Contacts of the helix formed by residues 1077 - 1088 (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 PRO1077 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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983B LYS* 5.1 1.1 - - - -
984B SER* 3.9 33.0 - - - -
987B LEU* 3.7 17.7 - - + +
1059B TYR* 5.8 2.5 - - + -
1076B VAL* 1.3 98.5 - - + +
1078B ASP* 1.3 59.0 - - - +
1080B PHE* 3.7 1.0 - - - +
1081B TYR* 2.8 39.6 + - - +
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Residues in contact with ASP1078 (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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983B LYS* 3.3 38.7 + - + +
984B SER* 4.2 3.8 + - - -
1075B PRO* 5.5 2.9 - - + -
1076B VAL 2.5 7.5 + - - +
1077B PRO* 1.3 84.8 - - - +
1079B GLY* 1.3 57.2 + - - +
1081B TYR* 3.2 2.4 + - - +
1082B ASP* 2.8 37.2 + - - +
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Residues in contact with GLY1079 (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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1073B MET 3.9 4.0 - - - -
1074B GLY* 4.1 5.2 - - - -
1075B PRO* 3.4 25.5 + - - +
1076B VAL 3.3 5.1 + - - -
1078B ASP* 1.3 75.2 - - - +
1080B PHE* 1.3 59.9 + - - +
1082B ASP* 3.1 11.4 + - - +
1083B TYR* 2.8 28.6 + - - +
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Residues in contact with PHE1080 (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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987B LEU* 3.9 27.6 - - + -
1055B LEU* 3.5 15.5 - - + -
1058B LYS* 3.9 3.1 - - + -
1059B TYR* 3.5 38.8 - + + -
1062B PHE* 3.7 33.9 - + - -
1073B MET* 3.4 32.7 + - + +
1075B PRO 2.8 16.2 + - - +
1076B VAL* 3.9 12.6 - - + -
1077B PRO 3.7 6.3 - - - +
1078B ASP 3.4 0.2 - - - -
1079B GLY* 1.3 73.2 - - - +
1081B TYR* 1.3 64.7 + - - +
1083B TYR* 3.3 8.4 + - - +
1084B PHE* 3.3 38.1 - + - -
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Residues in contact with TYR1081 (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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946B ASP* 5.7 1.3 - - - -
948B SER* 4.9 6.3 + - - -
949B LEU* 6.3 0.7 - - + -
952B GLU* 3.9 6.6 + - - -
983B LYS* 3.7 36.1 - - + +
986B LYS* 3.3 40.6 - - + +
987B LEU* 3.9 28.3 - - + -
990B LEU* 4.1 15.0 - - + -
1055B LEU* 6.2 1.6 - - + -
1077B PRO 2.8 24.2 + - - +
1078B ASP 3.4 2.7 - - - +
1080B PHE* 1.3 78.8 - - - +
1082B ASP* 1.3 66.3 + - - +
1084B PHE* 3.1 8.1 + - + +
1085B THR* 2.9 56.9 + - + +
1092B LEU* 3.5 15.2 - - - +
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Residues in contact with ASP1082 (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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946B ASP* 4.7 6.6 - - - +
983B LYS* 3.0 38.6 + - - +
1078B ASP* 2.8 27.1 + - - +
1079B GLY* 3.1 9.2 + - - +
1081B TYR* 1.3 73.1 - - - +
1083B TYR* 1.3 58.3 + - - +
1085B THR* 3.3 10.8 + - - -
1086B LYS* 2.9 34.7 + - - +
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Residues in contact with TYR1083 (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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1029B PHE* 3.8 21.4 - + - -
1030B ASP* 5.1 6.9 + - - +
1033B PHE* 4.2 16.0 - + - +
1069B ILE* 5.9 1.6 - - - +
1072B LEU* 3.3 33.9 - - + +
1073B MET* 3.6 40.4 - - + +
1079B GLY 2.8 12.3 + - - +
1080B PHE* 3.4 14.1 - - - +
1081B TYR 3.2 0.2 - - - -
1082B ASP* 1.3 77.2 - - - +
1084B PHE* 1.3 65.1 + + + +
1086B LYS* 4.4 2.1 - - - +
1087B ARG* 2.8 71.7 + - - +
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Residues in contact with PHE1084 (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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1029B PHE* 3.8 30.1 - + - -
1033B PHE* 4.4 13.0 - + - -
1051B LEU* 4.7 10.5 - - + -
1054B ALA* 4.8 0.7 - - + -
1055B LEU* 3.5 57.0 - - + -
1058B LYS* 4.5 1.8 - - + -
1073B MET* 3.6 26.7 - - + -
1080B PHE* 3.3 38.6 - + - -
1081B TYR* 3.1 8.0 + - + +
1083B TYR* 1.3 82.1 - + - +
1085B THR* 1.3 59.8 + - + +
1086B LYS 3.3 0.7 - - - -
1087B ARG* 3.3 4.0 + - - -
1088B PHE* 2.9 34.8 + + + +
1091B LEU* 4.4 8.0 - - + +
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Residues in contact with THR1085 (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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946B ASP* 5.1 4.8 + - - +
947B ARG* 5.9 0.2 - - - +
948B SER* 4.2 20.7 + - - -
990B LEU* 5.4 0.2 - - + -
1081B TYR* 2.9 63.9 + - + +
1082B ASP* 3.3 15.4 + - - -
1084B PHE* 1.3 74.8 - - + +
1086B LYS* 1.3 64.8 + - - +
1088B PHE 3.7 10.3 - - - +
1089B PRO* 3.2 24.9 - - - +
1091B LEU* 4.9 13.5 - - + -
1092B LEU* 5.2 2.7 - - + +
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Residues in contact with LYS1086 (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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946B ASP* 5.8 1.8 - - - -
947B ARG* 5.8 3.6 - - - +
1028B LYS* 5.5 1.4 + - - -
1082B ASP* 2.9 20.8 + - + +
1083B TYR* 4.4 4.0 - - - +
1085B THR* 1.3 78.7 + - - +
1087B ARG* 1.3 63.1 + - + +
1088B PHE 3.6 0.2 + - - -
1089B PRO* 4.1 6.9 - - - +
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Residues in contact with ARG1087 (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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1028B LYS* 3.3 64.4 + - + +
1029B PHE* 3.7 23.9 - - - +
1083B TYR* 2.8 68.2 + - - +
1084B PHE 3.3 5.4 + - - +
1086B LYS* 1.3 83.4 - - + +
1088B PHE* 1.3 81.3 + - + +
1089B PRO* 3.9 4.8 - - - +
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Residues in contact with PHE1088 (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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1019B VAL* 3.7 26.0 - - + +
1020B ILE* 4.4 8.5 - - + -
1021B PRO* 5.7 1.8 - - + -
1022B SER* 5.8 0.9 - - - -
1025B TRP* 3.4 40.2 - - + -
1028B LYS* 3.8 21.8 - - + -
1029B PHE* 3.7 22.9 - + - -
1051B LEU* 4.0 21.3 - - + -
1084B PHE* 2.9 19.5 + - + +
1085B THR* 3.3 10.8 - - - +
1087B ARG* 1.3 96.0 - - + +
1089B PRO* 1.3 68.6 - - - +
1090B ASN 3.2 2.5 - - - -
1091B LEU* 3.1 29.3 + - + +
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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