Contacts of the helix formed by residues 1295 - 1307 (chain A) in PDB entry 1WUF
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 ALA1295 (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* 4.3 3.6 - - + -
1029A LYS* 4.5 0.9 - - + +
1031A PHE* 3.7 34.1 - - + -
1047A GLU* 2.9 24.7 + - - +
1293A LEU 3.7 1.6 + - - -
1294A GLU* 1.3 78.9 - - - +
1296A GLY* 1.3 68.3 + - - +
1297A VAL 3.4 1.3 + - - -
1298A GLY 3.4 0.2 + - - -
1299A ARG* 3.1 16.2 + - - +
1324A PHE* 4.2 8.3 - - - -
1327A ASP* 3.6 13.5 - - - +
1328A ILE* 3.9 6.1 - - + -
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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 ALA* 1.3 74.1 - - - +
1297A VAL* 1.3 59.8 + - - +
1299A ARG* 3.5 5.7 + - - +
1300A ALA* 3.1 23.4 + - - +
1327A ASP* 2.8 29.4 + - - -
1328A ILE* 3.9 2.6 - - - +
1329A VAL* 3.5 27.0 - - - +
1333A PHE* 4.3 5.1 - - - -
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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 ILE* 3.5 21.8 - - + -
1045A TYR* 3.7 42.2 - - + +
1046A GLY 4.0 13.9 - - - -
1047A GLU* 3.5 7.6 + - + +
1295A ALA 3.4 0.6 - - - -
1296A GLY* 1.3 72.6 - - - +
1298A GLY* 1.3 68.4 + - - +
1300A ALA* 3.3 13.6 + - - +
1301A HIS* 3.3 19.3 + - - +
1328A ILE* 4.4 2.9 - - + +
1329A VAL* 4.4 4.7 - - + -
1348A ILE* 4.2 10.3 - - + -
1352A LEU* 3.8 24.9 - - + -
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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* 2.6 30.7 + - - -
1049A GLU* 4.2 4.3 - - - -
1106A LEU* 6.5 0.9 - - - -
1264A LEU* 5.5 0.3 - - - +
1294A GLU* 3.6 23.7 - - - +
1295A ALA 3.4 0.4 + - - -
1297A VAL* 1.3 74.2 - - - +
1299A ARG* 1.3 61.4 + - - +
1301A HIS* 3.4 6.9 + - - +
1302A ASN* 3.1 22.0 + - - +
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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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1294A GLU* 2.9 37.5 + - + +
1295A ALA 3.1 10.9 + - - +
1296A GLY 3.7 3.6 - - - +
1297A VAL 3.2 0.2 - - - -
1298A GLY* 1.3 73.9 - - - +
1300A ALA* 1.3 58.7 + - - +
1302A ASN* 3.2 6.2 + - - +
1303A ILE* 2.9 37.4 + - + +
1317A ILE* 3.6 21.6 - - + +
1318A SER* 3.2 34.5 + - - +
1320A SER* 3.8 16.6 + - - +
1323A PHE* 5.6 7.3 - - - -
1324A PHE* 3.9 12.1 - - - -
1327A ASP* 3.5 19.6 + - - -
1333A PHE* 3.5 34.5 - - + -
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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 3.1 17.6 + - - +
1297A VAL 3.3 6.0 + - - +
1299A ARG* 1.3 75.2 - - - +
1301A HIS* 1.3 62.0 + - - +
1303A ILE* 3.5 4.8 + - - +
1304A ALA* 3.4 19.2 + - - +
1333A PHE* 4.2 15.0 - - + -
1343A PRO* 5.1 4.8 - - - +
1348A ILE* 3.7 34.0 - - + +
1350A VAL* 3.8 19.5 - - + -
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Residues in contact with HIS1301 (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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1045A TYR 2.9 29.4 - - - -
1046A GLY* 4.5 1.5 - - - -
1047A GLU 5.6 0.6 + - - -
1106A LEU* 2.9 52.8 + - + +
1109A TRP* 5.4 0.7 - - + -
1110A ASP* 4.0 5.0 + - + +
1120A LEU* 4.5 17.6 - - + +
1264A LEU* 3.9 16.2 - - + +
1270A MET* 5.6 0.9 - - - +
1297A VAL* 3.3 23.2 + - + +
1298A GLY* 3.7 7.9 - - - +
1299A ARG 3.3 0.4 - - - -
1300A ALA* 1.3 75.5 - - - +
1302A ASN* 1.3 68.3 + - - +
