Contacts of the helix formed by residues 1152 - 1165 (chain A) in PDB entry 1DSZ
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 CYS1152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1121A ZN 2.4 36.6 - - - -
1135A CYS* 3.4 9.9 - - + +
1138A CYS* 3.7 6.7 - - - -
1140A ASP* 4.1 9.9 - - + +
1141A LYS 3.1 25.4 - - - +
1142A SER* 4.1 0.9 - - - +
1143A SER* 4.3 1.6 - - - +
1151A ALA* 1.3 77.6 - - - +
1153A GLU* 1.3 66.6 + - - +
1154A GLY* 3.3 6.0 + - - +
1155A CYS* 3.3 16.3 + - - -
1156A LYS* 2.9 23.4 + - - +
1184A ARG* 3.8 11.2 - - - -
1541D A 5.6 1.8 - - - +
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Residues in contact with GLU1153 (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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1141A LYS 4.8 0.2 + - - -
1143A SER* 2.3 37.0 + - - +
1146A HIS* 3.8 2.6 + - - -
1152A CYS* 1.3 73.5 - - - +
1154A GLY* 1.3 57.9 + - - +
1156A LYS* 2.8 38.5 + - - +
1157A GLY* 2.9 26.7 + - - -
1540D G 3.9 5.9 - - - +
1541D A 3.6 40.9 + - + +
1542D C 3.0 24.4 + - + -
1543D C 5.0 2.5 + - - -
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Residues in contact with GLY1154 (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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1152A CYS* 3.2 7.9 - - - +
1153A GLU* 1.3 75.6 - - - +
1155A CYS* 1.3 59.7 + - - +
1157A GLY 3.9 0.2 - - - -
1158A PHE* 2.9 31.0 + - - +
1161A ARG* 5.0 1.4 + - - -
1184A ARG* 5.1 2.6 - - - +
1191A ARG* 3.2 9.0 + - - -
1540D G 3.6 39.8 + - - +
1541D A 4.5 0.6 + - - -
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Residues in contact with CYS1155 (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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1121A ZN 2.3 35.9 - - - -
1135A CYS* 3.7 10.5 - - - -
1137A VAL* 3.8 20.6 - - + -
1138A CYS* 3.8 8.5 - - - -
1152A CYS* 3.3 5.9 + - - +
1154A GLY* 1.3 71.7 - - - +
1156A LYS* 1.3 60.4 + - - +
1158A PHE* 3.7 3.5 - - - +
1159A PHE* 2.9 32.9 + - - +
1191A ARG* 3.4 27.8 - - - +
1195A CYS* 4.5 4.6 - - - -
1200A MET* 4.3 12.6 - - + +
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Residues in contact with LYS1156 (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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1146A HIS* 3.5 42.5 + - + +
1147A TYR* 3.6 26.5 - - + +
1151A ALA* 4.9 0.2 - - + -
1152A CYS 2.9 18.4 + - - +
1153A GLU* 2.8 39.0 + - - +
1155A CYS* 1.3 76.5 - - - +
1157A GLY* 1.3 65.4 + - - +
1159A PHE* 3.8 0.2 - - - +
1160A ARG* 3.1 26.8 + - + +
1200A MET* 4.5 4.2 - - - +
1496C A 4.3 9.2 + - - +
1497C G 2.8 42.5 + - - -
1498C G 4.7 3.8 - - - -
1542D C 3.8 2.6 - - - +
1543D C 4.1 3.6 - - - +
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Residues in contact with GLY1157 (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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1153A GLU 2.9 19.4 + - - -
1154A GLY 3.9 0.4 - - - -
1156A LYS* 1.3 76.9 - - - +
1158A PHE* 1.3 62.5 + - - +
1160A ARG* 3.4 17.4 + - - +
1161A ARG* 2.9 45.2 + - - +
1540D G 5.0 3.6 - - - -
1541D A 5.9 2.2 - - - -
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Residues in contact with PHE1158 (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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1154A GLY 2.9 18.7 + - - +
1155A CYS 3.7 2.7 - - - +
1157A GLY* 1.3 76.9 - - - +
1159A PHE* 1.3 59.1 + - - +
1161A ARG* 3.8 15.0 - - - +
1162A SER* 2.6 49.1 + - - -
1169A TYR* 3.7 24.0 - + - -
1188A GLN* 3.4 30.3 - - + -
1191A ARG* 3.5 38.1 - - + +
