Contacts of the strand formed by residues 1293 - 1299 (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 VAL1293 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093B LEU* 4.9 0.4 - - - +
1288B TYR* 4.0 0.9 - - - +
1289B GLY* 3.3 3.6 - - - -
1290B ALA 2.9 31.9 + - - +
1291B GLY 3.8 9.6 - - - +
1292B GLY* 1.3 83.9 - - - +
1294B ILE* 1.3 69.3 + - - +
1295B LYS* 4.1 18.8 + - + +
1311B THR* 3.6 31.0 - - + -
1312B ILE 4.0 4.7 - - - +
1313B ASP* 6.1 1.6 - - - -
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Residues in contact with ILE1294 (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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1093B LEU* 3.5 32.8 - - + -
1238B VAL* 3.8 23.1 - - + +
1239B CYS 5.1 0.9 - - - -
1245B PRO* 3.8 28.3 - - + -
1287B CYS* 4.3 8.5 - - + -
1288B TYR 3.5 7.9 - - - +
1289B GLY* 4.2 2.0 - - - -
1293B VAL* 1.3 71.6 - - - +
1295B LYS* 1.3 62.2 + - - +
1296B CYS* 4.2 21.3 - - - -
1310B ILE 3.7 0.7 - - - +
1311B THR* 3.5 3.1 - - - -
1312B ILE* 2.7 51.9 + - + +
1314B PRO* 4.0 17.0 - - + -
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Residues in contact with LYS1295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1286B SER 3.9 0.5 - - - +
1287B CYS* 3.3 2.1 - - - -
1288B TYR* 3.0 62.6 + - + +
1293B VAL* 4.1 20.4 - - + +
1294B ILE* 1.3 76.4 - - - +
1296B CYS* 1.4 62.6 - - - +
1297B ILE* 4.1 9.1 - - + +
1309B VAL* 4.8 3.1 - - + -
1310B ILE 3.5 4.7 - - - +
1311B THR* 4.5 12.3 - - - +
1362B LEU* 2.7 32.4 + - + +
1363B ASP* 4.8 1.6 - - - +
1390B GLU* 3.1 34.2 + - - +
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Residues in contact with CYS1296 (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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1245B PRO 6.2 0.2 - - - -
1247B VAL* 4.1 7.2 - - + -
1285B CYS* 3.8 13.2 - - + -
1286B SER 3.6 4.0 - - - -
1287B CYS* 2.1 44.9 - - - -
1294B ILE* 4.2 3.4 - - - -
1295B LYS* 1.4 73.4 - - - +
1297B ILE* 1.3 63.0 + - - +
1298B CYS* 3.7 6.1 - - - -
1309B VAL* 3.3 5.4 - - - +
1310B ILE* 2.8 46.2 + - + +
1312B ILE* 3.9 27.6 - - - -
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Residues in contact with ILE1297 (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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1286B SER 2.8 33.9 + - - +
1288B TYR* 4.3 2.2 - - + -
1295B LYS* 4.1 20.2 - - + +
1296B CYS* 1.3 80.2 - - - +
1298B CYS* 1.3 62.0 + - - +
1307B ARG* 3.6 35.2 - - + -
1308B PRO 3.6 3.8 - - - +
1309B VAL* 4.4 7.4 - - + -
1324B LEU* 4.9 4.3 - - + -
1358B GLY 3.5 8.7 - - - +
1359B PHE* 3.8 16.2 - - - -
1360B ALA* 3.5 41.3 - - + +
1362B LEU* 3.9 25.1 - - + -
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Residues in contact with CYS1298 (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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1282B ILE* 4.1 17.7 - - + -
1283B GLU 3.3 8.5 - - - +
1284B GLU 4.4 2.2 - - - -
1285B CYS* 2.1 48.9 - - - +
1296B CYS* 3.7 14.1 - - - -
1297B ILE* 1.3 76.8 - - - +
1299B ARG* 1.3 60.8 + - - +
1307B ARG* 3.1 35.3 + - - +
1308B PRO* 2.9 17.8 + - - +
1310B ILE* 4.1 11.7 - - - -
1358B GLY 5.4 1.1 - - - -
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Residues in contact with ARG1299 (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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1281B HIS 4.3 0.7 - - - -
1282B ILE* 3.6 0.9 - - - -
1283B GLU* 2.8 50.7 + - + +
1284B GLU* 2.7 36.6 + - - -
1298B CYS* 1.3 77.9 - - - +
1300B ASP* 1.3 60.9 + - - +
1301B ASN* 2.9 34.8 + - - +
1307B ARG* 3.7 4.7 - - - +
1308B PRO* 4.2 1.8 - - - -
1331B ASP* 4.2 5.8 - - - +
1354B PRO* 4.8 4.0 - - - +
1355B GLY* 3.4 18.9 + - - +
1356B VAL* 3.5 30.6 - - - +
1357B LYS* 4.4 4.7 - - - -
1378B ARG* 4.2 0.2 - - - +
1412B TYR* 3.0 23.0 + - - -
2477B SIA 3.3 42.2 + - - -
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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