Contacts of the helix formed by residues 1270 - 1285 (chain B) in PDB entry 5XA0
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 ALA1270 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1269B GLU* 1.3 72.3 - - - +
1271B VAL* 1.3 69.7 + - - +
1272B THR 3.0 2.7 + - - -
1273B MET* 3.2 18.9 + - - +
1274B GLN 3.9 2.1 + - - -
1315B ILE* 3.2 35.8 + - + +
1316B VAL* 3.6 3.1 - - - +
1319B GLU* 3.1 35.7 - - + +
1326B CYS* 3.7 13.7 - - + +
1327B GLN* 4.6 1.6 - - - +
1330B VAL* 4.4 3.6 - - - +
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Residues in contact with VAL1271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1269B GLU* 4.8 1.0 - - + +
1270B ALA* 1.3 78.5 - - - +
1272B THR* 1.4 61.3 + - - +
1273B MET 3.3 0.3 + - - -
1274B GLN* 3.3 6.2 + - - +
1275B HIS* 3.1 25.9 + - + +
1319B GLU* 4.6 0.2 - - - +
1326B CYS* 3.3 32.3 - - + +
1329B MET* 4.9 6.2 - - + +
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Residues in contact with THR1272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1261B LEU* 4.0 18.5 - - - +
1268B LEU* 6.1 0.9 - - - -
1269B GLU* 3.9 25.9 - - - +
1270B ALA 3.0 0.8 - - - +
1271B VAL* 1.4 76.2 - - - +
1273B MET* 1.3 60.0 + - - +
1275B HIS* 4.6 5.4 - - - -
1276B ILE* 2.8 35.6 + - - +
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Residues in contact with MET1273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1260B ASN 5.6 0.4 - - - -
1261B LEU* 4.9 5.3 - - - +
1269B GLU 4.1 6.5 + - - +
1270B ALA* 3.2 13.9 + - - +
1272B THR* 1.3 74.7 - - - +
1274B GLN* 1.3 70.4 + - - +
1276B ILE* 3.0 12.9 + - - +
1277B PHE* 3.1 14.3 + - - +
1315B ILE* 5.6 4.3 - - + -
1330B VAL* 5.1 5.6 - - + -
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Residues in contact with GLN1274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1270B ALA 3.9 1.2 + - - -
1271B VAL 3.3 9.3 + - - +
1273B MET* 1.3 79.1 - - - +
1275B HIS* 1.3 66.3 + - + +
1277B PHE* 3.4 0.7 + - - +
1278B MET* 3.2 13.0 + - - +
1329B MET* 2.8 48.5 - - + +
1330B VAL* 3.1 11.2 - - + +
1333B GLU* 3.0 26.9 - - + +
1334B LEU 5.3 0.2 - - - +
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Residues in contact with HIS1275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1231B GLN* 6.2 4.3 - - + -
1271B VAL 3.1 15.0 + - - +
1272B THR* 4.4 4.3 - - - +
1274B GLN* 1.3 80.4 - - + +
1276B ILE* 1.3 58.0 + - - +
1278B MET* 3.2 7.2 + - - +
1279B ASN* 2.8 33.6 + - + +
1329B MET* 6.4 0.2 - - + -
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Residues in contact with ILE1276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1260B ASN* 3.2 33.9 - - - +
1261B LEU* 4.0 4.5 - - + -
1272B THR* 2.8 23.5 + - - +
1273B MET* 3.0 2.4 + - - +
1275B HIS* 1.3 76.4 - - - +
1277B PHE* 1.3 63.0 + - - +
1279B ASN* 3.8 6.1 - - - +
1280B ASN* 3.0 24.6 + - - +
1299B ILE* 4.5 1.8 - - - +
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Residues in contact with PHE1277 (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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1273B MET 3.1 10.3 + - - +
1274B GLN 3.9 6.5 - - - +
1276B ILE* 1.3 75.3 - - - +
1278B MET* 1.3 70.2 + - - +
1279B ASN 3.1 0.3 + - - -
1280B ASN* 3.2 2.6 + - - +
1281B PHE* 3.1 19.5 + - - +
1299B ILE* 4.3 24.6 - - + +
1300B GLU* 5.1 8.5 - - + -
1333B GLU* 5.1 10.5 - - + +
1334B LEU* 6.2 0.9 - - - -
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Residues in contact with MET1278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1274B GLN 3.2 10.0 + - - +
