Contacts of the helix formed by residues 1116 - 1138 (chain A) in PDB entry 1TXD
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 THR1116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095A LYS* 4.7 3.8 - - - +
1114A ALA* 3.4 5.9 - - - +
1115A GLN* 1.3 86.7 - - + +
1117A VAL* 1.3 66.4 + - - +
1118A SER* 3.9 9.0 + - - -
1119A GLU* 3.5 24.1 + - - +
1120A LYS* 3.4 20.0 + - - +
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Residues in contact with VAL1117 (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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1095A LYS* 3.7 36.3 - - + -
1116A THR* 1.3 72.6 - - - +
1118A SER* 1.3 64.2 + - - +
1119A GLU 3.3 0.7 + - - -
1120A LYS* 3.3 25.9 - - - +
1121A THR* 2.8 23.6 + - - +
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Residues in contact with SER1118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116A THR* 3.2 9.1 + - - -
1117A VAL* 1.3 80.8 - - - +
1119A GLU* 1.3 60.3 + - - +
1121A THR* 3.4 15.3 + - - -
1122A VAL* 3.5 15.5 + - - +
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Residues in contact with GLU1119 (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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1022A HIS* 4.1 12.8 - - + +
1023A GLU 4.5 0.5 - - - +
1024A GLY* 4.1 13.5 - - - -
1025A PRO* 4.3 11.9 - - - +
1114A ALA* 4.5 8.7 - - + -
1115A GLN* 5.1 10.4 + - - +
1116A THR* 3.5 18.9 + - - +
1117A VAL 3.3 0.6 - - - -
1118A SER* 1.3 75.2 - - - +
1120A LYS* 1.3 60.7 + - - +
1121A THR 3.1 2.0 - - - -
1122A VAL* 3.1 11.1 + - + +
1123A TRP* 2.9 51.4 + - + -
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Residues in contact with LYS1120 (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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1089A GLN* 2.5 41.0 + - - +
1095A LYS* 3.7 45.6 - - - +
1096A ALA 4.4 0.9 - - - +
1097A LEU* 3.9 24.8 - - + +
1112A LEU 6.2 0.2 - - - +
1114A ALA* 3.9 21.0 - - + +
1116A THR 3.4 6.8 + - - +
1117A VAL* 3.3 20.4 + - - +
1119A GLU* 1.3 77.8 - - - +
1121A THR* 1.3 71.3 + - - +
1123A TRP* 3.7 9.2 - - + +
1124A GLN* 3.0 34.6 + - - +
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Residues in contact with THR1121 (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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1117A VAL* 2.8 22.9 + - - +
1118A SER* 3.5 8.1 + - - -
1119A GLU 3.1 0.8 - - - -
1120A LYS* 1.3 89.2 + - - +
1122A VAL* 1.3 61.7 + - - +
1124A GLN* 4.0 8.7 - - - +
1125A ASP* 2.9 45.1 + - - +
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Residues in contact with VAL1122 (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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1022A HIS* 3.3 30.5 - - + +
1118A SER 3.5 11.8 + - - +
1119A GLU* 3.1 12.5 + - + +
1121A THR* 1.3 75.3 - - - +
1123A TRP* 1.3 59.8 + - - +
1125A ASP* 3.2 4.3 + - - -
1126A LEU* 2.8 51.4 + - + +
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Residues in contact with TRP1123 (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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1022A HIS* 3.6 20.3 - + - -
1023A GLU* 4.1 2.9 - - - -
1024A GLY* 3.4 27.1 - - - -
1026A LEU* 3.5 37.2 - - + +
1040A THR* 3.5 39.5 - - + -
1042A LEU* 3.8 25.6 - - + -
1047A LEU* 3.9 4.9 - - + -
1097A LEU* 4.2 10.8 - - + -
1114A ALA* 4.6 0.7 - - + -
1119A GLU* 2.9 54.9 + - + +
1120A LYS* 3.8 10.1 - - + +
1121A THR 3.4 0.2 - - - -
1122A VAL* 1.3 76.4 - - - +
1124A GLN* 1.3 58.4 + - - +
1126A LEU* 4.0 2.6 - - - -
1127A ILE* 2.9 56.5 + - + +
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Residues in contact with GLN1124 (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 VAL* 4.2 22.4 + - + +
1088A ARG* 4.4 5.3 - - - +
1089A GLN* 4.1 25.3 - - - +
1097A LEU* 3.9 26.7 - - + +
1120A LYS* 3.0 26.6 + - - +
1121A THR* 4.0 9.9 - - - +
1123A TRP* 1.3 75.9 - - - +
1125A ASP* 1.3 70.8 + - - +
1127A ILE* 4.1 1.5 - - - +
1128A CYS* 3.1 38.2 + - - -
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Residues in contact with ASP1125 (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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1121A THR* 2.9 32.0 + - - +
1122A VAL* 3.8 5.2 - - - +
1124A GLN* 1.3 85.5 - - - +
1126A LEU* 1.3 58.1 + - + +
1128A CYS* 3.8 4.3 + - - +
1129A ARG* 3.1 61.5 + - - +
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Residues in contact with LEU1126 (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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1021A ILE* 4.4 16.4 - - + +
1022A HIS* 3.2 41.1 - - + -
1042A LEU* 3.6 15.5 - - + -
1122A VAL* 2.8 28.7 + - + +
1123A TRP* 4.1 1.6 - - - +
1125A ASP* 1.3 76.4 - - + +
1127A ILE* 1.3 65.4 + - - +
1128A CYS 3.2 0.2 - - - -
1129A ARG* 3.1 35.4 + - + +
1130A MET* 2.9 29.7 + - + +
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Residues in contact with ILE1127 (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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1026A LEU* 6.2 1.1 - - + -