1192A LEU* 3.5 28.5 - - + -
1195A CYS* 4.3 7.4 - - - -
1539D T 3.7 30.7 - - - -
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Residues in contact with PHE1159 (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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1147A TYR* 3.9 24.5 - + + -
1155A CYS 2.9 19.1 + - - +
1156A LYS 3.8 3.1 - - - +
1158A PHE* 1.3 82.2 - - - +
1160A ARG* 1.3 64.6 + - - +
1162A SER* 3.1 4.8 + - - -
1163A ILE* 3.0 43.9 + - + +
1192A LEU* 3.8 10.1 - - + -
1195A CYS* 3.6 23.3 - - + -
1196A PHE* 3.7 29.6 - + - -
1200A MET* 3.7 25.6 - - + -
1201A SER 3.7 20.0 - - - -
1202A LYS* 3.7 22.7 - - - -
1205A VAL* 3.9 7.0 - - + -
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Residues in contact with ARG1160 (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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1147A TYR* 3.3 22.3 + - - +
1156A LYS* 3.1 13.5 + - - +
1157A GLY* 3.7 20.1 + - - +
1159A PHE* 1.3 78.5 - - - +
1161A ARG* 1.3 79.2 + - - +
1163A ILE* 3.3 0.9 + - - +
1164A GLN* 2.8 67.4 + - + +
1205A VAL* 4.6 8.1 - - + -
1497C G 3.5 44.7 + - - +
1498C G 3.7 34.3 + - - -
1499C T 4.0 20.2 + - - +
1540D G 5.1 0.4 + - - -
1541D A 5.1 2.0 - - - +
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Residues in contact with ARG1161 (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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1154A GLY 5.0 0.2 + - - -
1157A GLY* 2.9 34.3 + - - +
1158A PHE* 3.8 17.3 - - - +
1160A ARG* 1.3 95.7 - - - +
1162A SER* 1.3 65.0 + - - +
1164A GLN* 4.2 5.2 - - - +
1165A LYS* 2.8 59.9 + - + +
1167A MET* 4.6 0.7 - - + -
1169A TYR* 5.7 1.6 - - - +
1538D T 4.4 2.4 - - - +
1539D T 3.0 79.3 + - - +
1540D G 3.0 28.5 + - - -
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Residues in contact with SER1162 (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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1158A PHE* 2.6 32.3 + - - -
1159A PHE 3.1 4.7 + - - -
1161A ARG* 1.3 76.6 - - - +
1163A ILE* 1.3 61.3 + - - +
1166A ASN* 3.1 6.6 + - - -
1167A MET* 2.9 38.5 + - - +
1169A TYR* 2.9 28.7 + - - -
1192A LEU* 3.9 24.5 - - - -
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Residues in contact with ILE1163 (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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1159A PHE* 3.0 42.4 + - + +
1160A ARG 3.9 0.2 - - - +
1162A SER* 1.3 79.5 - - - +
1164A GLN* 1.3 68.1 + - - +
1165A LYS 3.1 1.8 - - - -
1166A ASN* 3.0 23.2 + - - +
1192A LEU* 5.1 2.0 - - + -
1196A PHE* 4.0 20.2 - - + -
1202A LYS* 3.6 35.2 - - + +
1205A VAL* 3.5 30.7 - - + +
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Residues in contact with GLN1164 (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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1160A ARG* 2.8 54.9 + - - +
1161A ARG* 4.2 4.8 - - - +
1163A ILE* 1.3 76.5 - - - +
1165A LYS* 1.3 64.8 + - + +
1166A ASN* 3.8 6.6 + - - +
1205A VAL* 3.8 18.4 - - + -
1206A ARG 5.2 6.3 + - - +
1497C G 3.8 17.4 + - - -
1498C G 2.9 26.9 + - - -
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Residues in contact with LYS1165 (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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1161A ARG* 2.8 55.0 + - + +
1164A GLN* 1.3 82.4 - - + +
1166A ASN* 1.3 74.7 + - - +
1167A MET* 3.1 27.5 + - + +
1538D T 4.9 12.7 + - - -
1539D T 5.8 1.2 - - - +
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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