Contacts of the helix formed by residues 1272 - 1284 (chain A) 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 THR1272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1222A TYR* 5.2 6.7 - - - -
1223A GLU 4.3 4.9 - - - -
1230A MET* 6.0 5.2 - - - -
1269A GLU* 4.6 15.7 - - - -
1270A ALA 2.7 12.8 + - - -
1271A VAL* 1.3 74.6 - - - +
1273A MET* 1.3 52.5 - - - +
1274A GLN 3.6 1.6 - - - -
1275A HIS* 4.4 5.6 - - - +
1276A ILE* 2.3 45.4 + - - +
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Residues in contact with MET1273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1268A LEU* 6.4 1.1 - - + -
1269A GLU 3.9 17.6 + - - +
1271A VAL* 3.8 1.0 - - - +
1272A THR* 1.3 76.3 - - - +
1274A GLN* 1.3 60.7 + - - +
1276A ILE* 3.7 3.8 - - - +
1277A PHE* 2.9 30.5 + - - +
1312A LEU 5.8 3.4 - - - +
1315A ILE* 5.9 1.6 - - + -
1326A CYS* 3.9 10.8 - - + +
1327A GLN* 5.7 0.2 - - - -
1330A VAL* 3.7 21.6 - - + +
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Residues in contact with GLN1274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1271A VAL* 5.3 5.5 - - - +
1272A THR 3.6 0.6 - - - +
1273A MET* 1.3 77.2 - - - +
1275A HIS* 1.3 65.6 + - - +
1276A ILE 3.0 2.3 + - - -
1278A MET 3.2 1.9 + - - -
1326A CYS* 4.1 3.4 + - + +
1329A MET* 3.4 39.0 - - + +
1330A VAL* 3.4 13.6 - - - +
1333A GLU* 2.6 30.9 - - + +
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Residues in contact with HIS1275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230A MET 4.9 5.4 - - - +
1231A GLN* 4.9 16.4 - - + +
1235A ARG* 4.8 19.5 - - + +
1271A VAL 5.6 3.3 - - - +
1272A THR* 4.2 8.5 + - - +
1274A GLN* 1.3 79.3 - - - +
1276A ILE* 1.3 56.8 + - - +
1278A MET* 3.6 8.1 - - - +
1279A ASN* 2.8 29.8 + - - +
1333A GLU* 4.8 0.2 - - - -
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Residues in contact with ILE1276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272A THR* 2.3 34.8 + - - +
1273A MET* 3.7 5.4 - - - +
1274A GLN 3.0 0.2 + - - -
1275A HIS* 1.3 74.5 - - - +
1277A PHE* 1.3 55.1 + - - +
1279A ASN* 2.5 28.0 + - - +
1280A ASN* 2.6 19.6 + - - +
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Residues in contact with PHE1277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1273A MET 2.9 21.5 + - - +
1274A GLN 3.9 0.4 - - - +
1276A ILE* 1.3 70.1 - - - +
1278A MET* 1.3 66.5 + - - +
1280A ASN* 3.2 9.3 + - - +
1281A PHE* 3.1 19.4 + - - +
1330A VAL* 3.7 5.6 - - + +
1333A GLU 3.6 4.2 - - - +
1334A LEU* 3.2 36.2 - - + +
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Residues in contact with MET1278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1274A GLN 3.7 0.7 - - - +
1275A HIS* 3.6 12.1 - - - +
1277A PHE* 1.3 78.2 - - - +
1279A ASN* 1.3 62.3 - - - +
1281A PHE* 2.9 18.7 + - - +
1282A GLN* 3.0 14.0 + - - +
1333A GLU* 3.1 33.2 - - + +
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Residues in contact with ASN1279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1235A ARG* 6.1 3.4 - - + -
1275A HIS 2.8 20.7 + - - +
1276A ILE* 2.5 18.5 + - - +
1278A MET* 1.3 72.0 - - - +
1280A ASN* 1.3 54.6 + - - -
1282A GLN* 3.2 8.4 + - - +
1283A LEU* 3.0 29.8 + - - +
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Residues in contact with ASN1280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1276A ILE 2.6 13.7 + - - +
1277A PHE* 3.5 13.2 - - - +
1279A ASN* 1.3 74.2 - - - +
1281A PHE* 1.3 62.2 + - - +
1282A GLN 3.1 1.2 + - - -
1283A LEU* 3.4 8.9 + - - +
1296A VAL* 2.8 42.7 - - - +
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Residues in contact with PHE1281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1277A PHE 3.1 9.7 + - - +
1278A MET* 2.9 12.7 + - - +
1280A ASN* 1.3 75.9 - - - +
1282A GLN* 1.4 56.3 + - - +
1284A CYS 4.0 2.4 - - - +
1285A SER* 3.0 29.8 - - - -
1296A VAL* 3.8 9.8 - - - +
1333A GLU 5.3 3.8 - - - +
1334A LEU 6.0 0.9 - - - +
1335A VAL 6.1 0.7 - - - +
1336A ASN 5.6 2.7 - - - +
1337A SER* 5.4 16.4 - - - -
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Residues in contact with GLN1282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1238A HIS* 5.1 19.1 - - + +
1278A MET 3.0 14.5 + - - +
1279A ASN* 3.8 8.3 - - - +
1280A ASN 3.1 0.2 - - - -
1281A PHE* 1.4 75.5 - - - +
1283A LEU* 1.3 63.9 + - - +
1284A CYS* 3.3 3.8 + - - -
1285A SER* 4.7 4.0 + - - -
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Residues in contact with LEU1283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1250A GLN 4.1 10.9 - - - +
1251A ASN* 4.4 2.0 - - - -
1255A LEU* 3.6 24.7 - - + +
1279A ASN 3.0 14.3 + - - +
1280A ASN* 3.4 9.0 + - - +
1282A GLN* 1.3 77.3 - - - +
1284A CYS* 1.3 61.9 + - - +
1295A PHE 4.3 12.1 - - - +
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Residues in contact with CYS1284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1251A ASN* 3.3 23.1 - - - +
1255A LEU* 5.0 1.6 - - + -
1280A ASN 4.2 3.2 + - - -
1281A PHE 4.1 0.7 - - - -
1282A GLN 3.3 0.6 - - - -
1283A LEU* 1.3 81.2 - - - +
1285A SER* 1.3 61.3 - - - +
1292A VAL* 2.7 33.3 - - - +
1295A PHE* 2.9 39.8 + - + -
1296A VAL* 3.6 8.0 - - - +
1344A PHE* 4.4 0.7 - - - +
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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