Contacts of the helix formed by residues 1311 - 1323 (chain B) in PDB entry 1U8C
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 THR1311 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1250B THR 3.4 1.9 + - - +
1251B ASP* 2.9 37.1 + - + -
1310B VAL* 1.3 77.1 - - - +
1312B GLU* 1.3 59.4 + - - +
1313B ASN* 2.6 24.0 + - - -
1314B VAL* 2.8 22.0 + - - +
1315B VAL* 2.9 11.2 + - - -
1333B LEU* 4.2 7.9 - - + -
1334B SER* 3.9 32.5 - - - +
1335B MET* 4.3 16.2 - - + +
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Residues in contact with GLU1312 (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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1310B VAL 3.9 1.6 + - - -
1311B THR* 1.3 72.1 - - - +
1313B ASN* 1.3 62.7 + - - +
1314B VAL 2.9 1.6 + - - -
1315B VAL* 3.1 40.9 + - - +
1316B ASN* 4.6 3.1 + - - +
1332B VAL* 4.1 21.5 - - + +
1333B LEU 4.7 1.0 + - - -
1335B MET* 6.1 0.4 - - - -
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Residues in contact with ASN1313 (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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1251B ASP* 3.4 13.3 + - - +
1252B ALA* 5.3 1.0 - - - +
1311B THR* 2.6 32.5 + - - -
1312B GLU* 1.3 78.6 - - - +
1314B VAL* 1.3 70.2 + - - +
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Residues in contact with VAL1314 (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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1250B THR 4.5 0.2 - - - +
1251B ASP 4.2 5.4 - - - -
1252B ALA 3.7 22.9 - - - +
1253B LYS* 4.2 9.6 - - + +
1310B VAL* 4.2 8.5 - - + -
1311B THR* 2.8 22.3 + - - +
1313B ASN* 1.3 92.3 - - - +
1315B VAL* 1.3 60.6 + - - +
1316B ASN 3.5 2.0 - - - -
1317B LEU* 3.2 36.5 - - + +
1318B TYR* 3.0 31.9 - - + -
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Residues in contact with VAL1315 (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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1310B VAL* 3.7 18.2 - - + -
1311B THR 2.9 11.4 + - - +
1312B GLU* 3.1 46.2 + - - +
1314B VAL* 1.3 72.7 - - - +
1316B ASN* 1.3 82.2 + - + +
1317B LEU 2.9 1.3 - - - -
1318B TYR* 2.7 16.3 + - - +
1319B GLN* 3.2 31.3 + - + +
1330B VAL* 4.5 8.5 - - + +
1331B GLY 4.9 1.1 - - - +
1332B VAL* 4.8 14.8 - - + -
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Residues in contact with ASN1316 (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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1312B GLU* 4.6 3.3 + - - +
1314B VAL 3.5 0.4 - - - -
1315B VAL* 1.3 87.4 - - + +
1317B LEU* 1.3 63.1 + - - +
1319B GLN* 2.9 27.3 + - - +
1320B ASN* 3.3 27.2 + - - -
3320B NAG 3.6 44.7 + - + +
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Residues in contact with LEU1317 (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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248A ARG* 4.3 28.5 - - + +
249A THR* 5.0 2.7 - - + -
272A MET* 4.9 2.5 - - - -
1253B LYS* 4.1 19.7 - - + -
1254B THR 4.8 0.9 - - - +
1314B VAL* 3.2 28.1 + - + +
1315B VAL 2.8 2.0 + - - -
1316B ASN* 1.3 80.4 - - - +
1318B TYR* 1.3 82.5 + - + +
1320B ASN* 3.4 7.0 - - - +
1321B TYR* 3.1 59.4 + - + +
3320B NAG 5.0 5.1 - - - +
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Residues in contact with TYR1318 (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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1223B PHE* 4.5 4.7 - + - -
1248B PHE* 4.0 19.1 - + - -
1250B THR* 3.5 11.2 - - + +
1252B ALA 2.7 26.8 + - - -
1253B LYS 3.3 14.7 + - - -
1254B THR* 3.5 18.3 - - + -
1308B PHE* 4.0 40.1 - + + -
1310B VAL* 4.0 14.1 - - + -
1314B VAL* 3.0 25.4 - - + -
1315B VAL 2.7 11.9 + - - +
1317B LEU* 1.3 91.4 - - + +
1319B GLN* 1.3 63.6 + - - +
1321B TYR* 3.5 13.1 - + - +
1322B SER* 2.9 24.3 + - - -
1330B VAL* 4.3 8.0 - - + +
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Residues in contact with GLN1319 (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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1315B VAL* 3.2 29.3 + - + +
1316B ASN* 2.9 35.8 + - - +
1318B TYR* 1.3 75.8 - - - +
1320B ASN* 1.3 68.0 + - - +
1322B SER* 2.6 24.2 + - - -
1323B GLU* 2.9 12.2 + - - +
1330B VAL* 3.8 23.2 - - + +
3320B NAG 5.0 10.0 - - - +
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Residues in contact with ASN1320 (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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272A MET* 3.5 23.1 - - - +
1316B ASN 3.3 7.8 + - - +
1317B LEU 3.4 9.9 - - - +
1319B GLN* 1.3 79.9 - - - +
1321B TYR* 1.3 59.6 + - - +
1323B GLU* 3.3 11.7 - - - +
1324B LEU* 2.8 27.1 - - - +
3320B NAG 1.5 78.8 + - - +
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Residues in contact with TYR1321 (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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249A THR* 3.2 40.0 + - - +
272A MET* 4.3 11.7 - - + -
273A ALA* 4.0 17.9 - - + -
1223B PHE* 4.9 7.0 - + + -
1254B THR* 4.1 20.0 + - + +
1256B ILE* 3.9 13.9 - - + +
1292B LEU* 4.3 19.5 - - + +
1308B PHE* 4.6 10.5 - - + -
1317B LEU* 3.1 53.8 + - + +
1318B TYR* 3.5 20.2 - + - +
1319B GLN 3.1 0.6 - - - -
1320B ASN* 1.3 78.7 - - - +
1322B SER* 1.3 62.3 + - - +
1324B LEU* 3.0 21.1 + - - +
1325B ILE* 3.3 15.8 - - + +
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Residues in contact with SER1322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1308B PHE* 4.4 9.6 - - - -
1318B TYR 2.9 12.3 + - - -
1319B GLN* 2.6 24.3 + - - -
1321B TYR* 1.3 70.7 - - - +
1323B GLU* 1.3 53.5 + - - +
1324B LEU 2.7 7.9 + - - -
1325B ILE* 2.5 43.6 + - - +
1326B PRO* 3.3 2.6 - - - +
1328B THR* 3.6 33.1 + - - +
1330B VAL* 4.3 9.1 - - - +
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Residues in contact with GLU1323 (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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303A ARG* 5.6 2.4 + - - -
309A LEU* 4.5 6.6 - - - +
1319B GLN 2.9 11.2 + - - +
1320B ASN* 3.3 17.0 - - - +
1321B TYR 3.2 0.2 - - - -
1322B SER* 1.3 77.1 + - - +
1324B LEU* 1.3 66.7 + - + +
1326B PRO* 4.5 7.0 - - - +
1568B MET* 5.4 10.9 - - - +
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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