Contacts of the helix formed by residues 1037 - 1052 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1035A SER 3.6 3.9 + - - -
1036A ALA* 1.3 75.5 - - - +
1038A LEU* 1.3 60.2 + - - +
1039A ARG* 3.1 39.0 + - - -
1040A GLU* 3.0 21.9 + - - +
1041A ARG* 2.9 26.4 + - - +
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Residues in contact with LEU1038 (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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1036A ALA 4.0 0.4 + - - -
1037A SER* 1.3 72.1 - - - +
1039A ARG* 1.3 57.5 + - - +
1041A ARG* 2.9 16.7 + - + +
1042A ILE* 2.8 57.1 + - + +
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Residues in contact with ARG1039 (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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1037A SER* 3.1 22.1 + - - -
1038A LEU* 1.3 80.3 - - - +
1040A GLU* 1.3 88.7 + - - +
1042A ILE* 3.7 11.5 + - - +
1043A GLU* 3.3 20.8 + - - +
1170A LEU* 5.3 15.1 - - - +
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Residues in contact with GLU1040 (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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1006A SER 5.4 0.5 - - - +
1007A PHE* 3.4 58.1 - - + +
1035A SER 5.0 0.2 - - - +
1036A ALA* 3.7 6.4 - - + -
1037A SER* 3.0 35.6 + - - +
1039A ARG* 1.3 97.1 + - - +
1041A ARG* 1.3 61.2 + - - +
1043A GLU* 3.4 5.7 + - - +
1044A PHE* 2.9 28.4 + - - +
1170A LEU* 5.9 1.9 - - - +
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Residues in contact with ARG1041 (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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1032A VAL* 3.7 27.2 - - + +
1033A ASN 3.4 4.6 + - - -
1034A GLU* 2.6 38.8 + - - +
1036A ALA 2.9 18.2 + - - -
1037A SER 2.9 14.5 + - - +
1038A LEU* 2.9 19.5 + - + +
1040A GLU* 1.3 75.1 - - - +
1042A ILE* 1.3 58.3 + - - +
1044A PHE* 3.3 9.0 + - + +
1045A LEU* 2.9 41.1 + - + +
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Residues in contact with ILE1042 (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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1038A LEU* 2.8 45.9 + - + +
1039A ARG* 3.8 9.2 - - - +
1041A ARG* 1.3 73.9 - - - +
1043A GLU* 1.3 60.6 + - - +
1045A LEU* 3.3 10.9 + - + +
1046A ASN* 2.8 29.6 + - + +
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Residues in contact with GLU1043 (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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1007A PHE* 3.2 28.5 - - + -
1039A ARG 3.3 12.2 + - - +
1040A GLU* 3.5 9.4 - - - +
1041A ARG 3.3 0.2 - - - -
1042A ILE* 1.3 82.2 - - - +
1044A PHE* 1.3 62.3 + - - +
1046A ASN* 2.9 18.0 + - - +
1047A GLU* 3.0 14.4 + - - +
1152A GLY* 3.4 27.5 - - - +
1153A MET* 3.9 22.0 - - - +
1155A ARG* 5.5 4.2 + - - +
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Residues in contact with PHE1044 (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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1007A PHE* 3.9 12.5 - + + -
1030A LYS* 3.7 39.5 - - + -
1031A THR* 4.1 3.8 - - - -
1032A VAL* 3.4 33.4 - - + -
1040A GLU 2.9 14.6 + - - +
1041A ARG* 3.4 9.9 - - + +
1043A GLU* 1.3 78.4 - - - +
1045A LEU* 1.3 72.5 + - + +
1046A ASN 3.4 0.2 + - - -
1047A GLU* 3.5 11.7 + - - +
1048A ALA* 3.5 17.8 + - - +
1072A THR* 3.6 37.7 - - + -
1074A VAL* 3.3 31.2 - - + +
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Residues in contact with LEU1045 (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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1041A ARG* 2.9 26.9 + - + +
1042A ILE* 3.7 9.0 - - + +
1044A PHE* 1.3 91.4 - - + +
1046A ASN* 1.3 60.7 + - - +
1048A ALA* 3.8 8.5 - - + +
