Contacts of the helix formed by residues 1097 - 1117 (chain A) in PDB entry 6AGF
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 TRP1097 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095A ASN* 3.1 26.4 + - - +
1096A ALA* 1.3 78.5 - - - +
1098A CYS* 1.3 59.4 + - - +
1099A TRP 3.1 1.3 - - - -
1100A LEU* 2.8 39.1 + - + +
1101A ASP* 3.2 16.8 + - - +
1140A LEU* 3.6 33.2 - - + -
1141A SER* 3.2 34.7 + - - +
1147A ARG* 3.9 34.2 - - + +
1150A VAL* 4.0 19.3 - - + -
1151A ASN* 4.6 14.1 + - - +
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Residues in contact with CYS1098 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1083A LYS* 4.6 10.5 - - - -
1087A TYR* 4.8 10.5 - - - -
1092A TYR* 3.3 68.6 + - + +
1093A PHE* 6.1 0.2 - - - -
1095A ASN* 2.7 33.9 - - + +
1097A TRP* 1.3 75.5 - - - +
1099A TRP* 1.3 64.2 + - - +
1101A ASP* 4.0 8.6 - - - +
1102A PHE* 3.3 12.6 + - - +
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Residues in contact with TRP1099 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092A TYR* 5.7 0.2 - - - -
1093A PHE* 2.5 67.8 + + + -
1094A THR* 5.0 0.2 - - - -
1095A ASN 4.3 0.4 - - - -
1096A ALA* 3.5 35.4 - - + +
1097A TRP 3.1 0.2 - - - -
1098A CYS* 1.3 78.0 - - - +
1100A LEU* 1.3 62.6 + - - +
1102A PHE* 3.1 30.9 + + - +
1103A LEU* 3.2 40.8 + - + +
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Residues in contact with LEU1100 (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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1096A ALA 4.0 7.5 + - - +
1097A TRP* 2.8 42.5 + - + +
1099A TRP* 1.3 75.4 - - - +
1101A ASP* 1.3 65.7 + - - +
1103A LEU* 3.8 7.7 + - + +
1104A ILE* 3.4 33.9 + - + +
1134A LEU* 6.3 0.4 - - + -
1137A LEU* 3.8 41.1 - - + +
1140A LEU* 5.4 3.6 - - + -
1141A SER* 4.4 3.4 - - - +
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Residues in contact with ASP1101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1079A GLU* 5.0 10.0 - - - +
1092A TYR* 5.0 4.9 - - - +
1097A TRP* 3.2 13.7 + - - +
1098A CYS* 4.3 9.9 - - - +
1099A TRP 3.2 0.2 - - - -
1100A LEU* 1.3 80.3 - - - +
1102A PHE* 1.3 64.7 + - - +
1103A LEU 3.3 0.2 - - - -
1104A ILE* 3.5 2.4 + - - +
1105A VAL* 3.3 30.5 + - + +
1138A ARG* 3.6 39.8 - - - +
1141A SER* 4.3 13.1 + - - -
1142A ARG* 4.4 17.0 + - - -
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Residues in contact with PHE1102 (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 MET* 3.6 26.2 - - + -
1084A TRP* 3.8 27.4 - + - -
1092A TYR* 3.9 12.6 - + + +
1093A PHE* 4.5 19.7 - + + -
1098A CYS 3.3 17.9 + - - +
1099A TRP* 3.1 21.9 + + - +
1101A ASP* 1.3 81.0 - - - +
1103A LEU* 1.3 70.4 + - + +
1105A VAL* 3.8 1.4 + - - +
1106A ASP* 2.8 61.0 + - - +
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Residues in contact with LEU1103 (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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1099A TRP* 3.2 49.6 + - + +
1100A LEU* 4.3 10.1 - - + +
1101A ASP 3.3 0.4 - - - -
1102A PHE* 1.3 84.8 - - + +
1104A ILE* 1.3 64.7 + - + +
1106A ASP* 3.4 6.6 + - - +
1107A VAL* 3.1 29.5 + - + +
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Residues in contact with ILE1104 (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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1100A LEU* 3.4 24.5 - - + +
1101A ASP 3.5 5.7 + - - +
1102A PHE 3.4 0.6 - - - -
1103A LEU* 1.3 76.7 - - + +
1105A VAL* 1.3 65.1 + - - +
1107A VAL* 3.4 9.4 + - + +
1108A SER* 3.3 19.9 + - - -
1131A LEU 6.1 1.1 - - - +
1134A LEU* 3.5 28.3 - - + +
1135A ARG* 4.2 22.4 - - + +
1137A LEU* 4.3 12.6 - - + -
1138A ARG* 3.1 46.6 + - + +
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Residues in contact with VAL1105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073A THR* 5.4 1.3 - - - +
1076A PHE* 3.4 41.3 - - + +
1077A ILE* 3.7 22.4 - - + -
1080A MET* 4.5 18.6 - - + -
1101A ASP* 3.3 20.2 + - + +
1102A PHE* 4.2 3.6 - - - +
1104A ILE* 1.3 76.6 - - - +
1106A ASP* 1.3 61.2 + - - +
1108A SER* 2.7 30.4 + - - +
1109A ILE* 3.2 12.0 + - + +
1138A ARG* 4.5 11.2 - - - +
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Residues in contact with ASP1106 (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 MET* 5.2 3.8 - - - +
1102A PHE* 2.8 62.4 + - - +
1103A LEU* 3.8 6.4 - - - +
1104A ILE 3.3 0.4 - - - -
1105A VAL* 1.3 80.1 - - - +
1107A VAL* 1.3 64.7 + - + +
1109A ILE* 3.4 9.6 + - - +
1110A ILE* 3.3 31.8 + - + +
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Residues in contact with VAL1107 (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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1103A LEU* 3.1 16.4 + - + +
