Contacts of the helix formed by residues 1295 - 1307 (chain A) in PDB entry 1WUE
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 SER1295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1013A LEU* 4.5 6.1 - - - -
1031A PHE* 3.4 36.8 - - - -
1047A GLU* 2.8 25.9 + - - -
1293A PHE 3.9 0.6 + - - -
1294A GLU* 1.3 77.2 - - - +
1296A GLY* 1.3 66.3 + - - +
1297A VAL* 3.0 10.0 + - - +
1298A GLY 3.2 1.0 + - - -
1299A ARG* 2.9 21.2 + - - +
1320A THR* 5.2 0.4 - - - -
1324A PHE* 4.9 2.2 - - - -
1327A ASP* 3.9 5.4 - - - -
1328A ILE* 3.4 15.2 - - - +
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Residues in contact with GLY1296 (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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1295A SER* 1.3 72.3 + - - +
1297A VAL* 1.3 57.1 + - - +
1299A ARG* 3.8 1.5 - - - +
1300A ALA* 3.0 30.5 + - - +
1320A THR* 4.2 0.4 - - - -
1327A ASP* 2.9 33.6 + - - -
1328A ILE* 4.4 0.2 - - - +
1329A ILE* 3.9 12.8 - - - -
1333A PHE* 3.4 19.4 - - - -
1350A VAL* 4.2 1.7 - - - +
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Residues in contact with VAL1297 (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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1033A LEU* 4.0 12.6 - - + -
1045A PHE* 4.0 15.9 - - + +
1046A GLY* 4.1 24.7 - - - +
1047A GLU* 3.6 9.0 - - + +
1295A SER* 3.0 1.7 + - - +
1296A GLY* 1.3 80.7 - - - +
1298A GLY* 1.3 63.5 + - - +
1300A ALA* 3.4 8.5 + - - +
1301A LEU* 3.5 10.0 + - - +
1328A ILE* 3.8 22.0 - - + -
1329A ILE* 4.2 4.5 - - + -
1348A ILE* 3.9 25.4 - - + +
1350A VAL* 4.8 3.1 - - + -
1352A LEU* 3.9 22.0 - - + -
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Residues in contact with GLY1298 (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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1047A GLU* 2.9 25.9 + - - -
1049A VAL* 5.8 0.4 - - - -
1294A GLU* 3.9 17.5 - - - -
1295A SER 3.2 0.6 + - - -
1297A VAL* 1.3 77.7 - - - +
1299A ARG* 1.3 56.4 + - - +
1301A LEU* 3.3 10.3 + - - +
1302A ASN* 2.9 32.4 + - - +
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Residues in contact with ARG1299 (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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1293A PHE* 4.2 4.4 - - - +
1294A GLU* 2.6 48.8 + - + +
1295A SER 2.9 21.4 + - - +
1298A GLY* 1.3 73.7 - - - +
1300A ALA* 1.3 65.5 + - - +
1302A ASN* 3.3 8.6 + - - +
1303A LEU* 3.1 25.8 + - + +
1317A ILE* 4.4 12.4 - - + +
1318A SER* 2.9 34.8 + - - +
1319A ALA 4.7 0.2 - - - -
1320A THR* 3.1 32.6 + - - +
1323A TYR* 4.3 20.0 - - - -
1324A PHE* 4.7 2.4 - - - -
1333A PHE* 3.6 33.4 - - + -
1340A MET* 5.1 0.2 - - - -
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Residues in contact with ALA1300 (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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1296A GLY 3.0 19.9 + - - +
1297A VAL 3.7 4.9 - - - +
1298A GLY 3.3 0.2 - - - -
1299A ARG* 1.3 75.5 - - - +
1301A LEU* 1.3 62.7 + - - +
1303A LEU* 3.5 2.6 + - - +
1304A GLN* 3.2 28.3 + - - +
1333A PHE* 3.7 14.8 - - + -
1343A PRO* 4.1 5.0 - - + +
1348A ILE* 3.5 18.4 - - + +
1350A VAL* 3.5 26.0 - - + -
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Residues in contact with LEU1301 (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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1106A THR* 3.6 36.3 - - + +
1120A LEU* 3.6 28.5 - - + -
1124A PHE* 4.1 11.4 - - + -
1264A ILE* 3.8 24.9 - - + -
1270A ILE* 3.6 14.6 - - + -
1297A VAL 3.5 9.4 + - - +
1298A GLY* 3.3 11.6 + - - +
1299A ARG 3.2 0.4 - - - -
1300A ALA* 1.3 77.7 - - - +
