Contacts of the helix formed by residues 1117 - 1133 (chain A) in PDB entry 3DKF
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 ASP1117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1053A ILE* 4.0 1.8 - - - -
1115A ILE* 3.7 1.6 - - - +
1116A THR* 1.3 84.6 - - + +
1118A ILE* 1.3 63.5 + - - +
1119A GLY* 3.1 25.3 + - - -
1120A GLU* 3.0 19.4 + - + +
1121A VAL* 2.9 25.6 + - - +
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Residues in contact with ILE1118 (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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1053A ILE* 3.9 13.0 - - + +
1054A ASP 5.2 2.7 - - - +
1055A LEU* 5.5 2.7 - - + +
1057A ALA* 3.9 19.1 - - + +
1058A LEU* 3.9 35.9 - - + +
1059A ASN 4.8 2.7 - - - +
1116A THR 4.0 0.2 + - - -
1117A ASP* 1.3 72.5 - - - +
1119A GLY* 1.3 58.8 + - - +
1121A VAL* 3.4 13.4 + - + +
1122A SER* 2.8 47.4 + - - +
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Residues in contact with GLY1119 (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 ASP* 3.1 11.7 + - - -
1118A ILE* 1.3 83.2 - - - +
1120A GLU* 1.3 55.8 + - - +
1122A SER* 3.1 10.9 + - - -
1123A GLN* 3.1 25.3 + - - +
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Residues in contact with GLU1120 (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 ILE* 3.8 17.7 - - + +
1117A ASP* 3.0 24.6 + - + +
1119A GLY* 1.3 71.9 - - - +
1121A VAL* 1.3 59.5 + - - +
1123A GLN* 3.5 8.3 + - - +
1124A PHE* 3.1 27.2 + - - +
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Residues in contact with VAL1121 (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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1053A ILE* 3.8 21.5 - - + -
1055A LEU* 4.5 12.8 - - + -
1058A LEU* 5.3 6.7 - - + -
1115A ILE* 3.6 22.9 - - + +
1117A ASP 2.9 16.8 + - - +
1118A ILE* 3.5 15.5 - - + +
1120A GLU* 1.3 76.9 - - - +
1122A SER* 1.3 56.1 + - - +
1124A PHE* 3.2 9.7 + - + +
1125A LEU* 3.0 46.2 + - + +
1147A LEU* 4.0 25.8 - - + -
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Residues in contact with SER1122 (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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1058A LEU* 5.5 2.9 - - - +
1059A ASN* 5.5 4.9 + - - +
1062A LEU* 5.8 6.8 - - - +
1118A ILE* 2.8 31.3 + - - +
1119A GLY* 3.1 11.6 + - - -
1121A VAL* 1.3 77.1 - - - +
1123A GLN* 1.3 52.0 + - - +
1125A LEU* 3.4 13.6 + - - +
1126A THR* 2.8 37.2 + - - -
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Residues in contact with GLN1123 (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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1119A GLY 3.1 12.3 + - - +
1120A GLU* 3.8 11.2 - - - +
1121A VAL 3.3 0.4 - - - -
1122A SER* 1.3 73.4 - - - +
1124A PHE* 1.3 59.7 + - - +
1126A THR* 3.8 7.0 - - - -
1127A GLU* 3.0 29.6 + - - +
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Residues in contact with PHE1124 (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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1112A LEU* 3.7 26.7 - - + -
1115A ILE* 4.0 22.9 - - + -
1120A GLU 3.1 14.6 + - - +
1121A VAL* 3.4 10.3 - - - +
1123A GLN* 1.3 77.2 - - - +
1125A LEU* 1.3 70.3 + - + +
1127A GLU* 3.7 6.4 + - - +
1128A GLY* 3.1 21.8 + - - -
1145A ILE* 3.8 37.5 - - + +
1146A CYS 4.5 8.1 - - - -
1147A LEU* 4.6 12.6 - - + -
1153A PRO* 3.7 20.6 - - + -
1154A LEU 4.5 1.1 - - - -
1155A VAL* 4.1 8.1 - - + -
1225A LEU* 3.7 26.2 - - + +
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Residues in contact with LEU1125 (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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1058A LEU* 5.2 11.4 - - + -
1062A LEU* 4.9 18.4 - - + +
1063A VAL* 5.3 2.2 - - + +
1066A VAL* 3.7 31.7 - - + +
1070A VAL* 5.7 1.6 - - + -
1121A VAL* 3.0 31.6 + - + +
1122A SER* 3.7 12.6 - - - +
1123A GLN 3.3 0.2 - - - -
1124A PHE* 1.3 84.7 - - + +