1275B HIS* 3.2 11.0 + - - +
1277B PHE* 1.3 76.6 - - - +
1279B ASN* 1.3 58.4 + - - +
1281B PHE* 2.9 24.7 + - - +
1282B GLN* 3.0 14.0 + - - +
1333B GLU* 4.7 10.7 + - + +
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Residues in contact with ASN1279 (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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1235B ARG* 6.3 3.8 - - + -
1275B HIS* 2.8 22.5 + - + +
1276B ILE* 3.8 7.0 - - - +
1278B MET* 1.3 69.0 - - - +
1280B ASN* 1.3 69.2 + - - +
1281B PHE 3.4 0.2 + - - -
1282B GLN* 3.5 5.4 + - - +
1283B LEU* 3.4 21.5 + - - +
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Residues in contact with ASN1280 (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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1260B ASN* 5.8 3.1 - - + -
1276B ILE 3.0 12.4 + - - +
1279B ASN* 1.3 76.0 - - - +
1281B PHE* 1.3 51.1 + - - +
1283B LEU* 3.6 2.8 - - - +
1284B CYS* 2.6 42.1 + - + +
1295B PHE 5.1 4.0 - - - +
1299B ILE* 3.1 36.3 - - + -
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Residues in contact with PHE1281 (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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1277B PHE 3.1 9.9 + - - +
1278B MET* 2.9 13.6 + - - +
1280B ASN* 1.3 76.6 - - - +
1282B GLN* 1.3 50.8 + - - +
1284B CYS* 4.3 3.8 - - - -
1285B SER* 2.2 47.8 + - - +
1296B VAL* 4.9 17.9 - - + +
1299B ILE* 5.0 0.6 - - + +
1337B SER* 6.4 1.8 - - - -
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Residues in contact with GLN1282 (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 ASN* 4.8 7.6 - - + -
1244B PHE* 2.5 52.9 - - + +
1248B ASN* 2.9 1.2 - - - +
1278B MET 3.0 10.5 + - - +
1279B ASN* 4.0 8.7 - - - +
1280B ASN 3.3 0.2 - - - -
1281B PHE* 1.3 76.6 - - - +
1283B LEU* 1.3 63.1 + - - +
1285B SER* 2.9 4.3 + - - -
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Residues in contact with LEU1283 (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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1235B ARG* 6.3 3.1 - - + -
1244B PHE* 3.7 2.2 - - - +
1248B ASN* 2.5 25.1 - - - +
1251B ASN* 2.4 36.8 - - + +
1252B GLN 4.7 0.2 + - - -
1255B LEU* 6.4 0.2 - - + -
1279B ASN 3.4 14.1 + - - +
1280B ASN* 4.1 2.2 - - - +
1282B GLN* 1.3 78.1 - - - +
1284B CYS* 1.3 55.5 + - - +
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Residues in contact with CYS1284 (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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1248B ASN* 4.8 0.2 - - - +
1249B GLN* 5.3 1.4 + - - -
1251B ASN* 3.8 7.1 - - + +
1252B GLN* 5.2 5.2 + - - +
1280B ASN* 2.6 27.7 + - + +
1281B PHE* 4.1 2.9 - - - +
1283B LEU* 1.3 73.8 - - - +
1285B SER* 1.3 64.7 + - - +
1286B GLU* 3.3 7.6 + - - +
1291B VAL* 5.0 3.8 - - - +
1292B VAL* 3.8 11.5 + - - +
1295B PHE* 3.2 38.5 - - + +
1296B VAL 4.6 1.1 - - - +
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Residues in contact with SER1285 (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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1244B PHE 3.0 17.3 - - - +
1245B CYS* 2.9 19.0 - - - +
1248B ASN* 3.3 13.5 + - - +
1281B PHE* 2.2 38.7 + - - +
1282B GLN* 2.9 9.3 + - - +
1284B CYS* 1.3 69.2 - - - +
1286B GLU* 1.3 57.4 + - - +
1292B VAL* 3.6 11.4 - - - +
1296B VAL* 6.1 0.9 - - - +
1340B ASP* 5.9 1.6 - - - -
1341B VAL* 3.6 15.9 - - - -
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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