Contacts of the helix formed by residues 1291 - 1308 (chain A) in PDB entry 5LUQ
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 LEU1291 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1232A PRO* 4.3 32.1 - - + -
1233A SER 5.5 6.3 - - - +
1234A GLY 5.9 1.8 - - - +
1236A LEU* 4.9 1.4 - - - +
1261A LEU* 5.5 11.4 - - + -
1265A GLU* 4.5 15.3 - - - +
1279A LEU* 5.9 1.3 - - + -
1282A LEU* 5.9 5.8 - - + -
1287A GLN* 4.9 12.6 - - - +
1288A SER* 2.8 21.0 + - - +
1290A LEU* 1.3 80.4 - - - +
1292A LYS* 1.3 88.8 + - + +
1293A ALA 3.4 1.4 - - - +
1295A ALA* 3.0 24.8 + - - +
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Residues in contact with LYS1292 (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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1265A GLU* 4.8 13.5 - - - +
1279A LEU* 3.0 41.0 + - - +
1282A LEU* 5.7 0.4 - - - +
1291A LEU* 1.3 98.0 - - + +
1293A ALA* 1.3 66.3 + - - +
1295A ALA* 3.0 20.1 + - - +
1296A PHE* 2.8 28.1 - - + -
1361A LYS* 2.4 51.4 - - + +
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Residues in contact with ALA1293 (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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1289A SER* 5.6 5.6 - - - -
1290A LEU 5.4 6.1 - - - +
1291A LEU 3.4 1.2 - - - +
1292A LYS* 1.3 76.9 - - - +
1294A VAL* 1.3 63.6 + - + +
1296A PHE* 2.8 38.4 + - - +
1297A PHE* 3.1 3.8 + - - +
1362A ASP* 6.4 0.4 - - - +
1364A CYS* 3.9 13.1 - - - +
1367A HIS* 5.6 0.2 - - - -
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Residues in contact with VAL1294 (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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1236A LEU* 3.5 35.4 - - + -
1238A GLN* 4.2 16.8 - - - +
1289A SER 4.6 2.5 - - - +
1290A LEU* 4.0 32.5 - - + +
1291A LEU 3.7 2.2 + - - -
1293A ALA* 1.3 79.3 - - + +
1295A ALA* 1.3 56.9 + - - +
1297A PHE* 2.8 28.1 + - + +
1298A LEU* 2.8 13.7 + - + +
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Residues in contact with ALA1295 (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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1236A LEU* 4.7 1.3 - - + +
1265A GLU* 6.1 0.4 - - - +
1291A LEU 3.0 17.7 + - - +
1292A LYS* 3.0 17.5 - - - +
1294A VAL* 1.3 75.6 - - - +
1296A PHE* 1.3 60.2 + - + +
1298A LEU* 3.0 25.9 + - + +
1299A GLU* 3.0 10.6 + - - +
1341A ILE* 5.2 4.3 - - - +
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Residues in contact with PHE1296 (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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1292A LYS* 2.8 49.2 + - + -
1293A ALA* 2.8 17.4 + - - +
1295A ALA* 1.3 71.3 - - - +
1297A PHE* 1.3 53.4 + - - +
1299A GLU* 2.4 60.8 + - - +
1300A SER 2.9 9.4 + - - -
1345A THR* 5.2 7.2 - - + -
1348A LEU* 5.6 10.8 - - + -
1362A ASP* 3.4 39.9 - - + -
1364A CYS* 3.4 29.8 - - + -
1367A HIS* 4.0 3.4 + - - +
1368A LEU* 4.2 11.7 - - + -
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Residues in contact with PHE1297 (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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1238A GLN* 3.5 25.8 - - - -
1293A ALA 3.1 6.4 + - - +
1294A VAL* 2.8 28.0 + - + +
1296A PHE* 1.3 72.0 - - - +
1298A LEU* 1.3 55.0 + - - +
1300A SER* 3.6 6.4 + - - +
1301A ILE* 2.9 50.0 + - + +
1367A HIS* 4.1 25.0 + + + -
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Residues in contact with LEU1298 (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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1236A LEU* 3.8 29.4 - - + -
1237A ALA* 4.2 9.6 - - - +
1238A GLN* 3.2 39.0 - - + +
1254A LEU* 5.0 6.3 - - + -
1258A ASP* 4.4 28.3 - - - +
1294A VAL* 2.8 20.2 + - + +
1295A ALA* 3.3 15.3 - - + +
1296A PHE 3.0 0.2 - - - -
1297A PHE* 1.3 73.6 - - - +
1299A GLU* 1.3 59.3 + - - +
1301A ILE* 3.6 14.5 - - + +
1302A ALA* 2.9 24.4 + - - +
1305A ASP* 5.1 0.2 - - - +
1341A ILE* 5.0 4.4 - - + +
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Residues in contact with GLU1299 (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 3.0 6.2 + - - +
1296A PHE* 2.4 69.6 + - - +
1298A LEU* 1.3 65.9 - - - +
1300A SER* 1.3 58.8 + - - +
