Contacts of the helix formed by residues 1179 - 1193 (chain E) in PDB entry 6LXT
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 ILE1179 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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945E LEU* 3.5 31.9 - - + +
949E GLN* 3.3 23.6 - - + +
1177E VAL* 3.8 8.1 - - + -
1178E ASN* 1.3 71.8 - - - +
1180E GLN* 1.3 65.6 + - - +
1181E LYS 3.1 3.4 - - - -
1182E GLU* 3.0 24.0 + - - +
1183E ILE* 3.1 15.0 + - + +
944F ALA* 3.8 27.8 - - + +
947F LYS* 3.4 37.9 - - + -
948F LEU* 3.9 22.9 - - + -
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Residues in contact with GLN1180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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949E GLN* 3.4 23.2 + - - +
950E ASP* 5.5 2.1 - - - +
1178E ASN* 3.4 13.2 + - - +
1179E ILE* 1.3 76.4 - - - +
1181E LYS* 1.3 53.7 + - + +
1183E ILE* 3.2 21.7 + - - +
1184E ASP* 2.8 69.1 + - - +
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Residues in contact with LYS1181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1184B ASP* 5.3 11.0 - - - +
1178E ASN* 5.2 6.3 - - - +
1179E ILE* 3.1 0.6 - - - -
1180E GLN* 1.3 79.5 - - + +
1182E GLU* 1.3 63.1 + - - +
1184E ASP* 3.6 12.0 + - + +
1185E ARG* 3.0 27.5 + - - +
947F LYS* 5.8 2.0 - - - +
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Residues in contact with GLU1182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945E LEU* 5.9 0.7 - - + -
1179E ILE* 3.0 25.8 + - - +
1181E LYS* 1.3 78.8 + - - +
1183E ILE* 1.3 65.6 + - - +
1185E ARG* 3.2 8.0 + - - +
1186E LEU* 3.0 30.5 + - + +
940F SER* 3.2 35.9 - - - +
943F SER* 2.9 25.4 + - - -
944F ALA* 4.0 13.9 - - + +
947F LYS* 2.7 29.3 + - - +
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Residues in contact with ILE1183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942E ALA* 3.5 21.3 - - + +
945E LEU* 3.9 16.8 - - + +
946E GLY* 3.4 32.5 - - - +
949E GLN* 3.3 26.5 - - - +
1179E ILE* 3.1 16.5 + - + +
1180E GLN* 3.2 23.5 + - - +
1182E GLU* 1.3 75.2 - - + +
1184E ASP* 1.3 62.6 + - - +
1186E LEU* 3.1 10.7 + - - +
1187E ASN* 3.1 36.7 + - - +
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Residues in contact with ASP1184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1180E GLN* 2.8 48.4 + - - +
1181E LYS* 3.7 13.4 - - - +
1183E ILE* 1.3 72.0 - - - +
1185E ARG* 1.3 51.8 + - - +
1187E ASN* 3.2 13.4 + - - +
1188E GLU* 2.8 35.7 + - - +
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Residues in contact with ARG1185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1184B ASP* 4.9 17.2 + - - +
1188B GLU* 5.0 13.7 + - - +
1181E LYS 3.0 18.8 + - - +
1182E GLU* 3.2 7.3 + - - +
1184E ASP* 1.3 75.3 - - - +
1186E LEU* 1.3 56.8 + - - +
1188E GLU* 3.3 11.3 - - + +
1189E VAL* 3.0 45.9 + - + +
936F ASP* 4.2 27.1 + - - +
937F SER* 5.6 0.7 - - - -
940F SER* 3.4 26.6 + - - +
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Residues in contact with LEU1186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938E LEU* 4.0 20.8 - - + +
941E THR* 3.8 29.2 - - + -
942E ALA* 3.8 18.6 - - + +
945E LEU* 3.8 18.2 - - + -
1182E GLU 3.0 16.8 + - - +
1183E ILE* 3.1 8.7 + - - +
1185E ARG* 1.3 72.4 - - - +
1187E ASN* 1.3 55.3 + - - +
1189E VAL* 3.2 5.4 + - - +
1190E ALA* 2.9 35.0 + - - +
937F SER* 3.4 42.8 - - - +
940F SER* 4.4 6.5 - - - -
941F THR* 3.6 8.1 - - - +
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Residues in contact with ASN1187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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939E SER* 3.6 17.0 + - - +
942E ALA* 3.2 24.5 - - - +
943E SER 5.2 0.2 - - - +
1183E ILE* 3.1 26.6 + - - +
1184E ASP* 3.5 12.2 - - - +
1186E LEU* 1.3 75.5 - - - +
1188E GLU* 1.3 61.7 - - - +
1190E ALA* 3.3 8.9 + - - +
1191E LYS* 3.2 25.3 + - - +
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Residues in contact with GLU1188 (chain E).
