Contacts of the strand formed by residues 1379 - 1385 (chain B) in PDB entry 1W21
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 SER1379 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1372B THR* 3.6 1.4 - - - -
1373B ILE 3.2 13.9 + - - -
1374B SER* 3.4 13.5 + - - -
1377B SER* 2.8 11.2 + - - -
1378B ARG* 1.3 74.9 - - - +
1380B GLY* 1.3 68.5 + - - +
1406B ASN* 2.4 34.9 + - - -
1408B ASN 3.4 4.0 - - - -
1409B TRP* 3.7 7.9 - - - -
1410B SER* 3.6 0.7 - - - -
2478B SIA 3.2 38.8 + - - -
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Residues in contact with GLY1380 (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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1372B THR* 3.4 7.4 - - - -
1373B ILE* 3.6 13.9 - - - -
1379B SER* 1.3 75.7 + - - +
1381B TYR* 1.3 61.4 + - - +
1404B VAL* 3.2 16.2 - - - -
1405B ASN 3.5 11.6 + - - -
1406B ASN* 3.9 1.8 - - - +
1408B ASN 2.8 14.9 + - - -
1410B SER* 2.7 24.9 + - - -
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Residues in contact with TYR1381 (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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1358B GLY* 5.1 0.3 - - - -
1359B PHE* 3.1 18.9 + + - -
1370B GLY* 3.2 18.8 + - - -
1371B ARG* 3.4 25.3 - - - -
1372B THR* 4.0 5.8 - - + -
1373B ILE* 3.5 5.1 - - - +
1380B GLY* 1.3 76.6 - - - +
1382B GLU* 1.3 89.5 + - - +
1383B MET* 4.0 10.3 - - - -
1402B VAL* 3.7 1.7 - - - -
1403B ILE* 2.8 34.1 + - + -
1404B VAL* 2.8 30.4 + - + +
1410B SER* 4.4 4.5 - - - -
1411B GLY 4.8 5.2 - - - -
1413B SER* 2.7 37.0 + - - -
1430B PHE* 4.4 0.4 - + - -
1432B VAL* 4.0 29.6 - - + -
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Residues in contact with GLU1382 (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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1369B LEU 3.9 0.3 - - - +
1370B GLY* 3.3 3.6 - - - -
1371B ARG* 2.9 77.1 + - + +
1372B THR 3.9 6.2 - - - +
1373B ILE* 3.9 21.8 - - + +
1381B TYR* 1.3 78.1 - - - +
1383B MET* 1.3 62.2 + - - +
1384B LEU* 3.8 13.3 - - + +
1401B GLN 3.4 9.6 - - - +
1402B VAL* 4.7 1.3 - - - -
1403B ILE 4.4 0.2 - - - +
2484B MAN 3.4 8.3 + - - -
2486B MAN 2.5 43.8 + - - +
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Residues in contact with MET1383 (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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1103B TRP* 3.6 49.4 - - + +
1359B PHE* 3.6 37.5 - - + -
1368B TRP* 3.8 20.6 - - + -
1369B LEU 3.5 6.5 - - - +
1370B GLY* 3.6 12.6 - - - +
1381B TYR* 4.0 5.2 - - - -
1382B GLU* 1.3 72.8 - - - +
1384B LEU* 1.3 63.2 + - - +
1400B ASN* 3.1 5.5 - - - -
1401B GLN* 2.8 36.4 + - + +
1403B ILE* 3.8 24.9 - - + +
1430B PHE* 3.8 12.1 - - + -
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Residues in contact with LEU1384 (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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1328B VAL* 3.8 20.6 - - + -
1368B TRP* 3.3 5.4 - - - -
1369B LEU* 2.7 46.6 + - + +
1371B ARG* 3.5 38.6 - - + +
1382B GLU* 3.8 21.5 - - + +
1383B MET* 1.3 78.0 - - - +
1385B LYS* 1.4 61.0 + - - +
1386B VAL* 3.5 13.5 + - + +
1397B PRO* 4.3 9.0 - - + -
1399B SER 3.5 4.0 - - - +
1400B ASN* 3.4 27.4 - - + -
2484B MAN 3.9 14.8 - - - +
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Residues in contact with LYS1385 (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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1099B GLU* 5.2 3.4 - - - +
1100B VAL 3.1 14.1 + - - -
1101B ASN* 2.9 28.4 + - - +
1365B GLU* 3.6 23.1 - - - +
1366B ASN* 4.3 11.0 + - - +
1367B SER 3.3 13.5 - - - +
1368B TRP* 3.4 28.1 - - + +
1384B LEU* 1.4 67.6 - - - +
1386B VAL* 1.3 60.1 + - - +
1387B PRO* 3.4 3.8 - - + +
1397B PRO* 3.4 1.4 - - - +
1398B ILE* 2.9 46.8 + - + +
1399B SER* 3.0 28.7 + - - +
1460B ARG* 5.1 5.8 - - - +
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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