Contacts of the helix formed by residues 1051 - 1067 (chain B) in PDB entry 1G24
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 ASN1051 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049B PHE* 3.7 1.8 - - - -
1050B THR* 1.3 83.5 + - - +
1052B ILE* 1.3 68.8 + - - +
1053B ASP* 3.3 21.4 + - - +
1054B GLN* 3.0 37.3 + - + +
1055B ALA* 3.0 20.8 + - - +
1178B MET* 3.8 2.9 - - - -
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Residues in contact with ILE1052 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050B THR 4.6 2.5 - - - +
1051B ASN* 1.3 75.6 + - - +
1053B ASP* 1.3 64.1 + - - +
1055B ALA* 3.2 2.7 + - - +
1056B LYS* 2.9 32.9 + - + +
1178B MET* 3.4 35.4 - - + -
1180B VAL* 6.0 2.5 - - + -
1212B GLN* 4.6 17.0 - - - +
1213B LEU* 4.3 19.7 - - + +
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Residues in contact with ASP1053 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1051B ASN* 3.2 17.7 + - - +
1052B ILE* 1.3 81.6 - - - +
1054B GLN* 1.3 59.2 + - + +
1056B LYS* 3.6 9.7 + - - +
1057B ALA* 3.1 26.0 + - - +
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Residues in contact with GLN1054 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049B PHE* 4.2 8.0 - - + -
1051B ASN* 3.0 27.6 + - + +
1053B ASP* 1.3 77.0 - - - +
1055B ALA* 1.3 57.0 + - - +
1056B LYS 3.2 0.2 - - - -
1057B ALA* 3.6 17.7 - - - +
1058B TRP* 2.7 36.5 + - - +
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Residues in contact with ALA1055 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049B PHE* 3.5 36.7 - - + -
1051B ASN 3.0 12.0 + - - +
1052B ILE 3.6 7.9 - - - +
1054B GLN* 1.3 77.2 - - - +
1056B LYS* 1.3 57.7 + - - +
1058B TRP* 3.6 0.5 - - - +
1059B GLY* 2.8 25.1 + - - -
1177B LEU* 3.5 23.3 - - + +
1178B MET* 4.2 2.0 - - - -
1213B LEU* 4.2 16.8 - - + -
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Residues in contact with LYS1056 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1052B ILE* 2.9 22.1 + - + +
1053B ASP* 3.7 8.7 - - - +
1055B ALA* 1.3 77.2 - - - +
1057B ALA* 1.3 57.5 + - - +
1059B GLY* 3.3 0.5 + - - -
1060B ASN* 2.8 58.6 + - - +
1202B TYR* 3.5 18.7 + - - +
1204B ASP* 5.2 9.6 + - - +
1205B PRO* 6.2 0.6 - - - +
1213B LEU* 3.9 7.7 - - + +
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Residues in contact with ALA1057 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1053B ASP 3.1 18.1 + - - +
1054B GLN* 3.6 18.8 - - - +
1056B LYS* 1.3 76.3 - - - +
1058B TRP* 1.3 58.5 + - - +
1060B ASN* 3.7 7.7 - - - +
1061B ALA* 2.9 28.8 + - - +
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Residues in contact with TRP1058 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1049B PHE* 3.3 33.5 - + + -
1054B GLN 2.7 20.6 + - - +
1055B ALA 3.6 3.1 - - - +
1057B ALA* 1.3 70.0 - - - +
1059B GLY* 1.3 72.6 + - - +
1061B ALA* 3.2 5.0 + - - +
1062B GLN* 3.0 52.9 + - + +
1120B THR* 3.7 19.5 - - - -
1121B PRO* 3.6 29.6 - - + +
1122B GLU* 4.2 22.6 + - + +
1124B ILE* 4.2 13.2 - - + -
1177B LEU* 4.1 23.3 - - + -
1215B MET* 4.1 14.4 - - + -
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Residues in contact with GLY1059 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1055B ALA 2.8 14.5 + - - -
1058B TRP* 1.3 87.8 - - - +
1060B ASN* 1.3 62.0 + - - +
