Contacts of the helix formed by residues 1120 - 1136 (chain A) in PDB entry 5ID6
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 ASP1120 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021A ILE* 5.9 1.6 - - - -
1102A TYR* 4.0 19.0 - - - -
1118A GLN* 3.7 6.7 + - - +
1119A SER* 1.3 87.4 + - - +
1121A LYS* 1.3 68.2 + - - +
1122A ALA* 3.2 22.9 + - - +
1123A PHE* 3.2 14.6 + - - +
1124A TYR* 3.4 15.9 - - - -
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Residues in contact with LYS1121 (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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1018A TYR* 3.8 38.0 - - + +
1021A ILE* 5.4 6.4 - - + +
1120A ASP* 1.3 71.8 - - - +
1122A ALA* 1.3 53.1 + - - +
1124A TYR* 2.7 13.5 + - - -
1125A SER* 2.5 60.0 + - - -
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Residues in contact with ALA1122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1102A TYR* 3.1 20.4 + - - +
1120A ASP* 3.2 14.3 - - + +
1121A LYS* 1.3 81.2 - - - +
1123A PHE* 1.3 62.6 + - - +
1125A SER* 4.3 3.8 - - - -
1126A SER* 3.1 26.3 + - - -
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Residues in contact with PHE1123 (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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1028A ILE* 4.5 3.1 - - + -
1098A LEU* 4.3 6.8 - - + +
1099A PHE* 4.5 12.1 - + - -
1102A TYR* 3.5 40.7 + + + -
1104A ILE* 3.5 21.5 - - + -
1115A LEU* 3.6 33.9 - - + -
1118A GLN* 3.5 22.9 - - + +
1120A ASP* 3.2 11.7 + - - +
1121A LYS 3.2 0.6 - - - -
1122A ALA* 1.3 78.3 - - - +
1124A TYR* 1.3 92.8 + + - +
1126A SER* 3.5 2.4 + - - -
1127A PHE* 2.8 47.2 + + + +
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Residues in contact with TYR1124 (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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1018A TYR* 4.2 9.9 - - + -
1021A ILE* 3.3 26.9 - - + -
1024A SER* 3.9 30.1 - - - +
1025A LYS* 3.8 9.8 - - + -
1028A ILE* 3.8 17.3 - - + -
1115A LEU 2.9 15.3 + - - -
1116A CYS* 2.8 28.6 + - - -
1118A GLN* 3.0 33.8 + - + -
1120A ASP 3.4 20.4 - - - -
1121A LYS 2.7 10.9 + - - +
1123A PHE* 1.3 94.6 - + - +
1125A SER* 1.3 65.0 + - - +
1127A PHE* 3.2 3.7 + + + +
1128A MSE 3.0 30.5 + - - +
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Residues in contact with SER1125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018A TYR* 3.7 25.8 - - - +
1121A LYS* 2.5 49.8 + - - -
1122A ALA* 4.3 4.7 - - - -
1124A TYR* 1.3 72.8 - - - +
1126A SER* 1.3 60.8 + - - +
1128A MSE 4.1 2.3 - - - +
1129A ALA* 3.4 22.5 + - - +
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Residues in contact with SER1126 (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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1098A LEU* 3.1 34.9 - - - +
1102A TYR* 4.9 0.3 - - - -
1122A ALA 3.1 19.5 + - - -
1123A PHE 3.5 0.9 + - - -
1124A TYR 3.1 0.4 - - - -
1125A SER* 1.3 80.3 - - - +
1127A PHE* 1.3 59.8 + - - +
1128A MSE 3.3 0.7 - - - -
1129A ALA* 4.0 5.6 - - - +
1130A LEU* 3.1 29.1 + - - +
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Residues in contact with PHE1127 (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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1027A PHE* 5.0 3.1 - + - -
1028A ILE* 3.7 32.8 - - + -
1031A PHE* 6.0 0.9 - + - -
1034A ILE* 4.4 5.8 - - + -
1045A PHE* 4.3 15.5 - + - -
1095A TYR* 4.5 13.2 - + - -
1098A LEU* 3.8 9.8 - - + +
1099A PHE* 4.4 19.7 - + - -
1115A LEU* 4.0 22.0 - - + -
1123A PHE* 2.8 40.0 + + + +
1124A TYR* 3.2 8.0 + + - +
1126A SER* 1.3 75.6 + - - +
1128A MSE 1.3 72.4 + - + +
1130A LEU* 3.5 5.0 - - - +
1131A MSE 3.0 48.0 + - + +
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Residues in contact with MSE1128 (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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1015A LYS 4.1 1.8 - - - +
1016A THR* 3.4 48.7 - - - +
1017A LYS 4.1 8.1 - - - +
1018A TYR* 4.5 14.1 - - - +
1024A SER* 4.0 26.2 - - - +
1027A PHE* 3.7 49.4 - - + -
1124A TYR* 3.0 20.3 + - - +
1125A SER 4.1 3.4 - - - +
1127A PHE* 1.3 88.1 - - + +
1129A ALA* 1.3 61.0 + - - +