1042A LEU* 3.9 15.5 - - + -
1047A LEU* 3.9 30.1 - - + -
1082A LEU* 4.0 19.0 - - + +
1085A VAL* 4.2 8.5 - - + -
1087A VAL* 3.7 25.8 - - + -
1097A LEU* 4.9 7.0 - - + -
1099A VAL* 4.8 13.5 - - + -
1112A LEU* 6.1 0.7 - - + -
1123A TRP* 2.9 43.2 + - + +
1124A GLN* 4.1 2.5 - - - +
1126A LEU* 1.3 75.6 - - - +
1128A CYS* 1.3 53.2 + - - +
1130A MET* 3.7 1.7 - - - +
1131A ALA* 2.7 36.5 + - + +
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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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1087A VAL* 4.0 29.8 - - - -
1124A GLN* 3.1 37.3 + - - +
1125A ASP* 4.0 4.3 - - - +
1127A ILE* 1.3 74.5 - - - +
1129A ARG* 1.3 65.2 + - - +
1131A ALA* 4.0 6.9 - - - +
1132A ALA* 3.0 27.7 + - - +
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Residues in contact with ARG1129 (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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1125A ASP* 3.1 52.8 + - - +
1126A LEU* 3.1 33.4 + - - +
1128A CYS* 1.3 76.4 - - - +
1130A MET* 1.3 74.7 + - + +
1132A ALA* 4.0 2.5 - - - +
1133A SER* 3.2 23.2 + - - -
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Residues in contact with MET1130 (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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1021A ILE* 3.8 38.8 - - + -
1042A LEU* 4.2 19.3 - - + -
1043A LEU 4.3 2.9 - - - +
1044A GLU* 3.9 12.9 - - - +
1082A LEU* 3.8 21.3 - - + -
1126A LEU* 2.9 21.4 + - + +
1127A ILE 3.8 2.0 - - - +
1129A ARG* 1.3 89.3 - - + +
1131A ALA* 1.3 64.0 + - - +
1133A SER* 3.4 9.7 + - - -
1134A VAL* 3.3 29.3 + - - +
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Residues in contact with ALA1131 (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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1082A LEU* 3.6 31.7 - - + +
1085A VAL* 4.5 19.3 - - + +
1087A VAL* 6.3 0.2 - - + -
1127A ILE* 2.7 25.6 + - + +
1128A CYS* 4.0 6.7 - - - +
1130A MET* 1.3 73.1 - - - +
1132A ALA* 1.3 60.7 + - - +
1134A VAL* 3.6 2.0 + - - +
1135A LYS* 3.3 33.1 + - - +
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Residues in contact with ALA1132 (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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1128A CYS 3.0 18.9 + - - +
1129A ARG* 4.2 2.9 - - - +
1131A ALA* 1.3 74.0 - - - +
1133A SER* 1.3 59.7 + - - +
1135A LYS* 4.1 9.7 - - - +
1136A GLU* 3.2 30.1 + - - +
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Residues in contact with SER1133 (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 ARG 3.2 19.8 + - - -
1130A MET* 3.5 14.8 - - - -
1131A ALA 3.2 0.4 - - - -
1132A ALA* 1.3 76.9 - - - +
1134A VAL* 1.3 65.7 + - - +
1136A GLU* 3.4 9.4 + - - +
1137A GLN* 3.2 31.2 + - - +
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Residues in contact with VAL1134 (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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1044A GLU 4.0 16.4 - - - +
1045A ASP* 4.3 19.3 - - + +
1082A LEU* 4.9 4.3 - - + -
1083A SER* 4.0 31.0 - - - +
1130A MET 3.3 16.7 + - - +
1131A ALA* 4.1 4.0 - - - +
1133A SER* 1.3 75.6 - - - +
1135A LYS* 1.3 64.7 + - - +
1136A GLU 3.1 0.2 - - - -
1137A GLN* 3.3 21.1 + - - +
1138A SER* 3.6 9.9 + - - -
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Residues in contact with LYS1135 (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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1082A LEU 3.9 5.3 + - - -
1083A SER* 3.1 39.9 - - - +
1084A THR* 4.2 2.6 - - - +
1085A VAL 2.4 32.2 + - - +
1086A LEU* 4.4 11.7 - - - +
1131A ALA* 3.3 20.8 + - - +
1132A ALA* 4.2 7.6 - - - +
1134A VAL* 1.3 76.4 - - - +
1136A GLU* 1.3 59.5 + - - +
1138A SER* 3.8 17.2 - - - -
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Residues in contact with GLU1136 (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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1132A ALA 3.2 20.5 + - - +
1133A SER* 3.4 10.2 - - - +
1134A VAL 3.1 0.2 - - - -
1135A LYS* 1.3 75.0 - - - +
1137A GLN* 1.3 62.9 + - + +
1138A SER 3.1 12.3 + - - -
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Residues in contact with GLN1137 (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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1133A SER* 3.2 21.3 + - - +
1134A VAL* 3.3 14.6 + - + +
1136A GLU* 1.3 76.3 - - + +
1138A SER* 1.3 63.5 + - - +
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Residues in contact with SER1138 (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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1134A VAL 3.6 8.0 + - - -
1135A LYS* 3.8 16.8 - - - -
1136A GLU 3.1 8.0 - - - -
1137A GLN* 1.3 82.8 - - - +
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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