Contacts of the helix formed by residues 1279 - 1288 (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 LYS1279 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1094O ARG* 4.4 0.2 - - - +
1276O GLU 4.2 13.9 + - - +
1277O GLU 2.7 18.2 + - - +
1278O LEU* 1.3 77.0 - - + +
1280O ASP* 1.3 63.7 + - - +
1281O SER* 4.2 9.9 - - - +
1282O GLU* 2.8 44.0 + - - +
1283O ILE 4.0 1.4 + - - -
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Residues in contact with ASP1280 (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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1094O ARG* 2.4 35.6 + - - +
1098O LYS* 4.7 3.0 + - - +
1277O GLU 4.9 0.2 - - - -
1278O LEU 3.3 0.6 + - - -
1279O LYS* 1.3 71.8 - - - +
1281O SER* 1.3 62.8 + - - +
1282O GLU 3.4 0.2 - - - -
1283O ILE* 4.2 4.4 - - - +
1284O ASN* 2.8 51.7 + - - +
1300O MET* 4.0 10.4 - - - +
1301O ASP* 2.9 27.8 - - - +
1304O ARG* 3.4 14.4 + - - -
1305O SER* 4.1 13.0 + - - -
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Residues in contact with SER1281 (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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1279O LYS* 2.9 9.6 + - - +
1280O ASP* 1.3 77.5 - - - +
1282O GLU* 1.3 73.5 + - - -
1284O ASN* 3.5 4.9 - - - +
1285O GLU* 2.9 37.1 + - - +
1294O MET* 4.2 4.2 - - - +
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Residues in contact with GLU1282 (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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1276O GLU 4.7 2.2 - - - +
1277O GLU* 4.0 29.6 - - + +
1279O LYS* 2.8 52.7 + - - +
1281O SER* 1.3 77.3 - - - +
1283O ILE* 1.3 57.3 + - - +
1285O GLU* 2.8 31.5 + - - +
1286O ILE* 2.9 26.6 + - + +
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Residues in contact with ILE1283 (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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1091O LEU* 4.6 19.1 - - + -
1094O ARG* 5.0 13.0 - - + +
1095O ILE* 4.4 12.1 - - + -
1098O LYS* 3.6 27.8 - - - +
1209O LEU* 5.8 0.9 - - + -
1277O GLU* 3.2 52.9 - - + +
1278O LEU* 4.9 3.4 - - - +
1279O LYS 4.0 1.7 + - - +
1280O ASP* 3.6 5.9 + - - +
1281O SER 3.6 0.2 - - - -
1282O GLU* 1.3 74.9 - - - +
1284O ASN* 1.3 63.0 + - - +
1286O ILE* 4.6 2.9 - - - +
1287O LEU* 2.9 49.6 + - + +
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Residues in contact with ASN1284 (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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1098O LYS* 3.1 29.8 + - - +
1280O ASP* 2.8 46.7 + - - +
1281O SER* 3.5 4.9 - - - +
1283O ILE* 1.3 77.6 - - - +
1285O GLU* 1.3 56.5 + - - +
1288O ALA* 2.5 37.5 + - - +
1294O MET* 3.4 23.9 + - + +
1297O LEU* 3.2 28.5 + - + +
1301O ASP* 4.5 5.9 + - - -
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Residues in contact with GLU1285 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1207O ARG* 4.2 1.6 + - - -
1281O SER* 2.9 28.1 + - - +
1282O GLU* 2.8 19.2 + - - +
1284O ASN* 1.3 72.9 - - - +
1286O ILE* 1.3 67.5 + - + +
1287O LEU 3.1 0.9 + - - -
1288O ALA 3.2 13.9 - - - +
1294O MET* 3.7 21.9 - - + +
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Residues in contact with ILE1286 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1009O LYS* 4.9 13.3 - - + +
1010O VAL 5.4 1.3 - - - +
1011O VAL* 5.2 4.3 - - + -
1207O ARG* 2.3 32.3 + - - +
1209O LEU* 4.1 22.4 - - + -
1277O GLU* 4.4 16.8 - - - +
1282O GLU* 2.9 44.4 + - + +
1283O ILE* 4.1 5.2 - - - +
1285O GLU* 1.3 77.5 - - + +
1287O LEU* 1.3 65.9 + - + +
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Residues in contact with LEU1287 (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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1095O ILE* 4.7 11.4 - - + -
1098O LYS* 4.0 24.7 - - + -
1099O LEU* 5.9 4.9 - - + -
1207O ARG* 2.8 25.1 + - + +
1209O LEU* 3.6 30.5 - - + -
1283O ILE* 2.9 46.9 + - + +
1284O ASN* 3.9 1.8 - - - +
1286O ILE* 1.3 85.1 - - + +
1288O ALA* 1.3 67.9 + - - +
1289O ARG* 3.2 13.2 + - - +
1293O GLU* 4.2 0.2 - - - +
1297O LEU* 5.6 1.1 - - + -
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Residues in contact with ALA1288 (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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1207O ARG* 4.0 2.6 + - - -
1284O ASN* 2.5 20.8 + - - +
1285O GLU* 3.2 16.6 - - - +
1287O LEU* 1.3 72.3 - - - +
1289O ARG* 1.3 61.0 + - - +
1290O ASN 3.4 1.8 + - - +
1293O GLU* 3.2 27.4 - - + -
1294O MET* 3.5 26.6 - - + +
1297O LEU* 3.9 13.2 - - + +
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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