1131A MSE 3.0 6.5 + - - +
1132A SER* 2.8 29.3 + - - -
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Residues in contact with ALA1129 (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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1016A THR 5.1 0.7 - - - -
1073A ARG* 6.0 6.7 - - - +
1125A SER 3.4 15.8 + - - +
1126A SER* 4.0 7.2 - - - +
1127A PHE 3.4 0.2 - - - -
1128A MSE 1.3 77.7 - - - +
1130A LEU* 1.3 60.3 + - - +
1132A SER* 2.4 26.9 + - - -
1133A LEU* 3.2 18.4 - - + +
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Residues in contact with LEU1130 (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 VAL* 6.2 1.1 - - + -
1091A LEU* 4.3 11.6 - - + +
1094A ALA* 3.5 44.9 - - + +
1095A TYR* 3.4 46.9 - - + +
1098A LEU* 3.9 22.7 - - + -
1126A SER 3.1 15.3 + - - +
1127A PHE* 3.5 6.3 - - - +
1129A ALA* 1.3 76.9 - - - +
1131A MSE 1.3 61.9 + - - +
1133A LEU* 3.2 21.7 + - + +
1134A MSE 3.3 10.4 + - - +
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Residues in contact with MSE1131 (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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1014A LEU* 4.8 0.4 - - + -
1016A THR* 4.5 4.9 - - + -
1027A PHE* 4.1 28.0 - - + -
1031A PHE* 4.4 12.6 - - + -
1045A PHE* 4.2 21.5 - - - -
1065A LEU* 4.9 0.4 - - + -
1095A TYR* 4.0 10.5 - - + +
1127A PHE* 3.0 40.0 + - + +
1128A MSE 3.0 12.0 + - - +
1130A LEU* 1.3 73.4 - - - +
1132A SER* 1.3 65.7 + - - +
1134A MSE 3.1 36.9 + - + +
1135A LEU* 3.3 39.5 + - + +
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Residues in contact with SER1132 (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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1012A ASN* 5.5 0.9 + - - +
1016A THR* 3.0 33.2 - - - -
1128A MSE 2.8 8.8 + - - -
1129A ALA* 2.4 30.6 + - - -
1131A MSE 1.3 75.8 - - - +
1133A LEU* 1.3 67.4 + - - +
1135A LEU* 3.0 6.4 + - - +
1136A GLN* 2.9 27.8 + - - +
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Residues in contact with LEU1133 (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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1071A ARG* 3.3 30.7 + - + +
1073A ARG* 3.4 45.5 - - + +
1089A VAL* 4.7 17.5 - - + -
1091A LEU* 4.5 9.9 - - + -
1129A ALA* 3.2 19.3 - - + +
1130A LEU* 3.2 14.1 + - + +
1131A MSE 3.2 0.4 - - - -
1132A SER* 1.3 90.6 + - - +
1134A MSE 1.3 60.8 + - - +
1136A GLN* 3.2 30.3 + - + +
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Residues in contact with MSE1134 (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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1045A PHE* 3.3 43.5 - - + -
1065A LEU* 3.7 28.5 - - + -
1066A TYR 3.0 30.1 - - - +
1067A SER* 4.6 3.1 - - - -
1071A ARG* 3.2 16.9 + - - +
1091A LEU* 3.9 26.1 - - + +
1095A TYR* 3.9 7.2 - - - +
1130A LEU 3.3 7.5 + - - +
1131A MSE 3.1 29.5 + - + +
1133A LEU* 1.3 80.5 - - - +
1135A LEU* 1.3 61.7 + - + +
1136A GLN 4.8 0.2 - - - -
1153A PRO* 3.5 16.4 - - + +
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Residues in contact with LEU1135 (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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1010A PHE* 3.8 32.8 - - + -
1012A ASN* 3.5 47.2 + - - +
1014A LEU* 3.9 13.0 - - + -
1016A THR* 3.9 15.9 - - + -
1065A LEU* 4.0 19.3 - - + -
1131A MSE 3.3 35.4 + - + +
1132A SER* 3.0 8.5 + - - +
1134A MSE 1.3 78.1 - - + +
1136A GLN* 1.3 59.8 + - - +
1137A MSE 3.0 18.2 + - - +
1153A PRO* 4.4 4.5 - - + -
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Residues in contact with GLN1136 (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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1071A ARG* 3.5 21.2 - - - +
1072A ILE 2.7 30.3 + - - +
1073A ARG* 4.8 2.5 - - - +
1074A ILE* 5.6 3.1 + - - +
1132A SER 2.9 12.0 + - - +
1133A LEU* 3.2 24.2 + - + +
1135A LEU* 1.3 73.2 - - - +
1137A MSE 1.3 60.6 + - - +
1138A ARG 3.3 17.2 + - - +
1139A ASN* 2.9 26.3 + - - +
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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
------------------------------------------------------------
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