Contacts of the helix formed by residues 1051 - 1066 (chain A) in PDB entry 3L2O
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1008A SER* 3.1 10.5 + - - -
1009A SER* 4.0 9.2 - - - -
1010A ASP* 4.6 7.6 - - - +
1049A ASN 3.6 4.6 + - - +
1050A VAL* 1.3 76.8 - - - +
1052A ALA* 1.3 60.2 + - - +
1053A ALA* 2.9 12.1 + - - +
1054A ILE* 2.7 41.2 + - - +
1055A LEU* 3.2 23.4 + - - +
1102A GLU* 3.7 19.4 + - - -
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Residues in contact with ALA1052 (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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1008A SER* 3.0 10.9 + - - +
1010A ASP* 4.0 9.8 + - - +
1012A GLU* 3.6 35.9 - - + -
1014A PHE* 3.8 11.4 - - + -
1051A ASN* 1.3 74.7 - - - +
1053A ALA* 1.3 70.6 + - - +
1054A ILE 3.2 1.3 - - - -
1056A LYS* 3.0 23.7 + - - +
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Residues in contact with ALA1053 (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 ASN* 2.9 13.7 + - - +
1052A ALA* 1.3 81.8 - - - +
1054A ILE* 1.3 65.8 + - + +
1056A LYS* 3.2 18.3 + - - +
1057A LYS* 3.3 10.7 + - - +
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Residues in contact with ILE1054 (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 VAL* 3.7 18.2 - - + -
1051A ASN* 2.7 26.7 + - - +
1053A ALA* 1.3 73.0 - - + +
1055A LEU* 1.3 67.7 + - - +
1056A LYS 3.0 1.6 - - - -
1057A LYS* 2.9 10.6 + - + +
1058A VAL* 2.9 22.8 + - + +
1099A THR* 4.3 19.3 - - + +
1102A GLU* 3.4 49.6 - - + +
1103A LEU* 4.0 11.7 - - + +
1106A ALA* 3.9 19.3 - - + -
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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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1006A LEU* 4.3 20.9 - - + -
1008A SER* 4.9 11.0 - - - +
1014A PHE* 3.4 35.9 - - + -
1047A LEU* 4.4 20.0 - - + -
1050A VAL* 3.5 17.0 - - + +
1051A ASN 3.2 21.1 + - - +
1052A ALA 3.4 2.4 + - - +
1054A ILE* 1.3 78.6 - - - +
1056A LYS* 1.3 56.5 + - - +
1058A VAL* 3.6 20.4 - - + -
1059A ILE* 3.0 39.8 + - + +
1110A LEU* 4.8 2.9 - - + -
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Residues in contact with LYS1056 (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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1014A PHE* 4.1 22.2 - - + -
1052A ALA 3.0 12.3 + - - +
1053A ALA* 3.3 12.6 - - - +
1054A ILE 3.0 1.0 - - - -
1055A LEU* 1.3 75.0 - - - +
1057A LYS* 1.3 67.6 + - + +
1059A ILE* 3.4 7.1 + - - +
1060A GLN* 3.1 24.0 + - - +
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Residues in contact with LYS1057 (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 ALA 3.3 8.2 + - - +
1054A ILE* 2.9 12.0 + - + +
1056A LYS* 1.3 80.0 - - + +
1058A VAL* 1.3 54.5 + - - +
1060A GLN* 2.7 43.3 + - - +
1061A TRP 2.8 12.8 + - - -
1092A PHE* 3.4 45.5 - - + -
1095A VAL* 3.1 30.9 - - - +
1099A THR* 4.7 7.2 - - + +
1103A LEU* 4.0 18.5 - - + +
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Residues in contact with VAL1058 (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 ILE* 2.9 33.9 + - + +
1055A LEU* 3.5 18.2 - - + +
1057A LYS* 1.3 75.9 - - - +
1059A ILE* 1.3 62.4 + - + +
1061A TRP* 3.6 6.8 + - - +
1062A CYS* 3.1 25.1 + - - -
1103A LEU* 4.2 9.0 - - + -
1106A ALA* 4.1 16.4 - - + -
1110A LEU* 3.9 13.2 - - + -
1112A ILE* 3.8 27.8 - - + -
1115A LEU* 4.3 12.6 - - + -
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Residues in contact with ILE1059 (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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1006A LEU* 4.9 3.8 - - + -
1014A PHE* 3.6 44.6 - - + -
1016A VAL* 3.9 24.9 - - + -
1020A ILE* 4.9 3.1 - - + -
1055A LEU* 3.0 37.0 + - + +
1056A LYS* 3.8 5.4 - - - +
1057A LYS 3.1 0.4 - - - -
1058A VAL* 1.3 75.2 - - + +
1060A GLN* 1.3 61.3 + - - +
1062A CYS* 3.8 4.6 - - - +
1063A THR* 2.8 43.1 + - + +
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Residues in contact with GLN1060 (chain A).
