Contacts of the helix formed by residues 1321 - 1331 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1319B PHE 3.5 5.4 + - - -
1320B LEU* 1.3 79.8 - - - +
1322B TYR* 1.3 66.7 + - - +
1323B ARG* 4.2 15.5 - - + +
1324B THR* 3.0 31.8 + - - -
1325B TYR 2.8 13.3 + - - -
1448B TYR* 4.0 5.8 - - - -
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Residues in contact with TYR1322 (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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1321B ASP* 1.3 72.4 - - - +
1323B ARG* 1.3 61.5 + - - +
1325B TYR* 3.4 26.0 - + - +
1326B ALA* 3.5 8.2 + - + +
1396B GLN* 3.7 10.6 + - - -
1445B PHE* 2.9 58.7 + + - +
1448B TYR* 3.4 46.5 + + + -
1836B GLN* 5.6 0.4 + - - -
1840B HIS* 3.5 30.2 - + + +
1843B GLN* 3.0 33.6 + - - +
1844B PHE* 3.3 27.0 - + - -
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Residues in contact with ARG1323 (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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1321B ASP* 2.9 14.5 + - + +
1322B TYR* 1.3 75.3 - - - +
1324B THR* 1.3 60.3 + - - +
1325B TYR 3.0 7.5 + - - -
1326B ALA 3.7 0.2 + - - -
1327B MET* 2.9 34.1 + - + +
1340B LEU* 3.5 36.6 + - + +
1842B SER 3.9 6.1 + - - -
1843B GLN* 2.9 66.2 + - - +
1844B PHE* 4.5 10.8 - - + +
1845B ASN 5.3 0.6 - - - +
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Residues in contact with THR1324 (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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1320B LEU* 3.2 34.8 - - + +
1321B ASP* 3.0 25.0 + - - -
1323B ARG* 1.3 76.6 - - - +
1325B TYR* 1.3 61.6 + - - +
1327B MET* 4.4 9.0 - - + -
1328B ARG* 3.9 14.9 + - + +
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Residues in contact with TYR1325 (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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1320B LEU* 3.6 10.5 - - - +
1321B ASP 2.8 14.1 + - - +
1322B TYR* 3.4 22.0 - + - +
1323B ARG 3.0 0.2 - - - -
1324B THR* 1.3 81.9 - - - +
1326B ALA* 1.3 64.5 + - + +
1328B ARG* 4.1 0.9 + - - +
1329B VAL* 3.2 32.2 + - + +
1444B THR* 2.7 44.5 + - + -
1447B LEU 4.1 1.6 + - - -
1448B TYR* 3.7 26.2 - + + -
1451B LEU* 3.9 22.3 - - + +
1747B PHE* 3.2 28.5 - + - -
1751B VAL* 6.1 4.3 - - + -
1757B PHE* 3.6 23.8 - - + +
1758B VAL* 4.6 7.6 - - + -
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Residues in contact with ALA1326 (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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1322B TYR* 3.5 11.5 + - + +
1323B ARG 4.6 2.0 - - - +
1325B TYR* 1.3 81.6 - - + +
1327B MET* 1.3 71.5 + - - +
1328B ARG 3.2 2.0 - - - -
1329B VAL* 2.8 12.4 + - - -
1330B LEU* 2.8 25.4 + - + +
1444B THR* 4.1 16.2 - - + -
1445B PHE* 3.9 29.4 - - + -
1844B PHE* 5.0 5.2 - - + -
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Residues in contact with MET1327 (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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1323B ARG* 2.9 28.7 + - + +
1324B THR* 4.7 8.3 - - + -
1325B TYR 3.6 0.2 - - - -
1326B ALA* 1.3 78.8 - - - +
1328B ARG* 1.3 56.4 + - - +
1330B LEU* 5.1 1.1 - - - -
1331B PHE* 3.1 50.4 + - + +
1334B ILE 5.1 9.7 - - - +
1337B HIS* 4.8 16.4 - - + -
1339B VAL* 3.7 37.9 - - + +
1340B LEU* 4.1 15.3 - - + +
1843B GLN 4.9 2.0 - - - +
1844B PHE* 3.6 31.2 - - + -
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Residues in contact with ARG1328 (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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1320B LEU* 5.2 3.1 - - + -
1324B THR* 3.9 20.7 + - + +
1325B TYR 4.4 2.7 - - - +
1326B ALA 3.2 0.6 - - - -
1327B MET* 1.3 79.0 - - - +
1329B VAL* 1.3 62.3 + - - +
1331B PHE 4.4 4.5 - - - -
1332B PRO* 3.9 11.8 - - - +
1333B GLY 4.8 2.2 + - - +
1334B ILE 5.8 1.6 - - - +
1756B GLN 5.4 0.2 - - - +
1757B PHE* 3.4 47.9 - - + -
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Residues in contact with VAL1329 (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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1325B TYR* 3.2 26.5 - - + +
1326B ALA* 2.8 11.5 + - - +
1328B ARG* 1.3 82.0 - - - +
1330B LEU* 1.3 72.3 + - + +
1332B PRO* 4.1 10.4 - - - +
1440B THR* 5.1 8.3 - - + +
1441B ASN* 5.2 1.3 - - - +
1444B THR* 3.5 28.0 - - + +
1747B PHE* 5.9 3.6 - - + -
1750B ASN* 4.5 17.9 + - - +
1751B VAL* 5.7 5.4 - - + -
1757B PHE* 4.2 24.8 - - + -
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Residues in contact with LEU1330 (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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1326B ALA* 2.8 27.4 + - + +
1327B MET* 5.1 0.7 - - - -
1329B VAL* 1.3 86.8 - - + +
1331B PHE* 1.3 75.8 + - + +
1332B PRO* 3.0 12.2 - - - +
1385B GLY 5.7 0.3 - - - +
1386B ASN* 4.8 5.4 + - - -
1389B SER* 3.4 42.7 + - - +
1392B MET* 5.6 0.2 - - + -
1393B THR* 5.7 2.7 - - - -
1441B ASN* 3.0 40.6 - - + +
1444B THR* 4.5 7.0 - - + +
1445B PHE* 4.6 18.8 - - + -
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Residues in contact with PHE1331 (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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1327B MET* 3.1 33.0 + - + +
1328B ARG* 4.3 2.4 - - - +
1330B LEU* 1.3 86.8 - - + +
1332B PRO* 1.3 67.5 - - - +
1333B GLY 3.2 0.9 + - - -
1334B ILE* 3.1 41.2 + - + +
1337B HIS* 4.8 14.1 - - + -
1339B VAL* 4.1 23.8 - - + -
1386B ASN* 4.3 30.5 - - + +
1389B SER* 3.3 37.5 - - - -
1390B LEU* 4.2 19.7 - - + -
1393B THR* 5.7 2.5 - - - -
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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