Contacts of the helix formed by residues 1123 - 1133 (chain A) in PDB entry 1RPM
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 ILE1123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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885A LEU* 4.9 4.5 - - + -
1107A VAL* 4.0 7.0 - - + -
1111A MET* 3.9 13.2 - - - -
1121A VAL* 3.7 19.4 + - + -
1122A ASP* 1.3 68.2 - - - +
1124A TYR* 1.3 65.6 + - - +
1126A CYS* 3.0 4.9 + - - +
1127A VAL* 3.0 34.1 + - + +
1144A TYR* 4.4 1.8 - - + -
1147A ILE* 3.6 19.7 - - + -
1148A HIS* 3.6 55.9 - - + +
1151A ILE* 3.8 30.3 - - + -
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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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903A GLU* 3.4 35.4 - - + +
906A SER* 2.7 42.0 + - - -
907A PHE* 3.3 30.1 - + - -
1122A ASP* 4.2 2.8 + - - +
1123A ILE* 1.3 77.3 - - - +
1125A ASN* 1.3 69.4 + - - +
1127A VAL 3.4 0.3 + - - -
1128A ARG* 2.9 69.9 + - + +
1144A TYR* 3.5 14.6 + - - +
1148A HIS* 5.4 0.4 + - - -
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Residues in contact with ASN1125 (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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879A ALA 5.6 1.2 - - - +
1122A ASP* 3.0 38.5 + - - +
1123A ILE 3.3 0.6 - - - -
1124A TYR* 1.3 85.3 - - - +
1126A CYS* 1.3 60.3 + - - +
1128A ARG* 2.6 39.4 + - - +
1129A GLU* 2.8 31.4 + - - +
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Residues in contact with CYS1126 (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* 3.8 26.9 - - + -
1110A ILE* 3.8 31.0 - - - -
1111A MET* 4.0 20.6 - - + -
1122A ASP 3.0 14.4 + - - +
1123A ILE* 3.0 12.7 + - - +
1125A ASN* 1.3 76.3 - - - +
1127A VAL* 1.3 57.2 + - - +
1129A GLU* 3.1 7.9 + - - +
1130A LEU* 2.8 33.0 + - - +
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Residues in contact with VAL1127 (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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907A PHE* 3.8 22.9 - - + -
1107A VAL* 4.2 11.0 - - + -
1123A ILE* 3.0 19.4 + - + +
1124A TYR 3.8 4.7 - - - +
1126A CYS* 1.3 75.2 - - - +
1128A ARG* 1.3 64.2 + - - +
1130A LEU* 3.1 8.2 + - - +
1131A ARG* 2.9 32.3 + - - +
1137A MET* 3.9 21.8 - - + +
1138A VAL* 3.9 22.4 - - + -
1144A TYR* 3.9 20.2 - - + -
1147A ILE* 4.9 0.9 - - + -
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Residues in contact with ARG1128 (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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907A PHE* 4.1 11.0 - - + -
1124A TYR* 2.9 57.7 + - + +
1125A ASN* 2.6 37.6 + - - +
1127A VAL* 1.3 78.9 - - - +
1129A GLU* 1.3 64.6 + - - +
1131A ARG* 3.4 8.2 + - - +
1132A SER* 3.3 17.8 + - - -
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Residues in contact with GLU1129 (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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959A ILE* 6.0 0.9 - - - +
960A ASP* 4.1 21.5 + - - +
1125A ASN 2.8 18.9 + - - +
1126A CYS* 3.1 6.9 + - - +
1128A ARG* 1.3 78.6 - - - +
1130A LEU* 1.3 68.1 + - + +
1132A SER* 2.7 51.6 + - - -
1133A ARG* 3.5 19.1 + - - +
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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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959A ILE* 3.2 37.1 - - + +
960A ASP 4.9 0.7 - - - +
1103A GLY* 4.1 13.9 - - - +
1106A ILE* 3.9 20.4 - - + -
1107A VAL* 3.8 25.4 - - + -
1110A ILE* 4.1 20.0 - - + -
1126A CYS* 2.8 25.4 + - - +
1127A VAL* 3.1 5.6 + - - +
1129A GLU* 1.3 73.7 - - + +
1131A ARG* 1.3 56.9 + - - +
1133A ARG* 2.9 25.8 + - - +
1134A ARG* 3.0 11.6 + - - +
1137A MET* 3.7 20.8 - - + +
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Residues in contact with ARG1131 (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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904A TYR* 2.8 38.8 + - - -
907A PHE* 3.8 25.7 - - - +
908A PHE* 2.8 37.4 + - + +
909A GLU* 3.7 7.9 + - - +
912A SER* 4.0 7.2 + - - -
935A TYR* 3.6 12.1 + - - -
1127A VAL* 2.9 23.8 + - - +
1128A ARG* 3.6 7.9 - - - +
1129A GLU 3.1 0.2 - - - -
1130A LEU* 1.3 77.3 - - - +
1132A SER* 1.3 58.9 + - - +
1133A ARG 3.1 0.2 - - - -
1134A ARG 3.2 16.9 - - - +
1135A VAL* 4.8 0.5 - - - -
1136A ASN* 3.5 25.2 + - - +
1137A MET* 3.1 28.5 + - + +
1138A VAL* 3.0 12.7 + - - +
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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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912A SER* 4.9 4.7 - - - -
913A ALA* 5.2 0.7 - - - +
935A TYR* 3.6 4.5 - - - -
937A HIS* 2.8 33.2 + - - -
1128A ARG 3.3 9.6 + - - -
1129A GLU* 2.7 34.0 + - - -
1131A ARG* 1.3 76.6 - - - +
1133A ARG* 1.3 64.5 + - - +
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Residues in contact with ARG1133 (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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935A TYR* 3.3 8.6 - - - -
937A HIS* 5.0 5.2 + - - -
938A SER* 2.7 35.7 + - - -
957A ASN* 3.5 8.5 + - + -
958A TYR* 3.2 32.7 + - - +
959A ILE* 3.8 21.5 - - + +
960A ASP* 3.3 31.1 + - - -
966A ASN* 3.0 24.9 + - - -
1129A GLU* 3.8 26.2 + - - +
1130A LEU* 2.9 9.4 + - - +
1132A SER* 1.3 84.4 + - - +
1134A ARG* 1.3 60.6 + - - +
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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