Contacts of the helix formed by residues 1090 - 1103 (chain B) in PDB entry 3LJ1
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 ASN1090 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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951B ALA* 3.0 29.7 - - - +
1018B PHE* 3.3 53.1 - - + +
1019B VAL* 3.6 12.1 + - - +
1021B PRO* 5.7 1.7 - - - +
1088B PHE 3.2 1.4 + - - -
1089B PRO* 1.3 83.3 - - - +
1091B LEU* 1.3 63.1 + - - +
1092B LEU 3.6 0.9 - - - -
1093B ILE* 4.2 5.2 - - - -
1094B GLY* 3.0 23.1 + - - -
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Residues in contact with LEU1091 (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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990B LEU* 3.7 25.6 - - + -
1019B VAL* 4.0 12.1 - - + +
1048B LEU* 4.0 26.5 - - + -
1051B LEU* 4.6 12.1 - - + -
1052B LEU* 4.0 17.5 - - + -
1055B LEU* 3.9 18.8 - - + -
1084B PHE* 4.4 17.5 - - + +
1085B THR* 4.9 7.9 - - + -
1088B PHE* 3.1 25.5 + - + +
1089B PRO 3.2 1.2 - - - -
1090B ASN* 1.3 76.9 - - - +
1092B LEU* 1.3 64.5 + - - +
1094B GLY* 3.8 0.3 - - - -
1095B VAL* 3.0 30.3 + - + +
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Residues in contact with LEU1092 (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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948B SER* 6.2 0.4 - - - -
952B GLU* 4.0 17.0 - - - +
978B PRO* 3.6 31.9 - - + -
981B TRP* 4.6 2.5 - - + -
986B LYS* 4.0 26.9 - - + +
989B PHE* 3.6 28.3 - - + -
990B LEU* 3.8 17.3 - - + -
1081B TYR* 3.5 28.0 - - + +
1085B THR* 5.2 1.9 - - + +
1089B PRO 4.6 2.4 + - - +
1091B LEU* 1.3 78.1 - - - +
1093B ILE* 1.3 63.5 + - - +
1095B VAL* 3.3 2.1 + - - +
1096B TYR* 2.8 32.1 + - + +
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Residues in contact with ILE1093 (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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951B ALA* 4.2 24.9 - - + +
952B GLU* 3.9 20.5 + - + +
955B ASP* 3.9 26.0 - - + +
977B HIS* 3.8 29.2 - - + -
978B PRO* 3.8 15.5 - - + -
1018B PHE* 4.0 16.4 - - + -
1089B PRO 4.9 1.1 + - - +
1090B ASN* 3.8 11.2 - - - +
1092B LEU* 1.3 81.1 - - - +
1094B GLY* 1.3 61.6 + - - +
1096B TYR* 3.6 8.9 - - + +
1097B MET* 2.9 35.9 + - + +
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Residues in contact with GLY1094 (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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1018B PHE* 3.8 21.1 - - - -
1019B VAL* 4.4 5.8 - - - -
1090B ASN 3.0 20.9 + - - -
1091B LEU 3.8 0.4 - - - -
1093B ILE* 1.3 79.7 - - - +
1095B VAL* 1.3 60.7 + - - +
1097B MET* 3.5 5.1 + - - +
1098B ILE* 3.2 31.4 + - - +
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Residues in contact with VAL1095 (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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989B PHE* 4.1 5.4 - - + -
990B LEU* 3.9 19.5 - - + -
993B VAL* 3.6 37.5 - - + -
1012B PHE* 4.1 5.4 - - + -
1048B LEU* 4.6 13.9 - - + -
1052B LEU* 4.1 19.1 - - + -
1091B LEU* 3.0 23.1 + - + +
1092B LEU 3.8 2.9 - - - +
1094B GLY* 1.3 72.6 - - - +
1096B TYR* 1.3 60.4 + - - +
1098B ILE* 3.3 8.4 + - - +
1099B VAL* 2.8 32.9 + - + +
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Residues in contact with TYR1096 (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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955B ASP* 5.2 2.2 - - - -
959B GLN* 6.3 0.4 - - - -
976B ARG* 4.6 5.0 + - - +
977B HIS* 4.9 8.6 - + - -
978B PRO* 3.6 35.9 - - + +
