Contacts of the helix formed by residues 1349 - 1362 (chain A) in PDB entry 5IRC
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 ASP1349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1347A ILE* 3.5 1.9 - - - +
1348A ASN* 1.3 75.5 - - - +
1350A ARG* 1.3 58.5 + - - +
1351A GLU* 3.7 11.2 + - - +
1352A GLN* 3.0 51.4 + - + +
1353A LYS* 2.6 35.0 + - - +
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Residues in contact with ARG1350 (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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1345A HIS* 5.7 0.4 + - - -
1348A ASN 3.0 9.2 + - - +
1349A ASP* 1.3 72.7 + - - +
1351A GLU* 1.3 59.2 + - - +
1353A LYS* 3.3 34.0 + - - +
1354A LEU* 2.9 44.2 + - + +
1427A LEU* 3.3 34.4 - - - +
1431A GLN* 4.8 9.5 - - - +
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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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1349A ASP* 3.3 11.9 + - - +
1350A ARG* 1.3 76.6 - - - +
1352A GLN* 1.3 66.8 + - + +
1354A LEU* 3.3 7.8 + - - +
1355A HIS* 2.9 55.8 + - + +
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Residues in contact with GLN1352 (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 ILE* 3.7 22.1 - - + +
1349A ASP* 3.0 34.7 + - + +
1351A GLU* 1.3 78.4 - - + +
1353A LYS* 1.3 58.2 + - - +
1355A HIS* 3.4 7.6 + - + +
1356A ALA* 2.8 31.9 + - - +
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Residues in contact with LYS1353 (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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1344A ALA 3.6 17.3 - - - +
1345A HIS* 2.8 53.0 + - + +
1347A ILE* 3.5 25.2 + - - +
1348A ASN 5.1 2.4 + - - -
1349A ASP 2.6 19.8 + - - +
1350A ARG* 3.4 37.5 - - - +
1352A GLN* 1.3 74.2 - - - +
1354A LEU* 1.3 59.9 + - + +
1356A ALA* 3.2 3.6 + - - +
1357A LEU* 2.9 40.1 + - + +
1427A LEU* 4.0 7.6 - - + -
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Residues in contact with LEU1354 (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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1350A ARG* 2.9 33.5 + - + +
1351A GLU* 3.8 6.7 - - - +
1353A LYS* 1.3 77.9 - - + +
1355A HIS* 1.3 63.5 + - - +
1357A LEU* 3.3 12.0 + - + -
1358A LYS 3.0 18.5 + - - -
1427A LEU* 4.4 20.6 - - + -
1431A GLN* 4.5 18.6 - - + -
1434A PHE* 3.5 34.9 - - + -
1435A PHE* 3.6 26.8 - - + -
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Residues in contact with HIS1355 (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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1351A GLU* 2.9 56.4 + - + +
1352A GLN* 3.8 6.7 - - - +
1354A LEU* 1.3 76.2 - - + +
1356A ALA* 1.3 62.0 + - - +
1358A LYS* 3.3 7.1 + - - +
1359A GLU* 3.0 29.8 + - + +
1434A PHE* 3.7 29.0 - + - -
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Residues in contact with ALA1356 (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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1344A ALA* 3.9 13.0 - - + +
1347A ILE* 3.5 26.2 - - + -
1352A GLN 2.8 18.5 + - - +
1353A LYS 3.2 4.2 + - - +
1355A HIS* 1.3 77.9 - - - +
1357A LEU* 1.3 61.3 + - - +
1359A GLU* 3.2 9.8 + - - +
1360A VAL* 3.1 24.9 + - - +
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Residues in contact with LEU1357 (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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1341A LEU* 3.7 47.7 - - + +
1344A ALA* 3.8 9.6 - - + -
1345A HIS* 4.3 8.5 - - + +
1353A LYS* 2.9 40.1 + - + +
1354A LEU* 3.6 13.5 - - + +
1356A ALA* 1.3 75.6 - - - +
1358A LYS* 1.3 63.8 + - - +
1360A VAL* 3.1 13.9 + - - +
1361A LEU* 3.1 14.2 + - - +
1424A ILE* 4.5 12.8 - - + -
1427A LEU* 4.1 19.3 - - + -
1428A PHE* 4.3 5.7 - - + -
1435A PHE* 3.8 15.3 - - + -
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Residues in contact with LYS1358 (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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1354A LEU 3.0 16.5 + - - +
1355A HIS* 3.6 8.1 - - - +
1356A ALA 3.3 0.2 - - - -
1357A LEU* 1.3 73.4 - - - +
1359A GLU* 1.3 67.3 + - - +
1361A LEU* 3.1 22.1 + - + +
1362A LYS* 3.3 26.6 + - + +
1434A PHE* 2.8 50.4 + - + +
1435A PHE* 3.7 31.6 - - + +
1437A TYR 5.3 4.9 + - - -
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Residues in contact with GLU1359 (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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1355A HIS* 3.0 19.9 + - + +
1356A ALA* 3.2 12.5 + - - +
1358A LYS* 1.3 77.1 - - - +
1360A VAL* 1.3 64.4 + - + +
1362A LYS* 3.0 53.5 + - - +
1363A LYS* 3.7 12.0 + - - +
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Residues in contact with VAL1360 (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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1337A MET* 4.0 10.1 - - - +
1340A ASP* 3.8 44.4 - - + +
1341A LEU* 3.6 25.8 - - + -
1344A ALA* 4.2 8.3 - - + -
1356A ALA 3.1 14.0 + - - +
1357A LEU 3.1 8.8 + - - +
1359A GLU* 1.3 75.5 - - + +
1361A LEU* 1.3 60.2 + - - +
1363A LYS* 2.8 31.9 + - + +
1364A PHE* 3.5 11.5 - - + -
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Residues in contact with LEU1361 (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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1341A LEU* 5.1 0.4 - - - +
1357A LEU 3.1 6.9 + - - +
1358A LYS* 3.1 13.6 + - + +
1360A VAL* 1.3 76.5 - - - +
1362A LYS* 1.3 62.4 + - + +
1364A PHE* 3.0 31.1 + - + +
1369A HIS* 3.4 36.1 - - + +
1372A PHE* 3.8 34.3 - - + -
1428A PHE* 3.6 27.8 - - + -
1435A PHE* 3.9 25.1 - - + +
1436A PHE* 3.7 24.2 - - + -
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Residues in contact with LYS1362 (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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1358A LYS* 3.4 31.4 - - + +
1359A GLU* 3.0 41.1 + - - +
1360A VAL 3.1 1.0 - - - -
1361A LEU* 1.3 76.1 - - + +
1363A LYS* 1.3 60.1 + - + +
1364A PHE 3.4 4.8 + - - +
1369A HIS* 5.2 2.5 - - - +
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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