Contacts of the strand formed by residues 1323 - 1337 (chain A) in PDB entry 5DGY
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 GLY1323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1066A PHE* 3.8 18.2 - - - -
1084A LEU* 4.0 9.7 - - - +
1128A PRO* 4.2 3.8 - - - -
1146A VAL* 4.6 0.2 - - - -
1247A ASN 3.9 0.5 - - - +
1249A VAL* 2.8 39.3 + - - +
1322A MET* 1.3 77.5 - - - +
1324A ILE* 1.3 63.8 + - - -
1325A LEU* 3.4 9.5 + - - +
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Residues in contact with ILE1324 (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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1066A PHE* 3.7 26.6 - - + -
1128A PRO* 4.7 7.4 - - - +
1129A CYS 5.1 0.7 + - - +
1131A VAL* 3.8 57.1 - - + +
1133A LEU* 4.1 33.9 - - + -
1144A CYS* 5.3 0.2 - - - -
1145A GLY* 4.2 8.3 - - - +
1146A VAL* 3.9 15.5 - - + +
1246A ALA* 5.5 2.9 - - + -
1247A ASN 4.0 2.2 - - - -
1248A VAL* 4.1 22.2 - - + +
1295A ALA* 5.0 0.9 - - + -
1311A THR* 4.2 2.8 + - - +
1323A GLY* 1.3 68.8 - - - -
1325A LEU* 1.3 67.4 + - - +
1326A VAL* 4.1 10.4 + - + -
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Residues in contact with LEU1325 (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 PRO* 4.4 8.1 - - + -
1246A ALA 3.9 0.3 - - - -
1247A ASN* 2.9 62.0 + - + +
1249A VAL* 4.8 3.8 - - + -
1311A THR* 3.8 26.5 - - + +
1313A ILE* 4.0 24.5 - - + -
1321A VAL* 3.9 38.8 - - + +
1323A GLY 4.1 9.0 - - - +
1324A ILE* 1.3 79.1 - - - +
1326A VAL* 1.3 63.7 + - - +
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Residues in contact with VAL1326 (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 VAL* 4.1 17.9 - - + -
1244A GLN* 4.1 16.8 - - + +
1245A ILE 3.8 4.9 - - - +
1246A ALA* 5.4 2.5 - - - -
1247A ASN* 6.1 0.2 - - - -
1295A ALA* 4.2 8.7 - - + -
1308A ALA* 4.0 24.0 - - + -
1309A SER 3.6 15.0 - - - +
1310A SER* 3.7 0.8 - - - -
1311A THR* 3.0 36.1 + - - +
1324A ILE* 4.2 7.0 - - + +
1325A LEU* 1.3 80.1 - - - +
1327A SER* 1.3 67.6 + - - +
1328A TYR* 3.8 24.5 - - + -
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Residues in contact with SER1327 (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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1244A GLN* 3.9 0.5 - - - -
1245A ILE* 3.0 48.0 + - - +
1310A SER* 4.6 5.6 - - - -
1311A THR 5.8 0.7 - - - -
1326A VAL* 1.3 80.1 - - - +
1328A TYR* 1.3 77.9 + - - +
1353A PRO* 5.3 4.7 - - - +
1354A PHE 4.5 2.9 + - - -
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Residues in contact with TYR1328 (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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1242A VAL* 4.3 15.9 - - + -
1243A GLU 3.7 4.5 - - - -
1244A GLN* 3.3 41.2 + - + -
1245A ILE* 5.4 0.2 - - - -
1260A VAL* 4.3 10.3 - - + -
1283A PRO* 5.7 0.7 - - + -
1307A LEU* 3.7 12.2 - - + +
1308A ALA 2.8 36.7 + - - -
1310A SER* 3.4 20.1 + - - +
1326A VAL* 3.8 14.4 - - + -
1327A SER* 1.3 84.6 + - - +
1329A HIS* 1.3 64.8 + - - +
1353A PRO* 3.6 2.8 - - - +
1354A PHE* 3.0 54.2 + + + +
1356A LEU* 4.1 24.0 - - + -
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Residues in contact with HIS1329 (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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1242A VAL* 4.0 0.3 - - - -
1243A GLU* 3.0 71.6 + - + +
1245A ILE* 4.5 20.9 - - + +
1257A VAL* 4.2 12.6 - - + -
1328A TYR* 1.3 77.5 - - - +
1330A ILE* 1.3 58.1 + - - +
1331A LYS* 3.5 7.3 + - + -
1351A GLU* 3.3 46.6 - - + +
1352A VAL 3.3 15.7 - - - +
1353A PRO* 3.8 9.2 - - + -
1354A PHE* 3.6 8.7 - - - -
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Residues in contact with ILE1330 (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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1208A VAL* 5.2 1.5 - - + +
1210A LEU* 3.9 20.4 - - + -
1221A ILE* 3.9 16.6 - - + -
1223A VAL* 3.7 21.8 - - + -
1240A VAL* 3.7 26.0 - - + -