1049A SER* 3.0 29.0 + - - -
1065A VAL* 6.2 2.7 - - + -
1067A SER* 6.2 0.2 - - - +
1072A THR* 4.6 13.9 - - + +
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Residues in contact with ASN1046 (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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1042A ILE* 2.8 16.9 + - + +
1043A GLU* 2.9 12.7 + - - +
1045A LEU* 1.3 76.0 - - - +
1047A GLU* 1.3 65.4 + - - +
1049A SER* 3.2 6.0 + - - -
1050A VAL* 2.9 36.3 + - - +
1151A PHE 3.4 11.1 + - - -
1152A GLY 2.9 23.8 + - - -
1154A THR 3.2 21.7 + - - +
1155A ARG* 3.2 11.1 + - - +
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Residues in contact with GLU1047 (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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1030A LYS* 2.7 41.5 + - - +
1043A GLU 3.0 8.5 + - - +
1044A PHE* 3.7 15.8 - - - +
1045A LEU 3.4 0.2 - - - -
1046A ASN* 1.3 76.6 - - - +
1048A ALA* 1.3 65.2 + - - +
1050A VAL* 3.3 2.2 - - - +
1051A MET* 3.1 40.3 + - - +
1074A VAL* 6.0 2.0 - - + -
1076A MET* 4.2 10.3 - - + +
1150A ASP* 3.4 8.9 + - - +
1151A PHE* 3.4 47.9 + - + +
1152A GLY* 3.8 6.3 + - - +
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Residues in contact with ALA1048 (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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1044A PHE 3.5 10.1 + - - +
1045A LEU* 3.8 13.0 - - + +
1046A ASN 3.2 0.4 - - - -
1047A GLU* 1.3 79.0 - - - +
1049A SER* 1.3 66.8 + - - +
1051A MET* 3.2 12.6 + - - -
1052A LYS* 3.3 11.9 + - - +
1062A LEU* 3.5 15.7 - - + +
1065A VAL* 4.7 16.4 - - + -
1074A VAL* 4.1 29.4 - - + +
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Residues in contact with SER1049 (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 LEU 3.0 17.4 + - - -
1046A ASN* 3.2 8.0 + - - -
1048A ALA* 1.3 81.2 - - - +
1050A VAL* 1.3 65.2 + - - +
1052A LYS* 3.3 31.0 + - - +
1053A GLY 4.3 0.7 + - - -
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Residues in contact with VAL1050 (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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1046A ASN* 2.9 38.4 + - - +
1047A GLU* 3.3 11.9 - - - +
1049A SER* 1.3 75.4 - - - +
1051A MET* 1.3 65.1 + - - +
1052A LYS 3.2 0.3 + - - -
1053A GLY* 3.3 9.7 + - - -
1054A PHE* 3.5 24.3 - - + -
1128A PHE* 3.7 35.0 - - + -
1151A PHE* 3.5 30.1 - - + +
1154A THR* 4.4 10.1 - - + +
1155A ARG* 5.8 0.2 - - - -
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Residues in contact with MET1051 (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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989A TRP* 5.1 1.0 - - - -
1047A GLU* 3.1 30.1 + - - +
1048A ALA* 3.2 4.9 + - - +
1050A VAL* 1.3 78.0 - - - +
1052A LYS* 1.3 64.2 + - - +
1054A PHE* 2.9 30.7 + - + +
1060A VAL* 3.1 34.3 - - + +
1061A ARG 3.9 2.5 - - - -
1062A LEU* 3.6 39.9 + - + +
1074A VAL* 5.3 0.2 - - - -
1076A MET* 3.7 32.3 - - + -
1151A PHE* 3.4 33.9 - - + -
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Residues in contact with LYS1052 (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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987A ASP* 5.7 6.3 - - - +
989A TRP* 3.4 68.4 + - + +
1048A ALA* 3.3 16.1 + - - +
1049A SER* 3.3 22.8 + - - +
1050A VAL 3.1 0.6 - - - -
1051A MET* 1.3 76.5 - - - +
1053A GLY* 1.3 59.4 + - - +
1054A PHE 3.5 2.1 + - - +
1055A THR* 5.7 0.2 + - - -
1062A LEU* 3.6 8.9 - - + +
1065A VAL* 4.5 16.3 - - - +
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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
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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