Contacts of the helix formed by residues 1335 - 1354 (chain P) in PDB entry 1YYL
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 LYS1335 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1333P LEU 3.3 5.7 + - - -
1334P SER* 1.3 70.7 + - - +
1336P THR* 1.3 61.5 + - - +
1338P TRP* 3.1 4.0 + - - +
1339P GLU* 2.8 36.1 + - + +
1412P ARG* 3.6 55.4 + - + +
1413P ASN 5.1 2.5 - - - +
1414P ILE* 3.3 30.7 - - + +
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Residues in contact with THR1336 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1334P SER* 3.5 4.8 + - - -
1335P LYS* 1.3 81.5 - - - +
1337P GLN* 1.3 62.9 + - - +
1339P GLU* 4.4 6.3 - - + -
1340P ASN* 3.1 40.0 + - - +
1412P ARG* 4.8 6.9 + - - +
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Residues in contact with GLN1337 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1290P GLU* 4.4 12.3 - - - +
1291P SER 3.6 16.9 + - - +
1292P VAL* 4.3 25.3 - - + +
1293P VAL* 4.5 8.1 + - - +
1334P SER* 3.3 32.5 + - - +
1335P LYS 3.1 0.8 - - - -
1336P THR* 1.3 79.4 - - - +
1338P TRP* 1.3 52.3 + - - +
1340P ASN* 3.5 4.6 + - - +
1341P THR* 2.3 37.1 + - - +
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Residues in contact with TRP1338 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1259P LEU* 3.5 25.8 - - + -
1288P LEU* 5.3 0.2 - - + -
1292P VAL* 4.2 11.4 - - + -
1333P LEU* 3.7 20.1 - - + +
1334P SER 3.0 17.0 + - - +
1335P LYS 3.6 3.8 - - - +
1337P GLN* 1.3 74.7 - - - +
1339P GLU* 1.3 65.9 + - - +
1341P THR* 3.0 18.6 + - + -
1342P LEU* 3.0 53.7 + - + +
1345P ILE* 5.9 0.7 - - + -
1389P GLN 5.2 1.3 - - - -
1390P LEU* 3.1 52.6 + - + +
1391P PHE* 4.3 6.1 - + - -
1414P ILE* 3.8 11.4 - - + -
1449P ILE* 3.7 26.9 - - + -
1452P LEU* 4.0 26.9 - - + -
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Residues in contact with GLU1339 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1335P LYS* 2.8 24.4 + - + +
1336P THR* 3.9 9.0 - - + +
1338P TRP* 1.3 79.2 - - - +
1340P ASN* 1.3 79.1 + - - +
1342P LEU* 3.7 7.1 + - - +
1343P GLU* 3.2 31.2 + - - +
1393P TRP* 3.5 29.3 + - + +
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Residues in contact with ASN1340 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1336P THR* 3.1 34.0 + - - +
1337P GLN* 3.9 5.2 - - - +
1339P GLU* 1.3 87.9 + - - +
1341P THR* 1.3 67.9 + - - +
1343P GLU* 3.1 24.1 + - - +
1344P GLN* 3.1 21.1 + - - +
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Residues in contact with THR1341 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270P ILE* 5.0 3.8 - - + -
1288P LEU* 3.5 39.7 - - + -
1290P GLU 5.9 0.2 - - - +
1292P VAL* 4.2 12.4 - - + +
1337P GLN 2.3 29.1 + - - -
1338P TRP* 3.0 21.0 + - + -
1340P ASN* 1.3 71.4 - - - +
1342P LEU* 1.3 69.7 + - - +
1343P GLU 2.9 0.9 - - - -
1344P GLN* 2.7 22.4 + - - +
1345P ILE* 3.0 19.2 + - + +
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Residues in contact with LEU1342 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1338P TRP* 3.0 54.1 + - + +
1339P GLU* 4.0 4.9 - - - +
1341P THR* 1.3 76.7 - - - +
1343P GLU* 1.3 56.0 + - - +
1345P ILE* 3.3 15.5 + - + +
1346P ALA* 2.9 31.2 + - - +
1361P PHE* 3.7 40.9 - - + -
1390P LEU 3.9 11.2 - - - +
1391P PHE* 4.9 5.4 - - + -
1393P TRP* 3.8 41.1 - - + -
1452P LEU* 5.5 1.1 - - + -
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Residues in contact with GLU1343 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1339P GLU* 3.2 31.9 + - - +
1340P ASN* 3.1 22.4 + - - +
1341P THR 2.7 0.6 + - - -
1342P LEU* 1.3 79.4 - - - +
1344P GLN* 1.3 70.9 + - - +
1346P ALA* 3.4 4.0 + - - +
1347P ILE* 3.1 35.5 + - + +
1393P TRP* 4.0 20.0 - - + -
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Residues in contact with GLN1344 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270P ILE* 3.2 28.3 - - + -
1340P ASN* 3.4 26.3 + - + +
1341P THR* 2.7 10.4 + - - +
1343P GLU* 1.3 83.1 - - - +
1345P ILE* 1.3 65.7 + - - +
1347P ILE* 3.1 21.7 + - - +
1348P LYS* 3.0 26.1 + - - +
1789P NAG 3.7 33.9 + - - +
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Residues in contact with ILE1345 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1270P ILE* 4.3 15.3 - - + -
