Contacts of the strand formed by residues 1345 - 1357 (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 SER1345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1236A LYS* 5.5 5.4 - - - +
1335A THR* 4.4 19.2 - - - +
1336A VAL 3.6 12.1 + - - -
1337A SER* 4.6 6.4 - - - -
1343A LEU 3.7 8.5 + - - -
1344A THR* 1.3 82.4 + - - +
1346A SER* 1.3 62.4 + - - +
1347A GLU* 3.8 8.1 + - - +
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Residues in contact with SER1346 (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* 4.1 28.1 - - - -
1233A LYS* 5.2 2.6 + - - -
1334A LEU 3.5 0.3 - - - +
1335A THR 3.9 0.2 - - - -
1336A VAL* 2.9 43.4 + - - +
1338A GLY* 4.7 8.1 - - - +
1344A THR* 4.3 3.7 + - - +
1345A SER* 1.3 71.9 - - - +
1347A GLU* 1.3 60.7 + - - +
1348A VAL* 3.8 4.5 - - - -
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Residues in contact with GLU1347 (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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1333A LYS* 5.4 14.8 + - + +
1334A LEU 3.5 5.8 - - - +
1335A THR* 4.2 30.3 + - + +
1345A SER* 3.8 8.5 + - - +
1346A SER* 1.3 74.8 - - - +
1348A VAL* 1.3 62.9 + - - +
1349A ALA* 4.1 2.1 + - - +
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Residues in contact with VAL1348 (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* 3.9 43.1 - - + +
1196A GLN 6.1 0.2 - - - +
1197A PHE* 4.5 22.2 - - + -
1204A LEU* 4.9 4.0 - - + -
1333A LYS* 3.4 1.2 - - - +
1334A LEU* 2.7 66.3 + - + +
1336A VAL* 4.1 8.7 - - + -
1346A SER* 3.8 3.5 + - - +
1347A GLU* 1.3 74.7 - - - +
1349A ALA* 1.3 60.6 + - - +
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Residues in contact with ALA1349 (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* 3.4 18.9 + - - +
1206A LEU* 6.0 0.4 - - - -
1331A LYS* 3.4 31.0 - - - +
1332A VAL 3.3 14.4 - - - +
1333A LYS* 3.5 9.2 - - + +
1334A LEU* 5.9 0.4 - - - -
1347A GLU 4.1 2.4 + - - +
1348A VAL* 1.3 78.9 - - - +
1350A THR* 1.3 60.5 + - - +
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Residues in contact with THR1350 (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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1191A ALA* 4.8 6.8 - - + +
1192A GLU* 5.5 1.4 - - - +
1193A ALA* 4.4 15.9 - - + +
1195A TRP* 3.9 10.8 - - + -
1206A LEU* 3.8 19.7 - - + -
1208A VAL* 4.1 11.2 - - + -
1330A ILE 4.0 0.3 - - - +
1331A LYS* 3.5 3.3 - - - +
1332A VAL* 3.0 50.8 + - + +
1349A ALA* 1.3 75.6 - - - +
1351A GLU* 1.3 79.4 + - - +
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Residues in contact with GLU1351 (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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1191A ALA* 3.9 9.0 - - - +
1208A VAL* 6.5 0.7 - - - -
1243A GLU* 4.4 0.7 - - - +
1329A HIS* 3.3 38.6 + - + -
1330A ILE 3.5 4.7 - - - -
1331A LYS* 3.5 32.2 - - + +
1350A THR* 1.3 87.4 + - - +
1352A VAL* 1.3 63.5 + - - +
1353A PRO* 4.7 1.4 - - + +
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Residues in contact with VAL1352 (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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1189A PRO* 3.7 30.5 - - + -
1190A SER 4.7 0.4 - - - +
1191A ALA* 3.8 24.7 - - + +
1208A VAL* 4.2 22.2 - - + -
1210A LEU* 4.2 10.3 - - + +
1329A HIS* 3.3 3.9 - - - -
1330A ILE* 2.8 54.1 + - + +
1351A GLU* 1.3 76.6 - - - +
1353A PRO* 1.3 76.4 - - + +
1354A PHE* 4.4 0.5 - - - -
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Residues in contact with PRO1353 (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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1189A PRO* 4.2 11.3 - - - +
1210A LEU* 4.6 0.2 - - - +
1213A GLU* 4.6 5.0 - - - +
1327A SER* 5.3 4.7 - - - +
1328A TYR 3.6 10.3 - - - +
1329A HIS* 3.8 6.1 - - + -
1351A GLU* 4.7 1.8 - - + +
1352A VAL* 1.3 97.7 - - + +
1354A PHE* 1.3 63.9 + - - +
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Residues in contact with PHE1354 (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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1189A PRO* 5.2 0.2 - - + -
1210A LEU* 4.3 13.2 - - + -
1212A LYS 4.9 0.4 - - - +
1213A GLU* 3.6 18.4 - - - +
1215A TYR* 3.7 20.2 - + + -
1221A ILE* 4.0 18.2 - - + -
1242A VAL* 3.6 20.4 - - + -
1283A PRO* 5.5 0.4 - - + -
1310A SER* 4.1 0.9 + - - -
1327A SER* 4.5 2.9 + - - -
1328A TYR* 3.0 56.4 + + + +
1329A HIS* 3.6 16.6 - - - -
1330A ILE* 3.4 35.7 - - + -
1353A PRO* 1.3 75.5 - - - +
1355A ARG* 1.4 91.9 + - - +
1356A LEU* 4.5 9.0 - - + -
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Residues in contact with ARG1355 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1182A PRO* 4.3 20.6 - - - +
1186A GLY* 5.9 0.6 - - - +
1213A GLU* 3.1 39.7 + - - +
1214A ILE* 4.0 9.1 - - - +
1215A TYR 2.5 33.2 + - - +
1310A SER* 3.4 16.8 - - - +
1312A ILE* 4.5 25.8 - - - +
1354A PHE* 1.4 90.1 - - - +
1356A LEU* 1.3 54.5 + - - +
1357A MET* 3.9 21.5 - - + -
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Residues in contact with LEU1356 (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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1215A TYR* 3.2 12.3 - - + +
1216A PHE 3.2 30.1 - - - +
1217A HIS* 3.4 32.0 - - + +
1218A GLY 5.1 0.7 - - - +
1219A GLU 6.0 0.4 - - - +
1221A ILE* 5.3 1.3 - - + -
1283A PRO* 4.7 18.8 - - + +
1307A LEU* 4.5 14.1 - - + -
1309A SER* 3.3 7.8 - - - -
1310A SER* 2.8 34.9 + - - +
1328A TYR* 4.1 38.5 - - + +
1354A PHE* 4.5 9.0 - - + -
1355A ARG* 1.3 73.1 - - - +
1357A MET* 1.3 58.4 + - - +
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Residues in contact with MET1357 (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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1179A GLN* 4.3 9.6 - - - +
1180A HIS 4.1 6.5 - - - +
1181A ALA* 3.8 22.0 - - + +
1182A PRO* 3.5 28.0 - - + -
1214A ILE* 4.1 4.5 - - + -
1215A TYR 3.4 6.4 + - - +
1216A PHE* 3.3 24.7 - - - -
1217A HIS* 3.4 15.6 + - - -
1309A SER* 4.3 7.0 - - - -
1310A SER* 3.6 28.5 - - - +
1312A ILE* 3.8 17.9 - - + -
1355A ARG* 3.9 31.6 - - + -
1356A LEU* 1.3 80.1 - - - +
1358A HIS* 1.3 65.4 + - - +
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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