1104A ILE* 3.7 10.3 - - + +
1105A VAL 3.2 0.2 - - - -
1106A ASP* 1.3 78.3 - - + +
1108A SER* 1.3 57.4 + - - +
1109A ILE 3.1 0.6 + - - -
1110A ILE* 3.3 11.2 + - + +
1111A SER* 3.1 28.1 + - - +
1128A LEU* 3.7 39.6 - - + +
1131A LEU* 4.4 23.6 - - + +
1132A ARG* 5.8 1.3 - - - -
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Residues in contact with SER1108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073A THR* 4.0 26.4 - - - +
1104A ILE 3.3 7.2 + - - -
1105A VAL* 2.7 30.1 + - - +
1107A VAL* 1.3 77.5 - - - +
1109A ILE* 1.3 63.4 + - - +
1111A SER* 3.5 13.0 + - - -
1112A LEU* 3.2 23.4 + - - +
1135A ARG* 6.5 1.3 - - - -
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Residues in contact with ILE1109 (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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1073A THR* 5.3 2.7 - - - +
1077A ILE* 3.6 31.9 - - + -
1105A VAL* 3.2 17.9 + - + +
1106A ASP* 3.9 12.3 - - - +
1107A VAL 3.1 0.6 - - - -
1108A SER* 1.3 87.2 - - - +
1110A ILE* 1.3 59.7 + - + +
1111A SER 3.2 1.3 - - - -
1112A LEU* 3.5 16.2 - - + +
1113A VAL* 2.7 50.9 + - + +
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Residues in contact with ILE1110 (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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1106A ASP* 3.3 20.4 - - + +
1107A VAL* 3.8 11.4 - - + +
1109A ILE* 1.3 78.9 - - + +
1111A SER* 1.3 59.2 + - - +
1113A VAL* 5.2 1.1 - - - -
1114A ALA* 3.3 27.6 + - + +
1119A TYR* 5.7 5.4 - - + +
1125A ILE* 4.3 20.4 - - + +
1128A LEU* 4.7 19.5 - - + -
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Residues in contact with SER1111 (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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1107A VAL* 3.1 18.6 + - - +
1108A SER* 3.5 12.6 + - - -
1110A ILE* 1.3 77.4 - - - +
1112A LEU* 1.3 61.3 + - - +
1115A ASN* 3.3 23.9 + - - +
1125A ILE* 5.2 14.0 - - - +
1128A LEU* 5.3 17.2 - - - +
1129A ARG* 5.9 10.5 + - - -
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Residues in contact with LEU1112 (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 ASP 5.2 0.7 - - - +
1070A LYS* 4.8 20.6 - - + -
1073A THR* 3.4 28.5 - - + +
1108A SER 3.2 20.4 - - - +
1109A ILE* 3.0 13.4 + - + +
1111A SER* 1.3 79.7 + - - +
1113A VAL* 1.3 70.7 + - + +
1114A ALA 3.4 0.4 - - - -
1115A ASN* 3.5 15.1 + - + +
1116A TRP* 3.7 43.9 + - + +
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Residues in contact with VAL1113 (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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1109A ILE* 2.7 40.5 + - + +
1110A ILE* 5.0 1.3 - - - +
1112A LEU* 1.3 80.6 - - + +
1114A ALA* 1.3 57.6 + - - +
1116A TRP* 3.0 41.3 + - + +
1117A LEU* 3.6 21.5 + - + +
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Residues in contact with ALA1114 (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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1110A ILE* 3.3 20.6 + - + +
1111A SER 4.6 0.2 - - - -
1113A VAL* 1.3 77.1 - - + +
1115A ASN* 1.3 63.7 + - - +
1116A TRP 3.2 0.2 - - - -
1117A LEU* 3.5 15.0 - - - +
1119A TYR* 3.5 29.2 - - + +
1120A SER* 3.4 25.7 + - - -
1125A ILE* 4.6 17.0 - - + -
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Residues in contact with ASN1115 (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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1070A LYS* 5.5 5.0 + - - -
1111A SER 3.3 21.9 + - - +
1112A LEU* 3.5 10.9 + - - +
1113A VAL 3.1 1.0 - - - -
1114A ALA* 1.3 78.3 - - - +
1116A TRP* 1.3 69.1 + - + +
1120A SER* 4.9 5.7 + - - -
1121A GLU* 3.4 24.6 + - - +
1125A ILE* 5.8 0.4 - - - +
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Residues in contact with TRP1116 (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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1070A LYS* 5.2 12.7 - - + +
1112A LEU* 3.7 38.1 + - + +
1113A VAL* 3.0 26.4 + - + +
1115A ASN* 1.3 85.1 - - + +
1117A LEU* 1.3 78.8 + - + +
1120A SER* 5.1 0.9 - - - -
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Residues in contact with LEU1117 (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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1113A VAL* 3.6 21.7 + - + +
1114A ALA* 3.5 16.7 - - - +
1115A ASN 3.4 2.2 - - - -
1116A TRP* 1.3 100.9 - - + +
1118A GLY* 1.3 66.9 + - - +
1119A TYR* 3.7 3.6 + - - -
1120A SER* 3.7 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
------------------------------------------------------------
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