Contacts of the helix formed by residues 1321 - 1331 (chain A) in PDB entry 3RYT
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 ASP1321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1319A PHE 3.1 7.0 + - - +
1320A LEU* 1.3 71.2 - - - +
1322A TYR* 1.3 77.8 + - - +
1323A ARG* 3.0 10.2 + - + +
1324A THR* 2.7 24.5 + - - +
1325A TYR 2.8 8.8 + - - -
1448A TYR* 3.6 7.6 + - - -
1452A LYS* 5.6 0.5 + - - -
1843A GLN* 4.8 10.4 + - - -
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Residues in contact with TYR1322 (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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1321A ASP* 1.3 80.3 + - - +
1323A ARG* 1.3 63.3 + - - +
1325A TYR* 4.0 2.7 - + - -
1326A ALA* 3.0 33.0 + - + +
1396A GLN* 5.9 2.1 - - - +
1444A THR 5.3 0.2 - - - -
1445A PHE* 2.9 55.6 + + - +
1448A TYR* 3.3 41.9 + + + -
1836A GLN* 5.4 1.1 + - - -
1840A HIS* 3.5 55.4 - + + +
1843A GLN* 4.6 8.3 - - - +
1844A PHE* 3.2 33.7 - + - -
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Residues in contact with ARG1323 (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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1321A ASP* 2.8 10.5 + - + +
1322A TYR* 1.3 81.1 - - - +
1324A THR* 1.3 60.6 + - - +
1326A ALA* 4.5 0.7 - - - +
1327A MET* 2.9 30.8 + - - +
1340A LEU* 4.5 24.0 - - + -
1843A GLN* 3.4 22.3 + - - +
1844A PHE* 4.1 10.2 - - - -
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Residues in contact with THR1324 (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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1320A LEU* 3.6 36.7 - - + +
1321A ASP* 2.7 18.7 + - - +
1323A ARG* 1.3 73.5 - - - +
1325A TYR* 1.3 65.8 + - - +
1327A MET* 3.3 6.0 + - - +
1328A ARG* 3.3 34.9 + - + +
1340A LEU* 6.3 0.7 - - - -
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Residues in contact with TYR1325 (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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1320A LEU* 3.5 23.3 - - + +
1321A ASP 2.8 11.8 + - - +
1322A TYR* 4.1 5.2 - + - -
1324A THR* 1.3 75.9 - - - +
1326A ALA* 1.3 79.2 + - + +
1327A MET 3.4 0.2 + - - -
1328A ARG* 3.4 5.2 + - - +
1329A VAL* 3.3 30.0 - - + +
1444A THR* 2.7 54.0 + - + +
1445A PHE* 5.3 0.7 - - - -
1448A TYR* 3.3 32.9 + + + -
1451A LEU* 3.8 22.4 - - + +
1747A PHE* 3.5 16.9 - + - -
1751A VAL* 5.4 2.0 - - + -
1757A PHE 3.5 28.3 - - - +
1758A VAL* 4.2 15.3 - - + -
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Residues in contact with ALA1326 (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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1322A TYR* 3.0 38.9 + - + +
1323A ARG 4.5 1.3 - - - +
1325A TYR* 1.3 91.3 - - + +
1327A MET* 1.3 63.9 + - - +
1329A VAL* 3.4 1.4 + - - +
1330A LEU* 3.2 32.5 + - + +
1444A THR* 4.5 4.5 - - + -
1445A PHE* 4.1 16.8 - - + -
1844A PHE* 4.7 6.5 - - + -
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Residues in contact with MET1327 (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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1323A ARG 2.9 24.5 - - - +
1324A THR* 3.3 6.3 + - - +
1325A TYR 3.3 1.2 - - - -
1326A ALA* 1.3 75.4 - - - +
1328A ARG* 1.3 68.9 + - - +
1329A VAL 3.0 9.1 + - - -
1330A LEU* 6.0 2.5 - - - -
1331A PHE* 3.2 52.0 + - + +
1334A ILE* 5.3 9.2 - - + +
1336A ASP 5.5 5.4 - - - +
1339A VAL* 3.5 49.8 - - + -
1340A LEU* 4.9 15.9 - - + -
1393A THR* 6.5 0.2 - - - -
1844A PHE* 4.7 10.8 - - + -
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Residues in contact with ARG1328 (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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1320A LEU* 5.0 6.1 - - + -
1324A THR* 3.3 27.5 + - + +
1325A TYR 3.4 4.7 + - - +
1326A ALA 3.4 0.2 - - - -
1327A MET* 1.3 85.6 - - - +
1329A VAL* 1.3 59.3 + - - +
1331A PHE 4.3 13.4 - - - +
1332A PRO* 4.7 4.5 - - - +
1333A GLY* 5.3 5.3 - - - +
1334A ILE 4.0 21.3 + - - +
1335A GLU* 3.1 44.3 + - - +
1756A GLN 5.4 1.1 - - - +
1757A PHE* 3.8 47.2 - - + +
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Residues in contact with VAL1329 (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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1325A TYR* 3.3 26.0 - - + +
1326A ALA 3.4 6.3 + - - +
1327A MET 3.0 0.8 - - - -
1328A ARG* 1.3 82.2 - - - +
1330A LEU* 1.3 65.8 + - + +
1331A PHE 3.3 2.4 + - - -
1332A PRO* 4.9 6.3 - - - +
1437A LYS* 4.7 7.4 + - - -
1440A THR* 5.2 6.1 - - + +
1441A ASN* 5.2 1.1 + - - +
1444A THR* 3.4 37.5 - - + +
1747A PHE* 5.8 2.9 - - + -
1750A ASN* 4.2 19.8 + - - +
1751A VAL* 5.4 3.8 - - + -
1757A PHE* 4.2 22.4 - - + -
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Residues in contact with LEU1330 (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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1326A ALA* 3.2 18.2 + - + +
1327A MET* 5.2 2.7 - - - -
1329A VAL* 1.3 87.3 - - + +
1331A PHE* 1.3 85.0 + - + +
1332A PRO* 4.0 5.5 - - - +
1385A GLY 4.8 0.7 - - - +
1386A ASN* 5.2 1.9 - - - +
1389A SER* 3.2 37.1 + - - +
1392A MET* 4.8 0.2 - - + -
1393A THR* 5.2 4.9 - - - +
1437A LYS* 4.7 3.8 + - - +
1441A ASN* 3.2 42.8 - - + +
1444A THR* 4.4 7.4 - - - +
1445A PHE* 3.3 33.4 - - + -
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Residues in contact with PHE1331 (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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1327A MET* 3.2 46.1 + - + +
1328A ARG* 4.3 7.2 - - - +
1329A VAL 3.3 0.6 - - - -
1330A LEU* 1.3 99.0 - - + +
1332A PRO* 1.3 70.4 - - - +
1333A GLY 3.3 1.0 + - - -
1334A ILE* 3.3 37.2 + - + +
1339A VAL* 4.4 12.1 - - + -
1386A ASN* 4.7 22.0 - - - -
1389A SER* 3.8 25.1 - - - -
1390A LEU* 4.1 25.4 - - + -
1393A THR* 5.1 6.5 - - - -
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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