1272P ILE* 4.7 2.8 - - + +
1286P VAL* 4.0 22.9 - - + -
1288P LEU* 4.2 0.7 - - + -
1338P TRP* 5.9 0.9 - - + -
1341P THR* 3.0 30.8 + - + +
1342P LEU* 3.5 18.6 - - + +
1344P GLN* 1.3 76.4 - - - +
1346P ALA* 1.3 51.8 + - - +
1348P LYS* 3.4 6.8 + - - +
1349P LEU* 2.8 55.2 + - + +
1361P PHE* 4.0 9.0 - - + -
1452P LEU* 4.0 29.8 - - + -
1454P LEU* 4.1 14.6 - - + -
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Residues in contact with ALA1346 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1342P LEU 2.9 17.7 + - - +
1343P GLU 3.5 5.2 - - - +
1345P ILE* 1.3 75.3 - - - +
1347P ILE* 1.3 57.9 + - + +
1349P LEU* 2.8 14.7 + - - +
1350P LYS* 2.7 41.4 + - - +
1359P ILE* 3.5 29.3 - - + +
1361P PHE* 4.2 0.7 - - + -
1393P TRP* 3.8 15.5 - - + -
1395P ASP* 4.9 2.0 - - - +
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Residues in contact with ILE1347 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1343P GLU* 3.1 25.5 + - + +
1344P GLN* 3.1 29.2 + - - +
1346P ALA* 1.3 76.0 - - + +
1348P LYS* 1.3 64.7 + - + +
1350P LYS* 3.1 30.6 - - + +
1351P GLU* 3.2 12.8 + - - +
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Residues in contact with LYS1348 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1232P LYS* 2.9 32.1 - - - +
1269P GLU* 3.5 27.0 + - - +
1270P ILE* 3.3 32.5 + - + +
1271P VAL* 5.5 0.7 - - - -
1272P ILE* 3.4 30.9 - - + +
1344P GLN 3.0 14.5 + - - +
1345P ILE* 3.7 8.1 - - - +
1347P ILE* 1.3 79.2 - - + +
1349P LEU* 1.3 66.5 + - - +
1351P GLU* 3.0 43.6 + - - +
1352P GLN* 3.4 5.5 + - - +
1789P NAG 4.5 7.6 - - - +
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Residues in contact with LEU1349 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272P ILE* 4.1 21.3 - - + -
1277P PHE* 5.2 0.2 - - + -
1284P ILE* 4.5 12.8 - - + -
1345P ILE* 2.8 26.7 + - + +
1346P ALA* 2.8 11.1 + - - +
1348P LYS* 1.3 78.3 - - - +
1350P LYS* 1.3 55.6 + - - +
1351P GLU 3.1 0.2 - - - -
1352P GLN* 3.2 3.2 + - - +
1353P PHE* 3.1 37.8 + - + -
1359P ILE* 4.2 6.7 - - + -
1361P PHE* 3.6 29.8 - - + -
1454P LEU* 4.5 6.7 - - + -
1468P PHE* 3.5 50.7 - - + -
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Residues in contact with LYS1350 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1346P ALA* 2.7 21.8 + - - +
1347P ILE* 3.1 30.1 - - + +
1349P LEU* 1.3 69.5 - - - +
1351P GLU* 1.3 56.8 + - - +
1352P GLN 3.0 5.4 - - - -
1353P PHE* 4.1 1.3 - - - +
1354P GLY* 2.8 50.2 + - - +
1355P ASN* 3.3 26.0 + - - +
1357P LYS 3.7 12.4 + - - -
1359P ILE* 3.6 29.8 - - + +
1395P ASP* 4.4 17.3 + - - -
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Residues in contact with GLU1351 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1232P LYS* 3.5 23.6 + - - -
1347P ILE* 3.2 15.9 + - - +
1348P LYS* 3.0 40.4 + - - +
1350P LYS* 1.3 78.7 - - - +
1352P GLN* 1.3 64.8 + - + +
1354P GLY 4.7 0.7 - - - -
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Residues in contact with GLN1352 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1232P LYS* 6.1 0.8 - - - +
1272P ILE* 3.5 29.8 + - + +
1277P PHE* 3.0 44.2 - - + +
1348P LYS 3.9 2.0 - - - +
1349P LEU 3.2 8.7 + - - +
1350P LYS 3.0 0.2 - - - -
1351P GLU* 1.3 88.0 + - + +
1353P PHE* 1.3 75.3 + - + +
1354P GLY 3.7 0.9 - - - -
1734P NAG 5.3 4.5 + - - -
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Residues in contact with PHE1353 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1277P PHE* 3.4 51.4 - + + -
1278P THR* 5.2 1.3 - - - -
1284P ILE* 4.8 2.5 - - + -
1349P LEU* 3.1 29.1 + - + +
1350P LYS* 4.9 0.7 - - - -
1352P GLN* 1.3 83.3 - - + +
1354P GLY* 1.3 58.9 + - - +
1357P LYS* 2.9 43.7 + - + +
1359P ILE* 6.2 0.9 - - + -
1456P ARG* 3.0 44.2 - - - -
1466P GLU* 4.3 15.0 - - + -
1468P PHE* 3.8 22.4 - + - -
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Residues in contact with GLY1354 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1350P LYS* 2.8 29.0 + - - +
1351P GLU 4.7 0.4 - - - -
1352P GLN 3.7 1.2 - - - -
1353P PHE* 1.3 80.4 - - - +
1355P ASN* 1.3 63.8 + - - -
1356P ASN 3.3 2.9 - - - -
1357P LYS* 3.2 16.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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