981B TRP* 3.8 32.3 - + - -
989B PHE* 3.9 20.6 - + + -
1092B LEU* 2.8 20.0 + - + +
1093B ILE* 3.6 16.6 - - + +
1095B VAL* 1.3 74.2 - - - +
1097B MET* 1.3 61.0 + - + +
1099B VAL* 3.1 1.7 + - - +
1100B LYS* 2.7 70.9 + - + +
1113B LEU* 3.9 28.3 + - + +
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Residues in contact with MET1097 (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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955B ASP* 4.0 24.2 - - - +
1018B PHE* 4.8 20.2 - - + -
1093B ILE* 2.9 34.2 + - + +
1094B GLY* 3.7 5.8 - - - +
1096B TYR* 1.3 80.6 - - + +
1098B ILE* 1.3 62.8 + - + +
1100B LYS* 3.5 4.4 + - - +
1101B GLU* 3.2 24.4 + - - +
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Residues in contact with ILE1098 (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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1011B LYS* 4.0 9.0 - - + +
1012B PHE* 3.5 69.3 - - + +
1015B GLY* 4.2 17.7 - - - +
1048B LEU* 4.2 9.6 - - + -
1094B GLY 3.2 16.6 + - - +
1095B VAL 3.6 6.3 - - - +
1097B MET* 1.3 77.4 - - + +
1099B VAL* 1.3 58.3 + - - +
1101B GLU* 4.8 0.4 - - - -
1102B ASN* 2.8 52.5 + - + +
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Residues in contact with VAL1099 (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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989B PHE* 4.0 16.8 - - + -
993B VAL* 3.9 26.0 - - + -
1012B PHE* 4.2 13.5 - - + -
1095B VAL* 2.8 28.9 + - + +
1096B TYR 3.7 2.7 - - - +
1098B ILE* 1.3 72.2 - - - +
1100B LYS* 1.3 60.3 + - - +
1101B GLU 3.1 0.2 - - - -
1103B LEU* 2.7 64.7 + - + +
1109B LEU* 3.9 12.1 - - + -
1113B LEU* 4.0 14.4 - - + -
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Residues in contact with LYS1100 (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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959B GLN* 6.3 0.9 - - - +
973B LYS* 3.3 38.6 - - - +
1096B TYR* 2.7 53.6 + - + +
1097B MET* 4.0 5.4 - - - +
1099B VAL* 1.3 73.6 - - - +
1101B GLU* 1.3 57.0 + - - +
1104B SER* 3.0 19.8 + - - -
1113B LEU* 3.9 18.1 - - + +
1114B TYR* 3.7 31.6 + - - +
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Residues in contact with GLU1101 (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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1097B MET 3.2 16.7 + - - +
1098B ILE* 4.8 0.4 - - - -
1099B VAL 3.1 0.4 - - - -
1100B LYS* 1.3 80.5 - - - +
1102B ASN* 1.3 77.2 + - - +
1103B LEU 3.7 0.2 - - - -
1104B SER* 4.0 8.6 + - - -
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Residues in contact with ASN1102 (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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1008B LEU* 3.9 20.8 - - + +
1011B LYS* 3.5 35.6 - - + +
1098B ILE* 2.8 41.0 + - + +
1101B GLU* 1.3 89.0 - - - +
1103B LEU* 1.3 69.5 + - + +
1104B SER 3.5 1.7 + - - -
1105B ASP* 5.1 3.8 - - - +
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Residues in contact with LEU1103 (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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993B VAL* 5.3 2.2 - - + -
996B ARG* 4.0 23.1 - - + +
997B LEU* 5.3 1.3 - - + -
1008B LEU* 3.6 36.1 - - + -
1012B PHE* 4.8 9.6 - - + -
1099B VAL* 2.7 44.6 + - + +
1102B ASN* 1.3 80.5 - - + +
1104B SER* 1.3 57.5 + - - +
1105B ASP* 3.4 3.8 - - - -
1106B ASP* 2.8 45.4 - - + +
1109B LEU* 3.5 19.4 - - + +
1113B LEU* 4.2 3.1 - - - +
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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