Contacts of the helix formed by residues 1123 - 1136 (chain A) in PDB entry 5LUQ
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 THR1123 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A ALA* 5.0 15.1 - - - +
720A GLN* 2.6 47.6 + - + +
721A TYR* 3.7 39.4 + - + -
1077A GLY* 5.9 0.7 - - - -
1080A LEU* 5.0 0.5 - - - +
1121A LEU* 3.8 1.8 - - + -
1122A GLY* 1.3 83.2 + - - +
1124A ILE* 1.3 73.5 + - - +
1125A GLN 4.4 0.2 - - - +
1126A GLN* 4.3 11.6 + - - +
1127A CYS* 3.6 26.7 + - - -
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Residues in contact with ILE1124 (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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720A GLN* 5.4 1.1 - - - +
1018A VAL* 6.1 1.6 - - + -
1072A ALA 5.8 0.2 - - - +
1073A PHE* 4.2 15.5 - - - +
1076A LEU* 3.5 38.6 - - + -
1077A GLY* 4.5 9.6 - - - +
1080A LEU* 3.8 7.4 - - + +
1115A HIS* 3.4 26.9 - - + -
1118A GLU 5.6 4.0 - - - +
1120A SER* 5.2 10.3 - - - +
1121A LEU 4.9 3.6 - - - +
1122A GLY 2.9 3.7 + - - +
1123A THR* 1.3 85.8 + - - +
1125A GLN* 1.3 57.0 + - - +
1126A GLN 2.7 15.6 + - - -
1127A CYS 3.3 1.7 + - - -
1128A CYS* 3.1 33.4 + - - -
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Residues in contact with GLN1125 (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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1115A HIS* 3.5 34.7 + - + +
1119A LYS* 3.3 38.6 - - + +
1121A LEU* 4.2 9.1 + - - +
1122A GLY* 3.9 22.6 + - - -
1123A THR 3.6 0.2 - - - -
1124A ILE* 1.3 78.6 - - - +
1126A GLN* 1.3 60.0 + - + +
1128A CYS* 4.2 2.6 - - - +
1129A ASP* 3.7 18.0 + - - +
1164A CYS* 4.8 13.4 - - - -
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Residues in contact with GLN1126 (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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596A GLU* 3.4 27.5 - - - +
721A TYR* 3.8 19.7 + - - -
1122A GLY* 5.5 3.1 - - - -
1123A THR* 4.1 13.7 + - - +
1124A ILE 2.7 3.0 + - - -
1125A GLN* 1.3 78.1 - - + +
1127A CYS* 1.3 69.5 + - - +
1128A CYS 3.0 1.1 - - - -
1129A ASP* 3.0 9.7 + - - +
1130A ALA* 2.9 20.4 + - - +
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Residues in contact with CYS1127 (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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593A ASN 5.1 5.2 - - - -
596A GLU* 4.9 13.9 - - - -
597A ALA* 4.0 26.9 - - - -
1080A LEU* 3.3 35.0 - - + -
1081A ALA 5.2 0.2 - - - +
1084A ASN* 3.9 3.1 + - - +
1123A THR 3.6 15.7 + - - +
1124A ILE 3.3 1.8 + - - -
1126A GLN* 1.3 80.3 - - - +
1128A CYS* 1.3 57.2 + - - +
1130A ALA* 3.0 12.7 + - - +
1131A ILE* 2.9 30.5 + - - +
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Residues in contact with CYS1128 (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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1080A LEU* 3.3 17.9 - - - -
1111A LEU* 3.4 26.7 - - + -
1112A ALA 5.0 0.7 - - - +
1115A HIS* 3.1 41.5 - - + -
1124A ILE* 3.1 26.1 + - - +
1125A GLN 4.2 0.7 - - - +
1126A GLN 3.0 0.6 - - - -
1127A CYS* 1.3 73.9 - - - +
1129A ASP* 1.3 58.2 + - - +
1131A ILE* 2.7 44.9 + - + +
1132A ASP* 3.0 5.8 + - - +
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Residues in contact with ASP1129 (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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1115A HIS* 5.1 0.6 - - - -
1125A GLN 3.7 11.4 + - - +
1126A GLN* 3.0 10.1 + - - +
1128A CYS* 1.3 78.7 - - - +
1130A ALA* 1.3 57.2 + - - +
1132A ASP* 3.0 13.1 + - - +
1133A HIS* 2.9 25.2 + - - +
1136A ARG* 4.5 12.0 + - - -
