Contacts of the strand formed by residues 1051 - 1058 (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 ARG1051 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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986A VAL 4.7 0.4 + - - -
987A TRP* 3.0 79.9 + - + +
990A ASN* 3.1 35.1 + - - +
991A THR 5.3 2.2 + - - -
1040A PHE 3.4 2.1 - - - +
1041A ALA* 3.6 1.1 - - - -
1042A VAL* 2.8 37.5 + - - +
1047A VAL* 5.8 0.6 - - - +
1049A GLU* 2.7 36.1 + - - +
1050A ILE* 1.3 75.2 - - - +
1052A GLU* 1.3 62.3 + - - +
1053A ILE* 3.5 16.2 + - + +
1027B ILE* 4.4 2.7 - - - -
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Residues in contact with GLU1052 (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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992A ALA* 4.0 13.3 - - - +
1027A ILE* 5.7 0.9 - - + -
1039A THR* 3.6 30.3 - - + +
1040A PHE 3.2 6.7 - - - +
1051A ARG* 1.3 72.9 - - - +
1053A ILE* 1.3 62.2 + - - +
1054A ARG* 2.9 33.8 + - - +
1027B ILE* 3.0 51.0 + - + +
1028B GLU* 3.1 15.7 - - - +
1039B THR* 3.4 14.6 - - - +
1052B GLU* 4.1 1.2 - - - +
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Residues in contact with ILE1053 (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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983A TRP* 4.6 3.6 - - + -
986A VAL* 3.6 25.6 - - + +
987A TRP* 5.2 3.1 - - + -
991A THR 3.6 17.7 - - - +
992A ALA* 3.3 16.2 - - - +
994A ILE* 4.0 31.0 - - + -
1040A PHE* 2.8 39.9 + - + +
1042A VAL* 3.7 35.9 - - + -
1051A ARG* 3.5 17.6 + - + +
1052A GLU* 1.3 77.1 - - - +
1054A ARG* 1.3 63.4 + - - +
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Residues in contact with ARG1054 (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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992A ALA 2.9 9.3 + - - +
993A SER* 3.3 6.0 + - - -
994A ILE* 2.8 31.2 + - - +
1037A ILE* 3.7 21.8 - - + -
1038A ARG 3.3 3.4 - - - +
1039A THR* 3.4 27.9 + - + +
1040A PHE* 5.2 0.2 - - - -
1052A GLU* 2.9 26.4 + - - +
1053A ILE* 1.3 77.9 - - - +
1055A GLN* 1.3 54.4 + - - +
1056A PHE* 3.6 29.1 - - + -
1083A LYS* 2.8 50.5 + - - +
1085A PRO* 4.7 6.7 - - - +
1028B GLU* 3.2 26.7 + - - -
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Residues in contact with GLN1055 (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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994A ILE* 3.1 22.7 - - + +
996A MET* 3.7 8.0 - - + -
1011A TYR* 2.7 38.9 + - + +
1012A TRP* 3.3 24.9 - - - +
1036A VAL 3.7 0.2 - - - +
1037A ILE* 3.5 5.5 - - - +
1038A ARG* 2.8 74.4 + - - +
1040A PHE* 4.1 12.7 - - + -
1053A ILE 4.1 0.2 + - - -
1054A ARG* 1.3 73.1 - - - +
1056A PHE* 1.3 65.5 + - - +
1057A HIS* 3.6 8.7 + - - +
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Residues in contact with PHE1056 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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993A SER* 3.6 30.1 - - - -
994A ILE 2.7 14.8 + - - +
995A ILE* 4.5 2.7 - - + -
996A MET 2.9 24.8 + - - -
1036A VAL 3.9 4.0 - - - -
1037A ILE* 4.0 31.9 - - + -
1054A ARG* 3.6 42.4 - - + -
1055A GLN* 1.3 70.4 - - - +
1057A HIS* 1.3 58.8 + - - +
1076A PHE* 3.2 30.1 - + + -
1079A GLN* 4.0 12.3 - - + -
1080A VAL* 3.6 36.3 - - + -
1083A LYS* 3.8 13.5 - - + -
1084A SER* 4.6 1.6 - - - -
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Residues in contact with HIS1057 (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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996A MET* 3.4 30.5 + - + +
998A THR 2.8 31.4 + - - -
999A ASN* 3.9 9.4 + - - -
1000A LEU* 4.9 4.4 + - - +
1012A TRP* 4.5 4.6 - + - -
1035A TYR* 3.2 5.4 - - - -
1036A VAL* 3.0 37.9 + - + +
1038A ARG* 3.2 39.5 - - - +
1055A GLN* 3.6 6.7 + - - +
1056A PHE* 1.3 71.2 - - - +
1058A PHE* 1.3 70.8 + - - +
1059A THR* 3.3 21.1 + - + +
1076A PHE* 4.0 0.2 - - - -
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Residues in contact with PHE1058 (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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996A MET 2.9 15.7 + - - +
997A VAL* 4.0 18.7 - - + -
998A THR* 4.1 11.4 + - - +
999A ASN* 5.1 0.3 + - - -
1034A GLU* 3.2 39.9 - - + -
1035A TYR* 3.8 3.6 - + + -
1057A HIS* 1.3 81.5 + - - +
1059A THR* 1.3 57.6 + - - +
1060A GLY* 3.5 24.9 - - - -
1061A TRP* 3.5 18.8 + + + +
1067A PRO* 4.6 5.6 - - + -
1072A GLY 3.7 7.6 - - - -
1073A LEU* 3.7 46.7 - - + -
1076A PHE* 3.6 39.8 - + + -
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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