1304A ALA* 3.0 18.3 + - - +
1305A LEU* 3.1 11.8 + - - +
1348A ILE* 3.2 27.8 - - + +
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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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1262A LEU 5.4 0.5 - - - +
1263A LYS* 5.9 0.8 - - - +
1264A LEU* 4.2 15.9 + - + +
1289A CYS* 3.6 19.9 - - - +
1290A GLY 3.5 18.3 + - - +
1291A GLY* 4.5 1.2 - - - -
1294A GLU* 3.1 26.2 + - - +
1298A GLY 3.1 11.6 + - - +
1299A ARG* 3.4 11.8 - - - +
1301A HIS* 1.3 79.9 - - - +
1303A ILE* 1.3 57.5 + - - +
1305A LEU* 3.3 9.2 + - - +
1306A ALA* 2.9 27.2 + - - +
1316A ASP 4.7 1.2 + - - -
1317A ILE* 3.8 21.9 - - + +
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Residues in contact with ILE1303 (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* 3.7 18.4 - - + +
1299A ARG* 2.9 25.7 + - + +
1300A ALA 3.9 5.2 - - - +
1301A HIS 3.1 0.4 - - - -
1302A ASN* 1.3 73.0 - - - +
1304A ALA* 1.3 65.3 + - - +
1306A ALA* 3.5 1.9 + - - +
1307A ALA* 3.1 21.7 + - - +
1317A ILE* 3.7 22.4 - - + -
1333A PHE* 3.4 40.2 - - + -
1340A LEU* 3.9 19.1 - - + -
1341A LYS 4.6 2.7 - - - +
1342A VAL* 4.1 14.6 - - + +
1343A PRO* 4.0 20.0 - - + -
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Residues in contact with ALA1304 (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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1120A LEU* 3.3 34.8 - - + -
1121A ALA* 3.7 27.8 - - + +
1124A ILE* 3.0 16.7 - - + +
1126A ALA* 4.2 1.0 - - - +
1300A ALA 3.4 9.1 + - - +
1301A HIS 3.0 5.9 + - - +
1303A ILE* 1.3 75.4 - - - +
1305A LEU* 1.3 67.5 + - - +
1307A ALA* 3.4 13.6 + - - +
1308A ARG 4.0 0.9 + - - -
1342A VAL* 4.9 1.3 - - - -
1343A PRO* 5.6 1.7 - - + +
1348A ILE* 6.3 0.2 - - - -
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Residues in contact with LEU1305 (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 ILE* 3.9 7.9 - - - -
1262A LEU* 4.5 10.1 - - + +
1264A LEU* 3.6 30.7 - - + +
1270A MET* 3.3 30.5 - - + -
1273A ALA* 3.8 15.5 - - + -
1274A LEU* 4.2 7.9 - - + -
1289A CYS* 3.9 17.3 - - + -
1301A HIS 3.1 11.0 + - - +
1302A ASN* 3.5 12.1 - - - +
1304A ALA* 1.3 77.5 - - - +
1306A ALA* 1.3 61.9 + - - +
1308A ARG* 3.0 16.1 + - - +
1311A PHE* 3.2 39.5 - - + -
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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 LYS* 3.2 17.7 + - - -
1131A ILE* 3.5 33.3 - - + +
1289A CYS* 3.6 22.2 - - + -
1302A ASN 2.9 17.7 + - - +
1303A ILE 3.6 0.2 - - - +
1305A LEU* 1.3 78.3 - - - +
1307A ALA* 1.3 58.7 + - - +
1308A ARG 3.2 2.0 + - - +
1311A PHE* 3.8 10.7 - - + +
1315A GLY* 6.1 2.7 - - - +
1317A ILE* 3.9 7.0 - - + -
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Residues in contact with ALA1307 (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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1126A ALA* 3.3 27.8 - - + +
1127A THR 4.0 1.6 + - - -
1128A LYS* 2.9 37.1 + - + +
1131A ILE* 3.9 3.8 - - + -
1303A ILE 3.1 12.3 + - - +
1304A ALA* 3.5 8.7 - - - +
1305A LEU 3.1 1.0 + - - -
1306A ALA* 1.3 72.4 - - - +
1308A ARG* 1.3 64.1 + - - +
1309A ASN* 3.8 0.9 + - - +
1342A VAL* 4.1 25.8 - - + -
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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