Contacts of the helix formed by residues 1337 - 1347 (chain O) in PDB entry 5Z3U
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 ARG1337 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1018O LEU* 5.6 0.2 - - - -
1021O ILE* 3.6 31.0 - - - +
1336O LYS* 1.3 77.0 - - + +
1338O GLU* 1.3 62.5 + - - +
1340O SER* 2.5 39.8 + - - -
1341O GLU* 2.7 37.4 + - - +
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Residues in contact with GLU1338 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071O GLN* 4.2 14.5 - - - +
1336O LYS 3.3 4.2 - - - +
1337O ARG* 1.3 77.0 - - - +
1339O GLU* 1.3 89.1 + - + +
1341O GLU* 2.9 15.4 + - + +
1342O SER* 2.9 31.2 + - - -
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Residues in contact with GLU1339 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018O LEU* 3.6 22.7 - - + +
1019O GLN* 5.4 1.7 + - - +
1072O ILE* 3.3 56.8 - - + +
1081O ASP* 4.8 10.4 - - - +
1336O LYS 3.3 15.7 + - - +
1337O ARG 3.2 1.0 - - - -
1338O GLU* 1.3 92.9 + - + +
1340O SER* 1.3 56.9 + - - +
1342O SER* 2.3 26.6 + - - -
1343O ALA* 2.9 15.1 + - - +
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Residues in contact with SER1340 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1018O LEU* 4.1 21.5 - - - +
1021O ILE* 5.1 5.3 - - - +
1022O MET* 3.6 21.1 - - - +
1336O LYS 3.7 4.8 + - - -
1337O ARG* 2.5 43.9 + - - -
1339O GLU* 1.3 76.8 - - - +
1341O GLU* 1.3 59.0 + - - +
1343O ALA* 4.3 2.0 - - - +
1344O ALA* 2.9 29.1 + - - +
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Residues in contact with GLU1341 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1337O ARG* 2.7 59.2 + - - +
1338O GLU* 2.9 13.9 + - + +
1340O SER* 1.3 77.1 + - - +
1342O SER* 1.3 59.1 + - - +
1344O ALA* 3.9 5.8 - - + +
1345O VAL* 3.0 38.0 + - + +
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Residues in contact with SER1342 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071O GLN* 3.2 36.1 + - - +
1072O ILE* 5.1 0.3 - - - +
1338O GLU* 2.9 23.0 + - - -
1339O GLU* 2.3 33.3 + - - +
1341O GLU* 1.3 77.0 - - - +
1343O ALA* 1.3 55.7 + - - +
1346O TYR* 2.9 48.9 + - - +
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Residues in contact with ALA1343 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1022O MET* 4.3 13.9 - - + -
1028O LYS* 3.7 2.4 - - - +
1071O GLN* 4.9 6.7 - - - +
1339O GLU 2.9 11.9 + - - +
1340O SER* 4.2 3.6 - - - +
1342O SER* 1.3 78.9 + - - +
1344O ALA* 1.3 59.0 + - - +
1347O ASN* 2.5 55.7 + - - +
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Residues in contact with ALA1344 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1022O MET* 4.2 8.2 - - + +
1028O LYS* 4.2 12.9 - - + +
1340O SER 2.9 19.9 + - - +
1341O GLU* 3.9 8.1 - - + +
1342O SER 3.3 0.4 - - - -
1343O ALA* 1.3 75.9 - - - +
1345O VAL* 1.3 62.0 + - + +
1347O ASN 3.7 0.2 - - - -
1348O GLY* 2.9 26.0 + - - -
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Residues in contact with VAL1345 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1341O GLU* 3.0 23.0 + - + +
1344O ALA* 1.3 77.6 - - + +
1346O TYR* 1.3 82.6 + - + +
1348O GLY* 2.9 18.6 + - - -
1349O ARG* 3.9 11.5 + - - +
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Residues in contact with TYR1346 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1067O GLU* 5.9 5.7 - - + +
1071O GLN* 5.3 14.1 - - + +
1342O SER* 2.9 38.9 + - - +
1343O ALA* 5.1 0.7 - - - -
1345O VAL* 1.3 94.1 - - + +
1347O ASN* 1.3 59.6 + - - +
1348O GLY 3.3 0.9 - - - -
1349O ARG* 4.3 34.2 + - - +
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Residues in contact with ASN1347 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028O LYS* 3.1 33.9 - - + +
1032O LEU* 5.1 1.0 - - - +
1048O PHE* 3.2 38.0 - - + -
1067O GLU* 4.5 21.2 + - - +
1071O GLN* 5.3 1.2 - - - +
1343O ALA* 2.5 48.0 + - - +
1346O TYR* 1.3 77.7 - - - +
1348O GLY* 1.3 55.1 + - - +
1349O ARG* 3.2 11.9 + - - -
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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