Contacts of the helix formed by residues 1037 - 1052 (chain B) in PDB entry 1RQQ
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 SER1037 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1035B SER 3.6 3.5 + - - -
1036B ALA* 1.3 73.4 - - - +
1038B LEU* 1.3 60.6 + - - +
1039B ARG* 3.9 8.6 + - - +
1040B GLU* 3.0 38.4 + - - +
1041B ARG* 2.9 28.1 + - - +
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Residues in contact with LEU1038 (chain B).
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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1037B SER* 1.3 73.6 - - - +
1039B ARG* 1.3 57.8 + - - +
1041B ARG* 2.9 33.1 + - + +
1042B ILE* 2.8 52.3 + - + +
1045B LEU* 6.4 0.2 - - + -
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Residues in contact with ARG1039 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037B SER* 3.2 9.0 - - - +
1038B LEU* 1.3 76.7 - - - +
1040B GLU* 1.3 62.7 + - + +
1042B ILE* 3.8 7.8 + - - +
1043B GLU* 3.3 21.3 + - - +
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Residues in contact with GLU1040 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006B SER 4.9 1.9 - - - +
1007B PHE* 3.6 49.8 - - + +
1032B VAL* 5.6 0.7 - - - -
1033B ASN* 5.6 0.3 + - - -
1035B SER 4.8 0.5 - - - +
1036B ALA* 3.5 11.3 - - + -
1037B SER* 3.0 37.9 + - - +
1039B ARG* 1.3 77.9 - - + +
1041B ARG* 1.3 59.8 + - - +
1042B ILE 3.3 0.2 - - - -
1043B GLU* 3.4 7.0 + - - +
1044B PHE* 2.9 28.6 + - - +
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Residues in contact with ARG1041 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032B VAL* 5.0 17.5 - - + +
1033B ASN 4.3 2.8 + - - -
1034B GLU* 3.7 20.0 + - - +
1035B SER 5.1 0.2 - - - -
1036B ALA* 2.6 38.2 + - + +
1037B SER* 2.9 24.1 + - - +
1038B LEU* 2.9 37.6 + - + +
1040B GLU* 1.3 74.7 - - - +
1042B ILE* 1.3 60.2 + - - +
1044B PHE* 3.2 7.8 + - - +
1045B LEU* 2.9 43.2 + - + +
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Residues in contact with ILE1042 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1038B LEU* 2.8 37.8 + - + +
1039B ARG* 3.9 7.9 - - - +
1041B ARG* 1.3 74.3 - - - +
1043B GLU* 1.3 63.0 + - - +
1045B LEU* 3.2 19.4 + - + +
1046B ASN* 2.8 28.6 + - + +
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Residues in contact with GLU1043 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007B PHE* 4.6 12.6 - - + -
1039B ARG 3.3 12.8 + - - +
1040B GLU* 3.6 10.8 - - - +
1041B ARG 3.3 0.2 - - - -
1042B ILE* 1.3 80.0 - - - +
1044B PHE* 1.3 63.9 + - - +
1046B ASN* 2.9 24.5 + - - +
1047B GLU* 3.0 14.4 + - - +
1152B GLY* 2.8 39.9 - - - +
1153B MET* 4.5 4.5 - - - +
1155B ARG* 3.2 25.4 + - - -
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Residues in contact with PHE1044 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007B PHE* 4.1 16.1 - + + -
1030B LYS* 3.5 46.2 - - + -
1031B THR* 3.9 13.2 - - - -
1032B VAL* 3.4 29.2 - - + -
1040B GLU 2.9 13.9 + - - +
1041B ARG* 3.3 9.0 - - - +
1043B GLU* 1.3 78.4 - - - +
1045B LEU* 1.3 72.1 + - + +
1046B ASN 3.4 0.2 + - - -
1047B GLU* 3.5 14.7 + - - +
1048B ALA* 3.5 17.5 + - - +
1072B THR* 4.2 23.6 - - + -
1074B VAL* 3.3 32.6 - - + +
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Residues in contact with LEU1045 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1041B ARG* 2.9 31.2 + - + +
