 5.4 - - + -
1473A LEU* 4.5 0.7 - - + -
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Residues in contact with ASN1384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1337A LYS* 3.6 27.7 - - - +
1338A ILE 2.8 15.0 + - - -
1339A LEU* 3.0 40.2 + - - +
1340A CYS* 5.2 1.7 - - - +
1382A ARG* 5.2 4.9 - - - +
1383A TRP* 1.3 75.1 + - - +
1385A GLU* 1.3 57.5 + - - +
1386A TRP* 4.3 1.4 + - - -
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Residues in contact with GLU1385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1337A LYS* 3.4 3.9 - - - -
1338A ILE* 3.0 30.8 + - - +
1372A ASN 4.2 2.9 - - - +
1373A THR* 3.2 9.7 - - + -
1374A GLN* 2.9 54.4 + - - +
1383A TRP* 4.1 14.2 - - + +
1384A ASN* 1.3 77.6 - - - +
1386A TRP* 1.3 73.5 + - - +
1387A LEU* 3.7 19.8 + - + +
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Residues in contact with TRP1386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1335A ARG* 3.5 75.3 - - + +
1336A ILE* 3.7 4.5 - - - -
1337A LYS* 3.6 63.0 - - + +
1384A ASN 5.2 0.9 - - - -
1385A GLU* 1.3 82.3 - - - +
1387A LEU* 1.3 63.2 + - - +
1388A ASN* 3.9 15.8 + - - +
1476A GLU* 4.3 16.4 - - - -
1477A PHE 4.6 2.0 - - - -
1478A ASP* 4.3 17.7 - - - -
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Residues in contact with LEU1387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1335A ARG* 3.2 6.2 - - - -
1336A ILE 2.9 38.6 + - - +
1338A ILE* 3.6 19.5 - - + -
1358A THR* 3.5 38.8 - - + +
1371A VAL* 3.7 20.6 - - + +
1372A ASN 3.7 20.6 - - - +
1373A THR* 3.8 18.8 - - + +
1385A GLU* 3.9 14.8 - - + +
1386A TRP* 1.3 77.0 - - - +
1388A ASN* 1.3 61.3 + - - +
1389A TYR* 3.4 14.8 - - + +
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Residues in contact with ASN1388 (chain A).
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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1334A LEU 3.9 4.0 - - - +
1335A ARG* 3.8 21.7 - - - +
1371A VAL* 3.6 17.9 - - - +
1386A TRP* 4.0 16.9 + - - +
1387A LEU* 1.3 72.7 - - - +
1389A TYR* 1.3 62.5 + - - +
1390A ASP 4.2 0.3 + - - -
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Residues in contact with TYR1389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1333A ALA* 4.3 6.2 - - - +
1334A LEU* 3.0 38.9 + - + +
1336A ILE* 3.9 29.9 - - + +
1358A THR* 2.7 38.6 + - - +
1359A GLY* 4.5 6.1 - - - -
1360A ILE* 3.9 26.0 - - + -
1368A CYS* 4.2 10.3 - - - -
1369A ASP 4.9 1.1 - - - -
1371A VAL* 3.4 24.2 - - + -
1387A LEU* 3.4 30.1 - - + +
1388A ASN* 1.3 73.9 - - - +
1390A ASP* 1.3 60.8 + - - +
1391A ILE* 3.3 25.5 + - + +
1402A LEU* 4.2 5.9 - - - +
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Residues in contact with ASP1390 (chain A).
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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1367A LEU 4.4 1.0 - - - +
1368A CYS* 3.1 27.3 - - + +
1369A ASP 5.7 0.8 + - - +
1371A VAL* 5.5 0.6 - - - +
1388A ASN 4.2 0.8 + - - -
1389A TYR* 1.3 68.8 - - - +
1391A ILE* 1.3 67.6 + - - +
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Residues in contact with ILE1391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1333A ALA* 3.6 10.4 - - - +
1334A LEU* 3.6 48.8 + - + -
1360A ILE* 5.2 2.5 - - + -
1367A LEU* 4.2 31.2 - - + +
1368A CYS* 4.6 6.1 - - + -
1389A TYR* 3.3 8.9 + - + +
1390A ASP* 1.3 81.6 + - - +
1392A TYR* 1.3 75.0 + - - +
1395A ASP* 4.3 12.1 - - + +
1396A LEU* 3.9 31.0 - - + -
1397A PRO* 4.8 0.4 - - + -
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Residues in contact with TYR1392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1330A ILE 4.4 0.3 + - - -
1331A ASN* 2.6 39.4 + - - +
1332A SER* 3.1 33.7 - - - -
1333A ALA* 4.8 2.2 - - + -
1391A ILE* 1.3 81.4 - - - +
1393A ILE* 1.3 56.8 + - - +
1394A PRO* 3.2 28.9 - - + +
1395A ASP* 2.5 54.0 + - - +
1396A LEU* 3.3 4.0 + - - -
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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