1241A SER 3.7 1.8 - - - +
1242A VAL* 3.7 27.1 - - + -
1329A HIS* 1.3 69.9 - - - +
1331A LYS* 1.3 62.6 + - - +
1332A VAL* 3.9 2.5 + - - +
1350A THR 4.0 0.5 - - - +
1351A GLU* 3.5 1.4 - - - -
1352A VAL* 2.8 45.3 + - + +
1354A PHE* 3.4 31.6 - - + -
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Residues in contact with LYS1331 (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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1239A LYS 4.0 0.3 - - - +
1240A VAL* 3.8 1.3 - - - -
1241A SER* 2.8 51.8 + - - +
1243A GLU* 3.3 29.5 + - - +
1329A HIS* 3.5 13.2 + - + -
1330A ILE* 1.3 71.2 - - - +
1332A VAL* 1.3 62.1 - - - +
1333A LYS* 3.8 22.1 + - - +
1349A ALA* 3.4 26.5 - - - +
1350A THR 3.5 7.2 - - - +
1351A GLU* 3.5 30.3 - - + +
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Residues in contact with VAL1332 (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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1206A LEU* 4.1 8.9 - - + +
1208A VAL* 3.6 24.5 - - + -
1223A VAL* 5.6 2.2 - - + -
1225A VAL* 4.3 12.3 - - + -
1238A ILE* 4.0 23.1 - - + -
1239A LYS 3.5 10.5 - - - +
1240A VAL* 4.0 18.2 - - + +
1330A ILE* 3.9 3.9 + - + +
1331A LYS* 1.3 73.3 - - - +
1333A LYS* 1.3 63.0 + - - +
1334A LEU* 4.3 6.3 - - + -
1349A ALA* 3.3 3.5 - - - +
1350A THR* 3.0 55.2 + - + +
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Residues in contact with LYS1333 (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 ILE* 3.9 0.9 - - - -
1239A LYS* 2.8 72.7 + - + +
1241A SER* 4.4 16.6 + - - -
1243A GLU* 4.7 8.2 + - - -
1331A LYS* 3.8 20.8 - - - +
1332A VAL* 1.3 74.4 - - - +
1334A LEU* 1.3 66.0 + - - +
1335A THR* 3.8 6.6 + - - +
1347A GLU* 5.4 15.7 - - + +
1348A VAL 3.4 5.4 - - - +
1349A ALA* 3.5 14.6 - - + -
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Residues in contact with LEU1334 (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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1195A TRP* 4.8 1.1 - - + -
1204A LEU* 4.7 13.5 - - + -
1206A LEU* 3.9 39.3 - - + -
1225A VAL* 5.3 0.2 - - + -
1227A VAL* 4.5 14.6 - - + -
1235A VAL* 4.4 10.8 - - + -
1237A LYS 3.7 2.9 - - - -
1238A ILE* 3.7 37.5 - - + -
1332A VAL* 4.3 9.0 - - + -
1333A LYS* 1.3 73.7 - - - +
1335A THR* 1.3 58.8 + - - +
1336A VAL* 3.2 14.9 + - + +
1347A GLU* 3.5 3.1 - - - -
1348A VAL* 2.7 52.7 + - + +
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Residues in contact with THR1335 (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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1235A VAL* 3.3 2.6 - - - +
1236A LYS* 2.5 47.0 + - + -
1237A LYS* 3.0 38.5 + - + +
1239A LYS* 5.5 2.4 - - - +
1333A LYS* 3.8 8.5 + - - +
1334A LEU* 1.3 69.7 - - - +
1336A VAL* 1.3 53.8 + - - +
1345A SER* 4.4 15.7 - - - -
1346A SER 4.0 2.0 - - - -
1347A GLU* 4.2 28.2 + - + +
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Residues in contact with VAL1336 (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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1197A PHE* 4.4 20.0 - - + -
1204A LEU* 4.7 7.9 - - + -
1231A THR* 6.1 0.2 - - - +
1233A LYS* 4.2 19.5 - - + -
1234A VAL 3.4 18.4 - - - +
1235A VAL* 3.8 15.3 - - + +
1236A LYS* 4.6 0.9 - - - -
1334A LEU* 3.5 26.2 - - + +
1335A THR* 1.3 73.5 - - - +
1337A SER* 1.4 60.5 + - - +
1338A GLY* 2.9 9.2 + - - +
1345A SER* 3.6 4.6 - - - -
1346A SER* 2.9 39.2 + - - +
1348A VAL* 4.1 12.3 - - + -
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Residues in contact with SER1337 (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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1233A LYS* 4.0 2.4 - - - +
1234A VAL* 2.4 64.6 + - - +
1236A LYS* 3.3 34.1 - - - +
1336A VAL* 1.4 70.0 - - - +
1338A GLY* 1.4 61.8 + - - +
1344A THR 4.9 0.7 - - - -
1345A SER* 4.6 8.5 - - - -
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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