Contacts of the helix formed by residues 1046 - 1062 (chain A) in PDB entry 4KEG
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 GLY1046 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045A THR* 1.3 81.2 + - - +
1047A LEU* 1.3 63.7 + - - -
1048A ALA 3.3 2.9 + - - -
1049A GLY 3.5 2.1 + - - -
1050A SER* 2.7 30.2 + - - -
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Residues in contact with LEU1047 (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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1046A GLY* 1.3 71.4 - - - -
1048A ALA* 1.3 57.9 + - - +
1050A SER* 3.2 2.3 + - - -
1051A LEU* 2.8 31.6 + - - +
1238A LEU* 3.8 25.7 - - + +
1241A ASP* 3.8 48.2 - - + +
1242A ILE* 4.1 12.7 - - + +
1245A MET* 3.9 24.0 - - - -
1252A PHE* 3.6 28.5 - - + +
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Residues in contact with ALA1048 (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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1046A GLY 3.3 0.8 - - - -
1047A LEU* 1.3 79.9 - - - +
1049A GLY* 1.3 60.8 + - - +
1051A LEU* 3.6 3.6 - - - +
1052A THR* 3.1 29.0 + - - +
1120A LEU* 3.9 23.0 - - + +
1252A PHE* 3.8 29.8 + - + +
1253A VAL* 4.2 9.4 - - + -
1254A ILE* 5.3 1.8 - - + +
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Residues in contact with GLY1049 (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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179A LYS* 4.9 9.2 - - - -
1045A THR* 3.5 23.3 + - - -
1046A GLY 3.5 3.8 + - - -
1048A ALA* 1.3 74.8 - - - +
1050A SER* 1.3 65.3 + - - +
1052A THR* 3.2 7.0 + - - -
1053A ASN* 2.9 30.5 + - - -
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Residues in contact with SER1050 (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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1045A THR* 3.2 20.3 + - - +
1046A GLY 2.7 23.0 + - - -
1047A LEU* 3.4 4.7 - - - +
1049A GLY* 1.3 77.7 - - - +
1051A LEU* 1.3 53.9 + - - +
1053A ASN* 3.8 5.6 - - - +
1054A ALA* 2.8 36.9 + - - +
1238A LEU* 3.5 24.7 - - - -
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Residues in contact with LEU1051 (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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1047A LEU 2.8 20.5 + - - +
1048A ALA 3.6 4.5 - - - +
1050A SER* 1.3 74.5 - - - +
1052A THR* 1.3 57.3 + - - +
1054A ALA* 3.4 1.7 - - - +
1055A LEU* 2.8 48.7 + - + +
1120A LEU* 3.9 20.6 - - + -
1129A LEU* 3.9 28.7 - - + -
1163A ILE* 4.1 16.8 - - + -
1175A LEU* 5.5 2.0 - - + -
1231A LEU* 4.9 1.8 - - + -
1234A LEU* 3.6 29.8 - - + -
1238A LEU* 4.0 7.7 - - + +
1242A ILE* 3.9 21.1 - - + -
1252A PHE* 5.3 1.8 - - + -
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Residues in contact with THR1052 (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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179A LYS* 4.8 5.5 - - - -
1048A ALA 3.1 14.9 + - - +
1049A GLY* 3.2 15.6 + - - -
1051A LEU* 1.3 75.6 - - + +
1053A ASN* 1.3 60.7 + - - +
1055A LEU* 4.8 1.1 - - + -
1056A SER* 2.7 34.7 + - - -
1118A LEU* 3.9 37.2 - - + +
1120A LEU* 4.2 32.5 - - + -
1131A VAL* 5.5 0.2 - - + -
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Residues in contact with ASN1053 (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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179A LYS* 3.2 36.8 - - - +
1045A THR* 4.1 12.3 - - - +
1049A GLY 2.9 25.1 + - - +
1050A SER* 3.8 4.5 - - - +
1052A THR* 1.3 74.9 + - - +
1054A ALA* 1.3 65.3 + - - +
1056A SER* 3.1 7.0 + - - -
1057A ASN* 2.9 27.8 + - - +
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Residues in contact with ALA1054 (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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1050A SER 2.8 22.0 + - - +
1051A LEU 3.4 4.0 - - - +
1053A ASN* 1.3 73.9 - - - +
1055A LEU* 1.3 57.3 + - - +
