Contacts of the strand formed by residues 1258 - 1265 (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 ALA1258 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1225B TRP* 3.0 36.7 + - + +
1226B ALA* 4.2 8.1 - - + -
1249B THR* 3.6 1.3 - - - -
1250B ASP 2.8 33.9 + - - +
1257B ALA* 1.3 74.2 - - - +
1259B THR* 1.3 59.8 + - - +
1260B LYS* 5.1 2.0 - - - -
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Residues in contact with THR1259 (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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1247B VAL* 3.8 23.8 - - + -
1248B MET 3.2 11.7 - - - +
1249B THR* 2.9 22.9 + - - +
1257B ALA* 3.8 5.0 + - - +
1258B ALA* 1.3 72.1 + - - +
1260B LYS* 1.3 69.8 + - - +
1261B ILE* 4.8 1.6 - - + -
1274B GLU* 3.7 2.6 - - - +
1275B LEU* 2.8 53.7 + - + +
1282B ILE* 3.6 23.2 + - + +
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Residues in contact with LYS1260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1225B TRP* 3.6 64.7 - - + +
1246B VAL 3.7 0.7 - - - +
1247B VAL* 3.6 3.8 - - - +
1248B MET* 2.8 33.8 + - - +
1258B ALA* 4.1 2.4 + - + -
1259B THR* 1.3 81.2 - - - +
1261B ILE* 1.3 67.0 + - - +
1262B ILE* 4.0 10.3 - - + -
1272B ILE* 3.9 21.7 - - + +
1273B GLU 3.1 11.0 - - - +
1274B GLU* 4.5 17.5 - - + -
1275B LEU 4.4 0.4 - - - +
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Residues in contact with ILE1261 (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* 4.1 15.5 - - + -
1246B VAL 3.5 7.9 - - - +
1247B VAL* 3.8 26.5 - - + -
1259B THR* 4.8 4.3 - - + -
1260B LYS* 1.3 79.2 - - - +
1262B ILE* 1.3 64.2 + - - +
1263B TYR* 3.7 34.7 - - + +
1272B ILE* 3.5 1.9 - - - -
1273B GLU* 2.7 41.4 + - + +
1275B LEU* 5.1 3.4 - - + -
1310B ILE* 4.5 18.4 - - + -
1312B ILE* 4.1 9.4 - - + -
1319B HIS* 4.0 32.1 - - + +
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Residues in contact with ILE1262 (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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1222B ILE* 4.2 11.0 - - + -
1225B TRP* 4.1 20.9 - - + -
1245B PRO* 3.4 0.9 - - - +
1246B VAL 2.7 38.9 + - - +
1248B MET* 3.6 30.1 - - + -
1260B LYS* 4.3 6.3 - - + -
1261B ILE* 1.3 77.5 - - - +
1263B TYR* 1.4 61.8 + - - +
1264B PHE* 3.5 33.2 - - + -
1269B ILE* 3.9 16.4 - - + -
1271B LYS 3.5 2.9 - - - +
1272B ILE* 3.9 35.4 - - + -
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Residues in contact with TYR1263 (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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1243B VAL* 4.1 8.5 - - + -
1244B CYS 4.0 3.1 - - - -
1245B PRO* 3.7 18.6 - - + -
1261B ILE* 3.7 30.5 - - + +
1262B ILE* 1.4 72.9 - - - +
1264B PHE* 1.3 56.4 + - - +
1269B ILE* 3.7 2.9 - - - -
1270B GLN* 2.7 33.9 + - + +
1271B LYS* 2.8 28.1 + - + +
1273B GLU* 2.9 31.5 + - + -
1312B ILE* 3.7 22.8 - - + +
1313B ASP 4.2 1.1 - - - -
1314B PRO* 4.7 0.4 - - + -
1317B MET* 3.4 64.9 - - + -
1318B THR 3.5 10.6 + - - -
1319B HIS* 4.3 1.4 - - - +
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Residues in contact with PHE1264 (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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1197B MET* 3.6 22.7 - - + -
1199B ILE* 3.8 10.1 - - + -
1212B VAL* 3.7 20.0 - - + -
1220B THR* 5.2 0.4 - - + -
1222B ILE* 3.9 7.9 - - + -
1242B GLY 3.4 0.3 - - - +
1243B VAL* 3.2 6.2 - - - -
1244B CYS* 2.8 46.2 + - + +
1246B VAL* 3.8 24.9 - - + -
1248B MET* 3.9 16.2 - - + -
1262B ILE* 3.5 34.5 - - + -
1263B TYR* 1.3 74.5 - - - +
1265B LYS* 1.3 60.4 + - - +
1267B GLY* 4.0 16.6 - - - +
1268B LYS 3.3 15.9 - - - +
1269B ILE* 3.8 20.4 - - + -
1270B GLN* 4.0 1.8 - - - -
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Residues in contact with LYS1265 (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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1090B PHE* 4.5 21.9 - - + -
1241B LYS 4.7 8.2 + - - -
1242B GLY* 3.3 21.8 - - - +
1243B VAL* 4.8 9.2 - - + -
1244B CYS* 5.8 0.4 - - - -
1264B PHE* 1.3 75.1 - - - +
1266B GLU* 1.3 86.7 + - + +
1268B LYS* 3.0 23.8 + - - +
1270B GLN* 3.6 30.9 - - + +
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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