1126A THR* 1.3 63.5 + - - +
1128A GLY* 3.4 1.0 + - - -
1129A ILE* 3.2 29.3 + - + +
1145A ILE* 3.8 23.1 - - + -
1147A LEU* 4.9 12.8 - - + -
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Residues in contact with THR1126 (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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1122A SER* 2.8 22.6 + - - -
1123A GLN* 3.8 8.2 - - - -
1124A PHE 3.4 0.2 - - - -
1125A LEU* 1.3 73.9 - - - +
1127A GLU* 1.3 64.2 + - - +
1129A ILE* 3.3 12.2 + - + +
1130A ILE* 3.2 39.4 + - + +
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Residues in contact with GLU1127 (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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1123A GLN 3.0 18.6 + - - +
1124A PHE* 3.8 4.9 - - - +
1126A THR* 1.3 76.4 - - - +
1128A GLY* 1.3 57.8 + - - +
1130A ILE* 3.4 8.9 + - - +
1131A MET* 2.9 34.0 + - - +
1224A GLY* 5.9 3.6 - - - -
1225A LEU* 3.9 22.0 - - + +
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Residues in contact with GLY1128 (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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1069A VAL* 4.3 7.2 - - - -
1124A PHE 3.1 13.3 + - - -
1125A LEU 3.4 5.3 + - - -
1126A THR 3.3 0.4 - - - -
1127A GLU* 1.3 76.9 - - - +
1129A ILE* 1.3 55.9 + - - +
1132A LYS* 2.9 31.4 + - - +
1142A LEU* 3.5 10.9 - - - +
1145A ILE* 4.6 7.9 - - - -
1225A LEU* 3.7 20.1 - - - +
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Residues in contact with ILE1129 (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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1062A LEU* 4.9 2.7 - - - +
1065A ALA* 3.8 36.8 - - + +
1066A VAL* 3.9 18.2 - - + -
1068A HIS* 4.2 15.3 - - + +
1069A VAL* 4.2 10.5 - - + -
1125A LEU* 3.2 20.2 + - + +
1126A THR* 3.3 10.5 + - + +
1128A GLY* 1.3 74.8 - - - +
1130A ILE* 1.3 64.5 + - + +
1132A LYS* 3.5 7.8 - - - +
1133A ASP* 3.1 28.2 - - - +
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Residues in contact with ILE1130 (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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1126A THR* 3.2 34.6 + - + +
1127A GLU* 3.9 6.7 - - - +
1129A ILE* 1.3 74.8 - - + +
1131A MET* 1.3 67.2 + - - +
1133A ASP* 3.1 15.7 + - - +
1134A PHE* 3.3 34.4 + - + -
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Residues in contact with MET1131 (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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1127A GLU 2.9 19.4 + - - +
1128A GLY 3.9 2.7 - - - +
1130A ILE* 1.3 76.0 - - - +
1132A LYS* 1.3 55.7 + - - +
1134A PHE* 2.8 38.8 + - - +
1140A LEU* 4.8 7.4 - - + +
1142A LEU* 4.0 28.7 + - + +
1157A LEU* 4.1 16.8 - - + -
1223A PHE* 3.5 44.6 - - + +
1224A GLY* 4.7 4.0 - - - -
1225A LEU* 3.4 33.2 - - - +
1226A ALA* 4.0 17.3 - - + +
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Residues in contact with LYS1132 (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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1068A HIS* 4.2 27.3 + - + +
1069A VAL* 3.9 31.2 - - + -
1128A GLY 2.9 20.9 + - - +
1129A ILE 3.5 8.1 - - - +
1131A MET* 1.3 75.2 - - - +
1133A ASP* 1.3 60.6 + - - +
1134A PHE 3.3 1.3 + - - -
1135A SER* 4.1 13.0 + - - -
1141A SER* 6.1 0.3 - - - -
1142A LEU* 3.3 29.1 + - + +
1143A LEU* 3.1 26.5 + - - +
1144A GLY* 4.9 0.4 - - - -
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Residues in contact with ASP1133 (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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1068A HIS* 4.6 6.6 + - - -
1129A ILE* 3.1 23.5 - - - +
1130A ILE* 3.1 11.2 + - - +
1131A MET 3.0 1.2 - - - -
1132A LYS* 1.3 79.8 - - - +
1134A PHE* 1.3 53.6 + - + +
1135A SER* 3.2 12.2 + - - -
1194A PHE* 4.1 1.4 - - - -
1198A LYS* 2.6 30.9 + - - +
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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