1057A ASN* 3.6 4.9 + - - +
1058A GLY* 2.9 26.3 + - - -
1230A VAL* 4.3 1.6 - - - +
1234A LEU* 3.3 28.7 - - + +
1235A ASP 5.9 0.4 - - - +
1238A LEU* 4.1 11.9 - - + -
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Residues in contact with LEU1055 (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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1051A LEU* 2.8 44.9 + - + +
1052A THR* 4.8 1.3 - - + -
1054A ALA* 1.3 70.0 - - - +
1056A SER* 1.3 66.9 + - - +
1058A GLY* 3.6 0.2 - - - -
1059A LEU* 2.9 37.0 + - + +
1118A LEU* 3.9 22.2 - - + -
1120A LEU* 5.7 0.2 - - + -
1131A VAL* 4.7 13.0 - - + -
1133A ILE* 6.2 2.5 - - + -
1163A ILE* 4.5 13.2 - - + -
1227A VAL* 4.8 11.2 - - + +
1230A VAL* 3.8 22.6 - - + +
1231A LEU* 4.1 28.7 - - + +
1234A LEU* 4.2 7.4 - - + -
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Residues in contact with SER1056 (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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1052A THR* 2.7 24.2 + - - -
1053A ASN* 3.5 6.0 - - - -
1055A LEU* 1.3 77.4 - - - +
1057A ASN* 1.3 65.6 + - - +
1059A LEU* 3.7 2.4 - - - +
1060A LEU* 3.0 31.5 + - - +
1115A LEU* 3.8 19.2 - - - +
1116A LEU 5.4 0.3 + - - -
1118A LEU* 3.9 19.2 + - - +
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Residues in contact with ASN1057 (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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1053A ASN 2.9 19.8 + - - +
1054A ALA* 4.0 4.5 + - - +
1056A SER* 1.3 72.8 - - - +
1058A GLY* 1.3 63.2 + - - +
1060A LEU* 3.4 9.2 + - - +
1061A SER* 2.9 35.5 + - - -
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Residues in contact with GLY1058 (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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1054A ALA 2.9 18.0 + - - -
1056A SER 3.1 0.2 - - - -
1057A ASN* 1.3 78.1 - - - +
1059A LEU* 1.3 51.2 + - - +
1061A SER* 3.2 7.2 + - - -
1062A GLY* 2.6 35.2 + - - -
1230A VAL* 3.4 23.7 - - - +
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Residues in contact with LEU1059 (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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1055A LEU* 2.9 34.9 + - + +
1056A SER* 3.8 2.0 - - - +
1058A GLY* 1.3 71.8 - - - +
1060A LEU* 1.3 61.1 + - - +
1062A GLY 3.2 2.1 + - - -
1063A GLY 3.1 6.1 + - - -
1064A LEU* 2.9 47.7 + - + +
1115A LEU* 4.1 17.9 - - + -
1118A LEU* 5.0 3.8 - - + -
1133A ILE* 4.4 25.6 - - + -
1223A VAL* 5.5 0.4 - - + -
1226A LEU* 4.0 19.8 - - + +
1227A VAL* 3.8 39.3 - - + -
1230A VAL* 3.5 10.7 - - + +
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Residues in contact with LEU1060 (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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1056A SER* 3.0 23.7 + - - +
1057A ASN* 3.8 8.3 - - - +
1059A LEU* 1.3 77.6 - - - +
1061A SER* 1.3 60.9 + - - +
1063A GLY* 3.0 14.7 + - - -
1064A LEU* 4.1 5.3 + - + +
1065A LEU* 3.8 39.7 + - + +
1115A LEU* 4.1 26.2 - - + -
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Residues in contact with SER1061 (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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1057A ASN* 2.9 33.9 + - - -
1058A GLY* 3.2 9.7 + - - -
1060A LEU* 1.3 68.8 - - - +
1062A GLY* 1.3 56.4 + - - +
1063A GLY* 2.9 12.1 + - - -
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Residues in contact with GLY1062 (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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1058A GLY 2.6 21.6 + - - -
1059A LEU 3.4 4.5 - - - -
1060A LEU 3.2 0.4 - - - -
1061A SER* 1.3 71.2 + - - +
1063A GLY* 1.3 61.9 + - - +
1064A LEU 3.6 0.2 - - - -
1067A ILE* 4.8 3.3 - - - +
1226A LEU* 3.6 26.5 - - - +
1230A VAL* 5.3 0.9 - - - -
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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