1302A ALA* 2.9 21.5 + - + +
1303A MSE 2.9 15.2 + - - +
1338A VAL* 5.1 2.8 - - + +
1341A ILE* 3.2 38.8 - - + +
1345A THR* 4.2 3.6 + - - -
1364A CYS 4.5 0.2 - - - +
1367A HIS* 4.1 9.4 - - + +
1368A LEU* 3.8 30.0 + - - +
1371A VAL* 4.5 15.6 - - + +
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Residues in contact with SER1300 (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 PHE 2.9 6.2 + - - -
1297A PHE* 3.8 11.9 - - - -
1299A GLU* 1.3 74.0 - - - +
1301A ILE* 1.3 58.8 + - - +
1302A ALA 3.0 4.0 + - - -
1303A MSE 3.3 13.9 + - - +
1304A HIS* 2.4 57.3 + - - -
1367A HIS* 3.9 35.2 - - - +
1371A VAL* 5.8 2.0 - - - -
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Residues in contact with ILE1301 (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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1238A GLN* 3.3 26.7 - - + +
1297A PHE* 2.9 50.2 + - + +
1298A LEU* 3.7 15.9 - - + +
1300A SER* 1.3 78.1 - - - +
1302A ALA* 1.3 56.9 + - - +
1304A HIS* 3.7 18.1 - - + +
1305A ASP* 2.8 43.7 + - + +
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Residues in contact with ALA1302 (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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1298A LEU 2.9 17.5 + - - +
1299A GLU* 2.9 19.3 + - - +
1301A ILE* 1.3 76.0 - - - +
1303A MSE 1.3 58.8 + - - +
1305A ASP* 2.6 24.7 - - - +
1306A ILE* 2.8 22.4 + - + +
1334A LYS* 5.6 1.3 - - + +
1337A VAL* 5.8 3.8 - - + -
1338A VAL* 4.0 22.0 - - + -
1341A ILE* 5.1 5.8 - - + -
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Residues in contact with MSE1303 (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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1299A GLU 2.9 8.1 + - - +
1300A SER* 3.8 14.6 - - - +
1302A ALA* 1.3 73.0 - - - +
1304A HIS* 1.3 79.9 + - + +
1306A ILE* 3.2 10.9 + - + +
1307A ILE* 3.0 40.2 + - + +
1367A HIS 5.5 0.7 - - - +
1370A ARG* 3.6 22.0 - - + +
1371A VAL* 3.5 45.2 - - + +
1374A GLN* 4.8 9.4 - - - -
1378A GLU* 5.0 7.0 - - - +
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Residues in contact with HIS1304 (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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1300A SER* 2.4 52.2 + - - +
1301A ILE* 3.7 19.3 + - + +
1303A MSE 1.3 86.7 - - + +
1305A ASP* 1.3 58.9 - - - +
1307A ILE* 3.0 17.1 + - + +
1308A ALA* 2.9 24.3 + - - +
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Residues in contact with ASP1305 (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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1254A LEU* 5.6 2.1 - - - +
1298A LEU 5.1 0.3 - - - +
1301A ILE* 2.8 39.6 + - + +
1302A ALA* 2.6 16.7 - - - +
1304A HIS* 1.3 71.3 - - - +
1306A ILE* 1.3 85.0 + - - +
1308A ALA 3.1 12.2 - - - +
1330A TYR* 2.4 42.9 + - - +
1334A LYS* 2.6 38.9 + - - +
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Residues in contact with ILE1306 (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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1302A ALA* 2.8 23.2 + - + +
1303A MSE 3.4 9.6 - - + +
1304A HIS 3.2 0.2 - - - -
1305A ASP* 1.3 81.8 + - - +
1307A ILE* 1.3 63.2 + - - +
1330A TYR* 4.8 0.2 - - - -
1331A ASN* 4.1 12.8 - - - +
1334A LYS* 3.2 33.7 - - + +
1335A CYS* 4.5 1.1 - - - +
1338A VAL* 3.5 44.4 - - + -
1378A GLU* 3.8 18.4 - - - +
1381A SER* 3.0 43.6 - - - +
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Residues in contact with ILE1307 (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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1303A MSE 3.0 29.8 + - + +
1304A HIS* 3.0 12.0 + - + +
1305A ASP 3.7 0.4 - - - -
1306A ILE* 1.3 80.3 - - - +
1308A ALA* 1.3 63.3 + - + +
1330A TYR* 5.3 1.0 - - - -
1331A ASN* 5.5 1.0 - - - +
1381A SER* 4.5 17.3 - - - +
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Residues in contact with ALA1308 (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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1304A HIS 2.9 9.2 + - - +
1305A ASP* 3.1 12.0 - - - +
1307A ILE* 1.3 83.7 - - + +
1330A TYR* 2.8 37.0 + - - -
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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