Contacts of the strand formed by residues 1318 - 1323 (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 THR1318 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1263B TYR* 3.6 5.7 + - - -
1271B LYS* 3.9 8.3 - - - +
1273B GLU* 3.6 13.0 - - - +
1312B ILE* 3.6 0.2 - - - -
1313B ASP* 2.9 32.2 + - - +
1316B MET* 3.6 27.3 - - + +
1317B MET* 1.3 82.7 - - - +
1319B HIS* 1.3 65.2 + - - +
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Residues in contact with HIS1319 (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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1261B ILE* 4.0 17.6 - - + +
1263B TYR* 4.3 2.0 - - - +
1273B GLU* 2.8 29.8 + - + -
1274B GLU 3.4 20.6 - - - -
1275B LEU* 3.7 9.3 - - + +
1276B ALA* 3.0 39.2 + - + +
1310B ILE* 4.1 11.7 - - + -
1311B THR 3.1 15.9 - - - +
1312B ILE* 4.1 15.0 - - + -
1318B THR* 1.3 78.9 - - - +
1320B THR* 1.3 85.1 + - - +
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Residues in contact with THR1320 (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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1276B ALA* 4.8 2.2 - - - -
1277B GLY* 5.4 1.8 - - - -
1310B ILE* 3.4 3.3 - - - +
1311B THR* 2.9 44.0 + - - +
1319B HIS* 1.3 86.8 - - - +
1321B SER* 1.3 63.6 + - - +
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Residues in contact with SER1321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1275B LEU* 3.9 13.8 - - - +
1276B ALA 2.8 24.9 + - - -
1277B GLY* 3.5 4.6 - - - -
1278B ASN* 2.9 22.7 + - - +
1279B ALA* 3.1 30.3 + - - +
1309B VAL 3.3 10.5 - - - -
1310B ILE* 4.0 6.7 - - - -
1320B THR* 1.3 76.1 - - - +
1322B LYS* 1.3 68.7 + - - +
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Residues in contact with LYS1322 (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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1278B ASN* 4.3 4.7 - - + -
1279B ALA* 4.0 9.9 - - - +
1308B PRO* 3.3 8.3 - - - +
1309B VAL* 2.7 41.9 + - + +
1321B SER* 1.3 78.7 - - - +
1323B TYR* 1.3 70.4 + - - +
1325B CYS* 4.7 6.8 - - - -
1343B CYS* 3.5 29.1 - - - +
1344B ASP* 3.7 24.7 + - - +
1390B GLU* 5.0 9.4 + - + +
1391B THR* 6.2 0.4 - - - +
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Residues in contact with TYR1323 (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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1278B ASN 3.5 22.2 - - - -
1279B ALA* 3.7 5.8 - - - -
1280B GLN* 3.0 26.6 + - - +
1281B HIS 4.2 0.2 + - - -
1300B ASP* 2.8 29.6 + - - -
1306B ASN* 3.4 50.0 - - - +
1307B ARG 3.6 2.0 - - - -
1308B PRO* 3.7 21.8 - - + -
1309B VAL* 4.0 5.7 - - - +
1322B LYS* 1.3 84.0 - - - +
1324B LEU* 1.4 64.3 + - - +
1325B CYS* 3.4 5.9 + - - -
1342B ASN 3.6 4.3 - - - +
1343B CYS* 2.8 24.5 + - - +
1344B ASP 4.1 2.5 - - - -
1345B ALA* 3.7 16.6 - - - -
1346B PRO* 3.7 22.0 - - + +
1390B GLU* 4.8 1.9 - - - +
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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