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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1056A LYS* 3.1 15.5 + - + +
1057A LYS* 2.7 37.0 + - - +
1059A ILE* 1.3 75.6 - - - +
1061A TRP* 1.3 66.4 + - - +
1063A THR* 3.0 10.1 + - - +
1064A HIS* 3.0 23.6 + - - +
1088A TRP* 4.4 12.0 - - + -
1092A PHE* 3.6 13.6 - - + -
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Residues in contact with TRP1061 (chain A).
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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1023A GLN* 3.9 16.8 - - - -
1057A LYS 2.8 8.3 + - - +
1058A VAL* 3.9 4.9 - - - +
1060A GLN* 1.3 78.7 - - - +
1062A CYS* 1.3 72.6 - - - +
1064A HIS* 3.1 8.0 + - - +
1065A HIS* 3.1 48.7 + + + -
1069A PRO* 6.5 0.4 - - + -
1088A TRP* 4.0 10.3 - + - -
1089A ASP* 2.8 28.4 + - - -
1092A PHE* 3.6 36.6 - + + -
1112A ILE* 3.8 19.5 - - + -
1114A GLY* 3.5 27.8 - - - -
1115A LEU* 3.4 35.7 - - + -
1118A VAL* 4.0 11.0 - - + +
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Residues in contact with CYS1062 (chain A).
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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1020A ILE* 3.7 23.3 - - + -
1023A GLN* 3.4 32.4 + - - +
1058A VAL* 3.1 26.7 + - - +
1059A ILE* 3.9 3.1 - - - +
1061A TRP* 1.3 92.1 - - - +
1063A THR* 1.3 64.2 + - - +
1065A HIS 3.3 0.7 + - - -
1066A LYS* 3.0 21.1 + - - +
1112A ILE* 3.7 30.5 - - - -
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Residues in contact with THR1063 (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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1016A VAL* 5.9 1.3 - - + -
1020A ILE* 3.8 29.4 - - + -
1059A ILE* 2.8 39.4 + - + +
1060A GLN* 3.0 16.7 + - - +
1062A CYS* 1.3 73.4 - - - +
1064A HIS* 1.3 60.6 + - - +
1066A LYS* 3.3 24.3 - - - +
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Residues in contact with HIS1064 (chain A).
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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1060A GLN 3.0 6.8 + - - +
1061A TRP 3.4 7.9 - - - +
1062A CYS 3.1 0.2 - - - -
1063A THR* 1.3 81.1 + - - +
1065A HIS* 1.3 76.4 + + - +
1066A LYS* 3.8 1.2 + - - +
1067A ASP 5.1 1.0 + - - -
1068A ASP* 4.5 3.1 - - - +
1088A TRP* 3.2 77.4 + + + +
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Residues in contact with HIS1065 (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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1023A GLN* 4.2 13.5 - - - +
1061A TRP* 3.1 55.7 + + + +
1062A CYS 3.3 1.1 + - - -
1064A HIS* 1.3 92.8 + + - +
1066A LYS* 1.3 66.0 + - - +
1067A ASP 3.0 4.0 + - - -
1068A ASP* 3.4 27.5 + - - +
1069A PRO* 3.0 21.9 - - + +
1086A PRO* 5.2 3.4 - - + +
1089A ASP* 2.8 41.4 + - - -
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Residues in contact with LYS1066 (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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1017A ASP* 5.9 2.3 + - - +
1019A GLU* 6.3 1.6 - - + -
1020A ILE* 3.3 36.3 - - + -
1023A GLN* 4.0 10.3 + - - +
1062A CYS 3.0 7.5 + - - +
1063A THR* 3.3 16.8 - - - +
1064A HIS 3.4 1.1 - - - +
1065A HIS* 1.3 77.7 - - - +
1067A ASP* 1.3 88.4 + - + +
1068A ASP 3.3 4.2 + - - -
1069A PRO* 3.7 7.3 - - - +
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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