Contacts of the helix formed by residues 1342 - 1353 (chain A) in PDB entry 5TJ4
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 GLU1342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370A ALA* 3.2 31.2 - - + +
1222A ALA* 3.7 4.9 - - + +
1223A GLY* 3.6 18.7 + - - -
1229A ARG* 3.4 18.2 + - - -
1339A LEU* 3.2 32.9 - - + +
1340A SER 3.4 5.8 - - - -
1341A GLU* 1.3 74.2 + - - +
1343A GLN* 1.3 54.1 + - - +
1344A GLN 3.2 2.2 - - - -
1345A PHE* 3.0 13.0 + - - +
1346A VAL* 2.8 35.7 + - - +
1388A ILE* 3.6 14.9 - - - +
1392A LEU* 3.9 24.2 - - + +
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Residues in contact with GLN1343 (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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1278A CYS 3.5 9.5 - - - +
1279A LEU* 3.5 10.9 - - + +
1280A GLY* 2.7 39.9 + - - +
1281A LYS 5.5 0.5 - - - -
1282A GLU* 4.9 10.3 + - - +
1285A ARG* 5.6 1.5 - - - +
1336A LEU* 3.3 36.8 + - + +
1337A LEU 5.0 0.2 + - - -
1339A LEU* 2.8 34.2 + - + -
1340A SER* 3.5 14.1 + - - +
1341A GLU 3.2 0.6 - - - -
1342A GLU* 1.3 77.9 - - - +
1344A GLN* 1.3 56.4 + - - +
1346A VAL* 3.1 11.5 + - - +
1347A ALA* 2.9 29.7 + - - +
173C ALA* 5.8 2.8 - - - +
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Residues in contact with GLN1344 (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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1279A LEU 5.8 0.7 - - - -
1280A GLY* 5.1 7.3 - - - +
1340A SER 4.7 0.2 + - - -
1341A GLU* 3.5 15.5 + - - +
1342A GLU 3.2 0.2 - - - -
1343A GLN* 1.3 79.6 - - - +
1345A PHE* 1.3 82.7 + - + +
1347A ALA* 3.4 8.4 - - - +
1348A GLU* 3.2 32.6 + - - +
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Residues in contact with PHE1345 (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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179A LYS* 4.9 18.8 - - + -
365A GLN* 6.3 1.1 - - + -
366A THR* 3.3 17.7 - - + +
369A ALA* 3.5 33.4 - - + -
370A ALA* 3.6 35.7 - - + -
1222A ALA* 4.6 4.5 - - + -
1341A GLU* 3.7 18.6 - - + -
1342A GLU* 3.0 16.0 + - - +
1344A GLN* 1.3 96.6 - - - +
1346A VAL* 1.3 66.3 + - - +
1347A ALA 3.2 1.3 - - - -
1348A GLU* 3.2 25.9 + - - -
1349A ALA* 2.9 20.1 + - - +
1358A LEU* 4.9 0.6 - - - +
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Residues in contact with VAL1346 (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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370A ALA* 5.4 1.1 - - + -
1279A LEU* 4.3 7.4 - - + -
1339A LEU* 4.6 5.8 - - + -
1342A GLU* 2.8 24.2 + - + +
1343A GLN* 3.5 11.0 - - - +
1345A PHE* 1.3 71.5 - - - +
1347A ALA* 1.3 57.0 - - - +
1349A ALA* 3.2 8.6 + - - +
1350A LEU* 3.0 26.7 + - - +
1355A LEU* 4.1 9.5 - - + +
1358A LEU* 4.3 6.7 - - + -
1392A LEU* 3.6 30.3 - - + -
1395A VAL* 4.2 7.6 - - + -
1396A VAL* 4.3 9.4 - - + -
1399A LEU* 3.5 31.6 - - + -
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Residues in contact with ALA1347 (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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1276A ALA 5.7 0.2 - - - +
1279A LEU* 3.8 28.7 - - + +
1343A GLN 2.9 12.5 + - - +
1344A GLN* 3.4 12.8 - - - +
1346A VAL* 1.3 74.4 - - - +
1348A GLU* 1.3 65.2 + - - +
1350A LEU* 3.3 6.3 + - + +
1351A GLU* 2.9 29.1 + - - +
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Residues in contact with GLU1348 (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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365A GLN* 5.7 2.3 - - - +
366A THR* 2.9 30.6 + - + +
1344A GLN* 3.2 19.8 + - - +
1345A PHE* 3.2 31.9 + - - +
1347A ALA* 1.3 77.2 - - - +
1349A ALA* 1.3 62.1 + - - +
1351A GLU* 3.2 13.7 + - - +
1352A LYS* 3.0 27.0 + - - +
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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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366A THR* 4.0 7.8 - - + +
1345A PHE 2.9 13.7 + - - +
1346A VAL 3.2 8.5 + - - +
1348A GLU* 1.3 75.1 - - - +
1350A LEU* 1.3 53.1 + - - +
1353A GLY* 2.8 15.1 + - - -
1354A THR* 2.8 51.1 + - - +
1355A LEU* 3.7 17.8 + - + -
1358A LEU* 4.0 15.9 - - + -
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Residues in contact with LEU1350 (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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1272A LEU* 4.0 26.5 - - + -
1276A ALA* 3.8 29.2 - - + -
1279A LEU* 4.3 14.8 - - + -
1346A VAL 3.0 13.4 + - - +
1347A ALA* 3.4 8.5 - - - +
1349A ALA* 1.3 76.4 - - - +
1351A GLU* 1.3 66.9 + - + +
1353A GLY* 3.4 8.4 + - - -
1355A LEU* 3.6 30.3 - - + +
1399A LEU* 4.3 13.5 - - + +
1403A ALA* 4.4 9.4 - - + -
1407A THR 5.1 0.5 - - - +
1408A SER* 4.0 23.1 - - - +
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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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1347A ALA* 2.9 16.0 + - - +
1348A GLU* 3.5 17.0 - - - +
1350A LEU* 1.3 80.9 - - + +
1352A LYS* 1.3 60.8 + - + +
1353A GLY* 3.3 1.0 + - - -
1408A SER* 4.3 13.0 - - - -
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Residues in contact with LYS1352 (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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1348A GLU 3.0 16.6 + - - +
1351A GLU* 1.3 73.1 - - + +
1353A GLY* 1.3 61.5 + - - +
1354A THR* 3.8 18.7 + - + +
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Residues in contact with GLY1353 (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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1349A ALA 2.8 9.8 + - - -
1350A LEU 3.4 7.2 + - - -
1351A GLU 3.2 4.6 - - - -
1352A LYS* 1.3 78.3 - - - +
1354A THR* 1.3 57.8 + - - +
1355A LEU* 3.5 4.9 - - - -
1356A PRO* 3.8 12.7 - - - +
1407A THR 5.4 6.7 - - - -
1408A SER* 6.1 0.7 - - - -
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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