1167A ASP* 6.1 0.5 - - - +
1168A LEU* 3.4 31.9 - - + +
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Residues in contact with ALA1130 (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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593A ASN* 4.8 10.8 - - - +
1084A ASN* 3.6 14.1 - - - +
1126A GLN 2.9 11.9 + - - +
1127A CYS* 3.1 17.7 - - - +
1128A CYS 3.0 0.2 - - - -
1129A ASP* 1.3 76.7 - - - +
1131A ILE* 1.3 55.6 + - - +
1133A HIS* 3.1 14.9 + - + +
1134A LEU* 3.0 30.7 + - + +
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Residues in contact with ILE1131 (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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1080A LEU* 3.4 19.7 - - + +
1083A ASN* 4.3 9.0 + - + +
1084A ASN* 3.3 16.2 - - - +
1107A TYR* 4.0 28.7 - - + -
1108A MSE 4.3 3.1 - - - +
1111A LEU* 3.7 32.3 - - + -
1127A CYS 2.9 16.2 - - - +
1128A CYS* 2.7 22.2 + - - +
1130A ALA* 1.3 69.1 - - - +
1132A ASP* 1.3 71.5 + - - +
1134A LEU* 2.7 32.4 + - + +
1135A CYS* 2.9 16.2 + - - -
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Residues in contact with ASP1132 (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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1108A MSE 3.2 33.3 - - + +
1112A ALA* 5.2 0.5 - - - +
1128A CYS 3.6 9.8 - - - +
1129A ASP* 3.0 15.2 + - - +
1131A ILE* 1.3 87.8 - - - +
1133A HIS* 1.3 53.4 + - - +
1134A LEU 2.8 4.3 - - - -
1135A CYS* 2.5 40.8 + - + +
1136A ARG* 3.0 12.8 + - - +
1168A LEU* 3.7 33.8 - - + +
1171A TRP* 5.2 5.0 - - + -
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Residues in contact with HIS1133 (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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1087A ARG* 4.6 14.1 + - - -
1129A ASP 2.9 11.3 + - - +
1130A ALA* 3.1 18.8 + - + +
1132A ASP* 1.3 72.9 - - - +
1134A LEU* 1.3 64.2 + - + +
1136A ARG* 3.3 53.0 + - + +
1137A ILE* 5.3 1.7 - - - +
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Residues in contact with LEU1134 (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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1083A ASN* 3.5 21.8 - - + +
1084A ASN* 3.2 52.9 - - + +
1087A ARG* 3.2 40.8 - - + +
1104A LEU* 4.3 8.3 - - + +
1130A ALA* 3.0 21.1 - - + +
1131A ILE* 2.7 18.2 + - - +
1133A HIS* 1.3 87.6 - - + +
1135A CYS* 1.3 57.6 + - - +
1136A ARG 3.1 5.6 - - - -
1137A ILE* 3.2 27.2 + - + +
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Residues in contact with CYS1135 (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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1104A LEU* 3.6 43.3 - - + -
1105A VAL* 6.4 0.2 - - - -
1108A MSE 4.6 11.0 - - + -
1131A ILE* 2.9 21.8 + - - -
1132A ASP* 2.5 34.8 + - + +
1134A LEU* 1.3 69.3 - - - +
1136A ARG* 1.3 61.9 + - - -
1137A ILE 3.1 2.1 + - - -
1138A ILE* 3.6 24.4 + - + +
1139A GLU* 4.2 6.6 - - - +
1171A TRP* 5.2 4.5 - - + -
1172A LEU* 5.5 9.1 - - + +
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Residues in contact with ARG1136 (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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1129A ASP* 4.5 13.7 + - - -
1132A ASP* 3.7 7.8 + - - +
1133A HIS* 3.3 54.1 + - + +
1134A LEU 3.1 1.2 - - - -
1135A CYS* 1.3 78.7 - - - +
1137A ILE* 1.3 63.7 + - + +
1138A ILE 3.3 0.2 - - - -
1139A GLU* 3.2 26.7 + - - +
1140A LYS* 5.3 1.9 - - - -
1168A LEU* 6.2 0.4 - - - +
1171A TRP* 3.1 54.4 - - + +
1175A HIS* 4.7 4.9 + - + +
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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