1302A ASN* 1.3 68.1 + - - +
1304A GLN* 3.2 3.8 + - - +
1305A PHE* 2.9 21.7 + - + +
1348A ILE* 4.1 14.5 - - + +
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Residues in contact with ASN1302 (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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1264A ILE* 4.1 18.7 + - - +
1265A PRO* 5.1 1.6 - - - +
1289A LEU* 3.4 27.9 - - + +
1290A GLY 4.4 7.5 + - - -
1291A GLY* 4.9 1.8 - - - -
1294A GLU* 3.1 38.5 + - - +
1298A GLY* 2.9 17.8 + - - +
1299A ARG* 3.3 11.5 + - - +
1301A LEU* 1.3 77.4 - - - +
1303A LEU* 1.3 57.0 + - - +
1305A PHE* 3.9 2.0 - - - -
1306A ALA* 2.8 34.1 + - - +
1316A ASP 5.5 1.0 + - - -
1317A ILE* 4.1 14.2 - - + +
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Residues in contact with LEU1303 (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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1131A ILE* 3.8 19.1 - - + +
1133A VAL* 4.7 0.2 - - + -
1299A ARG* 3.1 17.9 + - + +
1300A ALA 3.8 3.8 - - - +
1302A ASN* 1.3 75.6 - - - +
1304A GLN* 1.3 57.9 + - - +
1306A ALA 3.7 0.7 - - - -
1307A SER* 3.0 31.2 + - - -
1317A ILE* 3.3 30.1 - - + -
1333A PHE* 3.5 40.2 - - + -
1340A MET* 3.9 30.5 - - + -
1341A THR 3.8 15.3 - - - +
1342A VAL* 4.0 5.7 - - - +
1343A PRO* 3.8 11.2 - - + -
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Residues in contact with GLN1304 (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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1119A SER* 3.4 5.9 + - - -
1120A LEU* 3.2 33.0 - - - +
1121A THR* 3.5 20.2 - - + +
1124A PHE* 3.5 16.2 - - + -
1127A THR* 4.1 4.5 - - - +
1300A ALA 3.2 10.1 + - - +
1301A LEU* 3.2 7.4 + - - +
1303A LEU* 1.3 80.5 - - - +
1305A PHE* 1.3 58.6 + - - +
1307A SER* 2.7 19.6 + - - -
1342A VAL* 3.8 16.4 - - + -
1343A PRO* 3.2 20.1 - - + +
1347A GLY 2.9 17.5 - - - +
1348A ILE* 3.4 28.9 - - - +
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Residues in contact with PHE1305 (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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1124A PHE* 3.7 25.3 - + + -
1262A LEU* 3.6 11.2 - - + -
1264A ILE* 3.9 20.4 - - + -
1270A ILE* 4.3 5.2 - - + -
1273A ALA* 3.6 37.5 - - + -
1274A LEU* 3.4 29.4 - - + -
1277A ALA* 4.5 2.0 - - + -
1289A LEU* 4.2 11.9 - - + -
1301A LEU 2.9 15.9 + - - +
1302A ASN* 3.9 2.7 - - - +
1304A GLN* 1.3 73.6 - - - +
1306A ALA* 1.3 62.9 + - - +
1307A SER 3.1 4.5 - - - -
1308A GLN* 2.9 41.1 + - - +
1311A PHE* 3.4 31.4 - + - -
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Residues in contact with ALA1306 (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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1128A ARG* 3.2 19.6 + - - -
1131A ILE* 4.2 7.8 - - + +
1289A LEU* 4.1 16.4 - - + -
1302A ASN 2.8 18.4 + - - +
1303A LEU 3.7 2.2 - - - +
1305A PHE* 1.3 74.1 - - - +
1307A SER* 1.3 59.8 + - - +
1308A GLN 3.2 2.4 + - - -
1311A PHE* 3.5 23.6 - - + +
1315A GLY* 6.2 1.6 - - - +
1317A ILE* 3.6 23.6 - - + -
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Residues in contact with SER1307 (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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1121A THR* 4.4 0.5 - - - +
1127A THR* 3.2 17.0 - - - -
1128A ARG* 2.9 52.1 + - - -
1131A ILE* 3.7 11.2 - - - -
1303A LEU 3.0 15.9 + - - -
1304A GLN* 2.7 22.0 + - - -
1305A PHE 3.1 0.2 - - - -
1306A ALA* 1.3 74.3 - - - +
1308A GLN* 1.3 66.4 + - - +
1309A PRO 3.2 0.5 - - - -
1342A VAL* 3.6 14.1 - - - +
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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