1042B ILE* 3.6 19.1 - - + +
1044B PHE* 1.3 86.3 - - + +
1046B ASN* 1.3 60.6 + - - +
1048B ALA* 3.6 8.6 + - + +
1049B SER* 3.0 28.2 + - - -
1067B SER* 6.5 0.4 - - - -
1072B THR* 4.6 17.7 - - + +
1074B VAL* 6.2 0.9 - - + -
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Residues in contact with ASN1046 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1042B ILE* 2.8 15.3 + - + +
1043B GLU* 2.9 19.3 + - - +
1045B LEU* 1.3 75.3 - - - +
1047B GLU* 1.3 66.2 + - - +
1049B SER* 3.1 7.7 + - - -
1050B VAL* 2.9 37.9 + - - +
1151B PHE 3.3 22.2 + - - -
1152B GLY 3.5 12.3 + - - -
1154B THR 3.7 13.9 + - - +
1155B ARG* 3.9 5.2 + - - +
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Residues in contact with GLU1047 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1030B LYS* 3.3 40.1 + - - +
1043B GLU 3.0 8.3 + - - +
1044B PHE* 3.8 15.3 - - - +
1046B ASN* 1.3 80.0 - - - +
1048B ALA* 1.3 64.3 + - - +
1050B VAL* 3.2 5.4 - - - +
1051B MET* 3.1 43.6 + - - +
1074B VAL* 5.6 3.9 - - - +
1076B MET* 5.0 4.9 - - - +
1150B ASP* 3.5 8.4 + - - -
1151B PHE* 3.3 51.2 + - + -
1152B GLY* 4.3 4.0 - - - +
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Residues in contact with ALA1048 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1044B PHE 3.5 9.8 + - - +
1045B LEU* 3.8 12.3 - - + +
1046B ASN 3.2 0.4 - - - -
1047B GLU* 1.3 80.0 - - - +
1049B SER* 1.3 66.1 + - - +
1051B MET* 3.1 14.3 + - - -
1052B LYS* 3.3 18.7 + - - +
1062B LEU* 3.6 6.3 - - + +
1065B VAL* 4.7 16.4 - - + -
1074B VAL* 4.2 31.8 - - + +
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Residues in contact with SER1049 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045B LEU 3.0 13.4 + - - -
1046B ASN* 3.3 13.0 - - - -
1048B ALA* 1.3 80.4 - - - +
1050B VAL* 1.3 65.2 + - - +
1052B LYS* 3.2 33.2 - - - +
1053B GLY 4.3 1.0 + - - -
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Residues in contact with VAL1050 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046B ASN* 2.9 34.9 + - - +
1047B GLU* 3.2 12.1 - - - +
1049B SER* 1.3 70.9 - - - +
1051B MET* 1.3 71.8 + - - +
1052B LYS 3.2 0.3 + - - -
1053B GLY* 3.3 9.7 + - - -
1054B PHE* 3.7 24.1 - - + -
1128B PHE* 4.4 29.4 - - + -
1151B PHE* 3.7 28.9 - - + +
1154B THR* 4.9 8.5 - - + +
1155B ARG* 6.3 0.2 - - - -
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Residues in contact with MET1051 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989B TRP* 5.2 0.9 - - - -
1047B GLU* 3.1 38.2 + - - +
1048B ALA* 3.1 6.7 + - - +
1050B VAL* 1.3 82.3 - - + +
1052B LYS* 1.3 63.7 + - - +
1054B PHE* 2.9 30.7 + - + +
1060B VAL* 3.1 37.7 - - + +
1061B ARG 3.8 4.7 - - - +
1062B LEU* 3.6 42.0 + - + +
1074B VAL* 5.3 2.7 - - - -
1076B MET* 4.4 13.7 - - + +
1151B PHE* 3.6 28.0 - - + -
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Residues in contact with LYS1052 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987B ASP* 3.9 22.0 + - - +
989B TRP* 3.3 55.8 - - + +
1048B ALA* 3.3 16.8 - - - +
1049B SER* 3.2 24.6 - - - +
1050B VAL 3.1 0.4 - - - -
1051B MET* 1.3 79.8 - - - +
1053B GLY* 1.3 58.3 + - - +
1054B PHE 3.5 2.8 + - - +
1055B THR* 5.7 0.2 + - - -
1062B LEU* 3.5 17.9 - - + +
1065B VAL* 4.8 8.7 - - - -
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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