1062B GLN* 3.1 5.4 + - - +
1063B TYR 2.9 18.7 + - - -
1202B TYR* 3.1 41.8 - - - -
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Residues in contact with ASN1060 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056B LYS* 2.8 49.5 + - - +
1057B ALA* 3.7 7.1 - - - +
1059B GLY* 1.3 71.4 - - - +
1061B ALA* 1.3 57.3 + - - +
1063B TYR* 3.3 10.2 + - + +
1064B LYS* 2.9 30.1 + - - +
1202B TYR* 3.4 19.8 + - - -
1204B ASP* 5.1 0.6 + - - -
1205B PRO* 3.8 20.0 - - - +
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Residues in contact with ALA1061 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057B ALA 2.9 17.3 + - - +
1058B TRP* 3.4 8.7 - - + +
1060B ASN* 1.3 77.4 - - - +
1062B GLN* 1.3 71.0 + - - +
1064B LYS* 3.5 19.1 + - - +
1065B LYS* 3.6 16.0 + - - +
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Residues in contact with GLN1062 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1058B TRP* 3.0 65.7 + - + +
1059B GLY* 3.1 6.5 + - - +
1061B ALA* 1.3 81.4 - - - +
1063B TYR* 1.3 67.4 + - - +
1065B LYS* 3.0 32.7 + - - +
1066B TYR* 3.2 38.0 + - + +
1119B LYS 4.9 2.5 - - - +
1121B PRO* 3.3 32.7 - - + +
1202B TYR* 5.1 0.7 - - + -
1215B MET* 6.3 0.4 - - + -
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Residues in contact with TYR1063 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1059B GLY 2.9 11.8 + - - +
1060B ASN* 3.5 11.2 - - + +
1062B GLN* 1.3 77.9 - - - +
1064B LYS* 1.3 66.7 + - + +
1065B LYS 3.1 1.0 + - - -
1066B TYR* 3.1 38.1 + + + +
1067B GLY 4.4 1.7 + - - -
1068B LEU* 4.3 4.9 - - + -
1073B LYS* 2.9 39.8 + - - +
1202B TYR 4.3 4.0 - - - +
1205B PRO* 3.7 37.5 + - + -
1206B ILE* 3.4 35.7 - - + +
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Residues in contact with LYS1064 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060B ASN 2.9 16.8 + - - +
1061B ALA* 3.6 11.0 - - - +
1062B GLN 3.2 0.4 - - - -
1063B TYR* 1.3 81.7 - - + +
1065B LYS* 1.3 62.1 + - + +
1066B TYR 3.8 0.3 + - - -
1067B GLY* 4.6 3.3 + - - -
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Residues in contact with LYS1065 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061B ALA 3.7 16.6 - - - +
1062B GLN* 3.0 25.8 + - - +
1064B LYS* 1.3 82.0 - - + +
1066B TYR* 1.3 64.5 + - + +
1067B GLY* 3.4 2.1 + - - -
1117B LYS 5.2 0.7 - - - +
1121B PRO* 5.8 4.0 - - - +
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Residues in contact with TYR1066 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062B GLN* 3.2 33.7 - - + +
1063B TYR* 3.1 32.0 + + + +
1065B LYS* 1.3 80.6 - - + +
1067B GLY* 1.3 63.6 + - - +
1068B LEU* 3.7 21.1 - - + +
1117B LYS* 3.4 38.7 - - - +
1118B MET* 3.7 42.4 - - + -
1119B LYS 4.6 8.3 + - - -
1200B ALA 3.9 4.0 + - - -
1201B GLY* 3.7 3.5 - - - -
1202B TYR* 3.0 41.2 + - - +
1215B MET* 5.2 2.1 - - - +
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Residues in contact with GLY1067 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063B TYR 4.4 2.6 + - - -
1064B LYS 4.6 3.0 + - - -
1065B LYS* 3.4 3.1 - - - +
1066B TYR* 1.3 79.4 - - - +
1068B LEU* 1.3 63.6 + - - +
1069B SER* 4.6 0.3 - - - -
1117B LYS* 2.8 21.2 + - - -
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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