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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1184E ASP 2.8 13.6 + - - +
1185E ARG* 3.3 17.3 - - + +
1186E LEU 3.2 0.2 - - - -
1187E ASN* 1.3 77.6 - - - +
1189E VAL* 1.3 60.3 + - + +
1191E LYS* 3.5 27.6 + - - +
1192E ASN* 2.9 50.9 + - - +
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Residues in contact with VAL1189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938E LEU* 3.9 20.0 - - + -
1185E ARG* 3.0 30.7 + - + +
1186E LEU 3.8 3.4 - - - +
1188E GLU* 1.3 76.8 - - + +
1190E ALA* 1.3 65.3 + - - +
1192E ASN* 3.8 8.2 - - + +
1193E LEU* 3.1 27.4 + - + +
933F LYS* 3.7 45.5 - - + +
936F ASP* 5.1 4.5 - - + -
937F SER* 4.2 9.9 - - - +
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Residues in contact with ALA1190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935E GLN* 2.7 61.5 + - - +
938E LEU* 4.1 15.0 - - + +
939E SER* 4.2 16.4 - - - +
1186E LEU 2.9 16.7 + - - +
1187E ASN* 3.3 8.7 + - - +
1189E VAL* 1.3 76.5 - - - +
1191E LYS* 1.3 51.4 + - - +
1193E LEU* 5.0 0.2 - - - -
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Residues in contact with LYS1191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1187E ASN 3.2 11.2 + - - +
1188E GLU* 3.6 22.7 + - - +
1190E ALA* 1.3 73.9 - - - +
1192E ASN* 1.3 80.4 + - - +
1193E LEU 3.1 3.6 + - - -
1194E ASN* 3.2 33.5 + - - +
1195E GLU* 3.9 2.1 - - - +
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Residues in contact with ASN1192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1188E GLU* 2.9 43.9 + - - +
1189E VAL* 3.4 9.3 + - - +
1191E LYS* 1.3 92.8 + - - +
1193E LEU* 1.3 51.5 + - - +
1194E ASN 3.1 1.8 - - - -
1195E GLU* 3.1 27.2 + - - +
933F LYS* 2.6 38.1 + - + +
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Residues in contact with LEU1193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931E ILE* 3.6 22.4 - - + +
934E ILE* 4.2 14.4 - - + -
935E GLN* 3.6 28.9 - - + +
938E LEU* 4.0 23.6 - - + -
1189E VAL* 3.1 25.2 + - + +
1191E LYS 3.1 1.2 + - - -
1192E ASN* 1.3 72.7 - - - +
1194E ASN* 1.3 64.0 + - - +
1195E GLU 3.2 1.1 - - - -
1196E SER* 3.2 18.1 + - - -
1197E LEU* 3.9 2.6 + - - +
930F ALA* 3.9 28.0 - - + +
933F LYS* 3.6 28.0 - - + +
934F ILE* 4.5 8.1 - - + -
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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