Contacts of the helix formed by residues 1354 - 1365 (chain H) 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 THR1354 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355H GLN* 5.4 2.5 + - - -
362H ALA 5.6 0.2 - - - -
363H ALA* 3.3 38.7 - - + +
366H THR* 5.1 5.4 - - - +
367H ASN* 4.2 6.6 + - - +
1349H ALA* 2.8 29.9 + - + +
1352H LYS* 4.5 15.7 - - + -
1353H GLY* 1.3 73.4 - - - +
1355H LEU* 1.3 64.9 + - - +
1356H PRO* 3.3 4.5 - - - -
1357H LEU* 3.4 14.7 + - - +
1358H LEU* 3.2 18.9 + - - +
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Residues in contact with LEU1355 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1346H VAL* 4.1 18.4 - - + +
1349H ALA* 3.8 17.0 - - + +
1350H LEU* 3.8 33.7 - - + +
1353H GLY* 5.3 2.0 - - - -
1354H THR* 1.3 78.2 - - - +
1356H PRO* 1.3 64.5 - - + +
1358H LEU* 3.1 6.9 + - + +
1359H LYS* 2.7 32.3 + - - +
1396H VAL* 3.9 22.5 - - + +
1399H LEU* 4.1 11.4 - - + +
1400H LEU* 3.6 38.8 - - + +
1403H ALA* 4.5 8.5 - - + -
1405H GLY 6.0 0.2 - - - +
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Residues in contact with PRO1356 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1353H GLY 3.8 14.4 - - - +
1354H THR* 3.3 5.4 - - - -
1355H LEU* 1.3 94.1 - - + +
1357H LEU* 1.3 55.2 - - - +
1359H LYS* 3.6 5.6 + - + +
1360H ASP* 3.0 28.8 + - - +
1400H LEU* 3.6 24.9 - - + -
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Residues in contact with LEU1357 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345H THR* 5.5 11.4 - - + -
355H GLN* 5.9 4.3 - - - +
363H ALA* 5.1 3.8 - - + -
367H ASN* 3.4 16.7 + - - +
1354H THR* 3.4 18.4 + - - +
1355H LEU 3.3 0.6 - - - -
1356H PRO* 1.3 75.9 - - - +
1358H LEU* 1.3 66.3 + - - +
1360H ASP* 3.3 7.3 + - - +
1361H GLN* 2.9 23.7 + - - +
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Residues in contact with LEU1358 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366H THR* 5.7 0.4 - - + -
367H ASN* 3.3 27.0 - - + +
370H ALA* 4.2 23.8 - - + -
1220H MET* 4.4 8.3 - - + -
1345H PHE 4.9 0.7 - - - +
1346H VAL* 4.3 17.0 - - + -
1349H ALA* 4.0 20.6 - - + -
1354H THR 3.2 13.3 + - - +
1355H LEU* 3.1 10.6 + - + +
1357H LEU* 1.3 75.6 - - - +
1359H LYS* 1.3 64.0 + - - +
1361H GLN* 3.0 6.3 + - + +
1362H VAL* 2.8 38.5 + - + +
1392H LEU* 5.2 2.9 - - + -
1396H VAL* 3.8 26.9 - - + -
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Residues in contact with LYS1359 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253H LEU* 5.7 1.0 - - - +
1257H GLU* 4.3 11.3 + - - -
1355H LEU 2.7 20.3 + - - +
1356H PRO* 3.7 6.5 - - + +
1358H LEU* 1.3 73.1 - - - +
1360H ASP* 1.3 63.3 + - - +
1362H VAL* 3.1 7.0 + - - +
1363H LYS* 2.9 24.6 + - + +
1393H TYR* 3.5 40.4 + - + -
1396H VAL* 3.7 15.2 - - + +
1397H SER* 3.9 24.2 + - - +
1400H LEU* 3.6 25.9 - - + +
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Residues in contact with ASP1360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1356H PRO 3.0 19.3 + - - +
1357H LEU* 3.3 8.9 + - - +
1359H LYS* 1.3 76.8 - - - +
1361H GLN* 1.3 60.5 + - - +
1363H LYS* 3.4 7.6 + - - +
1364H SER* 3.1 22.2 + - - -
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Residues in contact with GLN1361 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341H TYR* 5.7 9.2 - - + -
342H ALA* 6.2 2.9 - - - +
367H ASN* 5.0 9.2 - - + +
1220H MET* 4.6 16.2 - - + -
1357H LEU 2.9 13.1 + - - +
1358H LEU* 3.4 10.8 - - + +
1360H ASP* 1.3 74.1 - - - +
1362H VAL* 1.3 67.3 + - - +
1364H SER* 2.9 23.1 + - - +
1365H VAL* 3.2 12.9 + - + +
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Residues in contact with VAL1362 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220H MET* 3.8 23.6 - - - -
1358H LEU* 2.8 38.8 + - + +
1359H LYS* 3.7 7.4 - - - +
1361H GLN* 1.3 72.7 - - - +
1363H LYS* 1.3 62.3 + - - +
1365H VAL* 3.4 4.6 + - - +
1366H MET* 3.1 24.0 + - - +
1389H LEU* 3.8 30.5 - - + +
1392H LEU* 4.0 17.9 - - + -
1393H TYR* 3.8 21.5 - - + +
1396H VAL* 5.0 4.0 - - + -
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Residues in contact with LYS1363 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1359H LYS* 2.9 18.3 + - + +
1360H ASP* 3.5 8.5 - - - +
1362H VAL* 1.3 76.7 - - - +
1364H SER* 1.3 61.2 + - - +
1366H MET* 3.2 27.5 + - - +
1367H GLU* 3.6 4.7 + - - +
1393H TYR* 4.5 20.3 - - + +
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Residues in contact with SER1364 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341H TYR* 4.7 20.8 + - - +
1360H ASP 3.1 13.3 + - - -
1361H GLN* 2.9 22.7 + - - +
1363H LYS* 1.3 72.0 - - - +
1365H VAL* 1.3 61.2 + - - +
1366H MET 3.1 4.0 - - - -
1367H GLU* 2.9 31.1 + - - +
1368H GLN 4.1 1.2 + - - -
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Residues in contact with VAL1365 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337H SER* 5.4 4.9 - - - -
338H ALA* 5.7 0.4 - - - -
341H TYR* 3.7 40.2 - - + -
1220H MET* 3.0 37.9 - - + -
1224H LEU* 6.5 0.7 - - + -
1361H GLN* 3.2 7.3 + - + +
1362H VAL* 3.4 13.0 - - - +
1364H SER* 1.3 72.2 - - - +
1366H MET* 1.3 57.1 + - - +
1367H GLU 3.4 0.9 - - - -
1368H GLN* 4.2 16.2 + - + +
1369H ASN* 4.5 4.9 + - - -
1389H LEU* 4.0 26.3 - - + +
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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