Contacts of the helix formed by residues 1341 - 1353 (chain B) 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 GLU1341 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B LYS* 3.3 37.6 - - + +
1222B ALA* 4.1 18.4 - - + +
1225B ASP* 5.7 4.0 - - - +
1229B ARG* 4.9 1.3 - - - +
1340B SER* 1.3 91.1 + - - +
1342B GLU* 1.3 67.7 + - - +
1343B GLN 3.3 0.5 + - - -
1344B GLN* 3.4 34.1 + - - +
1345B PHE* 3.6 6.2 - - + -
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Residues in contact with GLU1342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B ALA* 3.4 13.2 - - - +
1222B ALA* 3.5 6.7 - - - +
1223B GLY* 2.4 46.7 + - - +
1229B ARG* 2.5 35.2 + - - -
1339B LEU* 3.7 20.0 - - + -
1340B SER 2.9 19.5 + - - -
1341B GLU* 1.3 77.4 + - - +
1343B GLN* 1.3 64.2 + - - +
1345B PHE* 3.1 18.2 + - - +
1346B VAL* 3.2 15.2 + - - +
1388B ILE* 3.8 6.4 - - + +
1392B LEU* 4.5 14.4 - - + -
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Residues in contact with GLN1343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1278B CYS 3.4 9.2 - - - +
1279B LEU* 3.5 11.1 - - + +
1280B GLY* 2.7 40.0 + - - +
1281B LYS 5.5 0.5 - - - -
1282B GLU* 4.9 9.9 + - - -
1285B ARG* 5.6 1.7 - - - +
1336B LEU* 3.3 36.3 + - + +
1337B LEU 5.0 0.2 + - - -
1339B LEU* 2.8 33.6 + - + +
1340B SER* 3.6 13.9 + - - +
1342B GLU* 1.3 77.0 - - - +
1344B GLN* 1.3 63.4 + - - +
1346B VAL* 3.1 10.9 + - - +
1347B ALA* 2.9 23.6 + - - +
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Residues in contact with GLN1344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LYS* 3.9 20.4 - - - +
1279B LEU 5.8 0.9 - - - -
1280B GLY* 5.2 6.4 - - - +
1340B SER 4.8 0.2 + - - -
1341B GLU* 3.4 23.6 + - - +
1343B GLN* 1.3 77.3 - - - +
1345B PHE* 1.3 89.1 + - + +
1347B ALA* 3.4 9.3 - - - +
1348B GLU* 3.2 27.9 + - - +
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Residues in contact with PHE1345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179B LYS* 4.4 27.6 - - + -
365B GLN* 6.4 0.9 - - + -
366B THR* 3.3 17.3 - - + +
369B ALA* 3.5 34.3 - - + -
370B ALA* 3.5 38.4 - - + -
1222B ALA* 4.5 5.8 - - + -
1341B GLU* 3.6 17.5 - - + -
1342B GLU* 3.1 3.8 + - - +
1344B GLN* 1.3 101.5 - - + +
1346B VAL* 1.3 60.3 + - - +
1347B ALA 3.2 1.6 - - - -
1348B GLU* 3.2 29.2 + - - -
1349B ALA* 2.9 25.1 + - - +
1358B LEU* 5.2 0.2 - - - -
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Residues in contact with VAL1346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ALA* 5.4 1.6 - - + -
1279B LEU* 4.3 7.9 - - + -
1339B LEU* 4.6 5.8 - - + -
1342B GLU 3.2 14.8 + - - +
1343B GLN* 3.1 11.1 + - - +
1345B PHE* 1.3 74.5 - - - +
1347B ALA* 1.3 58.1 + - - +
1349B ALA* 3.2 7.5 + - - +
1350B LEU* 3.0 26.7 + - - +
1355B LEU* 4.1 9.1 - - + +
1358B LEU* 4.3 6.5 - - + -
1392B LEU* 3.6 30.5 - - + -
1395B VAL* 4.2 7.6 - - + -
1396B VAL* 4.3 9.0 - - + -
1399B LEU* 3.5 31.6 - - + -
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Residues in contact with ALA1347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1276B ALA 5.8 0.2 - - - +
1279B LEU* 3.8 29.3 - - + +
1343B GLN 2.9 12.7 + - - +
1344B GLN* 3.4 13.0 - - - +
1346B VAL* 1.3 73.2 - - - +
1348B GLU* 1.3 66.3 + - - +
1350B LEU* 3.3 6.6 + - + +
1351B GLU* 2.9 29.3 + - - +
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Residues in contact with GLU1348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B GLN* 5.2 4.0 - - - +
366B THR* 3.0 30.2 + - + +
1344B GLN* 3.2 13.1 + - - +
1345B PHE* 3.2 32.1 + - - +
1347B ALA* 1.3 76.6 - - - +
1349B ALA* 1.3 63.2 + - - +
1351B GLU* 3.2 13.4 + - - +
1352B LYS* 2.9 27.4 + - - +
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Residues in contact with ALA1349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B THR* 4.0 7.4 - - + +
1345B PHE 2.9 13.4 + - - +
1346B VAL 3.5 7.9 - - - +
1348B GLU* 1.3 75.7 - - - +
1350B LEU* 1.3 54.0 + - - +
1353B GLY* 2.8 30.3 + - - -
1354B THR* 2.8 36.3 + - - +
1355B LEU* 3.7 18.1 + - + -
1358B LEU* 4.0 16.4 - - + -
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Residues in contact with LEU1350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272B LEU* 4.0 24.5 - - + -
1276B ALA* 3.8 28.3 - - + -
1279B LEU* 4.3 15.3 - - + -
1346B VAL 3.0 12.3 + - - +
1347B ALA* 3.4 10.1 - - - +
1349B ALA* 1.3 77.8 - - - +
1351B GLU* 1.3 65.0 + - + +
1353B GLY* 3.5 5.9 + - - -
1355B LEU* 3.6 29.7 - - + +
1399B LEU* 4.3 10.1 - - + -
1403B ALA* 4.2 6.7 - - + -
1405B GLY 4.2 1.6 - - - +
1406B PRO* 3.8 2.3 - - - +
1407B THR* 3.4 39.2 + - + +
1408B SER 5.4 2.0 - - - +
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Residues in contact with GLU1351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1347B ALA* 2.9 16.8 + - + +
1348B GLU* 3.5 16.2 - - - +
1350B LEU* 1.3 80.2 - - + +
1352B LYS* 1.3 57.5 + - + +
1353B GLY 3.2 0.2 - - - -
1406B PRO* 3.2 22.5 - - - +
1407B THR 3.5 20.3 + - - +
1408B SER* 5.0 2.9 - - - -
1409B VAL* 4.2 24.7 - - + +
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Residues in contact with LYS1352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1348B GLU 2.9 16.4 + - - +
1349B ALA 4.6 0.4 - - - +
1351B GLU* 1.3 73.4 - - + +
1353B GLY* 1.3 60.8 + - - +
1354B THR* 3.5 18.1 - - + +
1406B PRO* 4.1 10.2 - - - +
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Residues in contact with GLY1353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1349B ALA 2.8 13.8 + - - -
1350B LEU* 3.5 7.6 + - - -
1351B GLU 3.2 4.2 - - - -
1352B LYS* 1.3 76.4 - - - +
1354B THR* 1.3 57.1 + - - +
1355B LEU* 3.5 5.8 - - - -
1356B PRO* 3.8 11.9 - - - +
1405B GLY* 4.5 4.0 - - - -
1406B PRO* 4.1 21.2 - - - +
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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
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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