Contacts of the helix formed by residues 1070 - 1078 (chain A) in PDB entry 5DGY
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 GLN1070 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A THR* 5.2 7.4 - - + -
1068A TYR 4.4 0.5 - - - +
1069A GLY* 1.3 74.5 - - - +
1071A GLU* 1.3 64.2 + - - +
1072A ASP 3.5 2.2 - - - +
1073A ILE* 3.4 32.5 - - + +
1074A ASP* 3.4 23.7 + - - +
1141A GLY 5.3 9.0 + - - +
1143A SER* 5.6 0.7 - - - -
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Residues in contact with GLU1071 (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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1067A ARG* 5.0 16.2 + - - +
1069A GLY 5.1 3.4 - - - +
1070A GLN* 1.3 74.9 - - - +
1072A ASP* 1.3 73.5 + - - +
1074A ASP* 4.4 1.8 - - - +
1075A VAL* 3.5 24.9 + - - +
1081A ARG* 6.3 4.0 - - - +
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Residues in contact with ASP1072 (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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67A LYS* 4.6 17.3 - - + +
312A GLN* 3.8 25.0 + - + +
1070A GLN* 3.5 1.4 - - + +
1071A GLU* 1.3 88.2 - - - +
1073A ILE* 1.3 66.5 + - + +
1074A ASP 3.6 0.2 + - - -
1075A VAL* 3.6 6.7 + - - +
1076A MET* 3.4 19.9 + - - +
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Residues in contact with ILE1073 (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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67A LYS 4.3 2.9 - - - +
70A THR* 3.3 39.5 - - + +
72A LEU* 3.7 32.5 - - + -
73A ASN* 4.6 7.0 - - - +
145A ASN* 5.6 2.5 - - - +
312A GLN* 3.5 26.2 - - - +
1069A GLY* 5.3 2.5 - - - -
1070A GLN* 3.4 32.8 - - + +
1072A ASP* 1.3 76.4 - - + +
1074A ASP* 1.3 73.2 + - + +
1076A MET* 3.2 3.6 + - - +
1077A GLY* 3.1 20.4 + - - -
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Residues in contact with ASP1074 (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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139A VAL* 5.2 5.5 - - - +
145A ASN* 5.7 0.4 - - - +
1068A TYR* 3.8 31.1 + - - +
1069A GLY* 5.7 0.2 - - - -
1070A GLN 3.4 18.3 + - - +
1071A GLU* 4.4 2.5 - - - +
1072A ASP 3.4 0.4 - - - -
1073A ILE* 1.3 85.8 - - + +
1075A VAL* 1.3 66.0 + - + +
1076A MET 3.3 0.2 + - - -
1077A GLY* 3.7 6.5 + - - +
1078A LEU 4.3 1.0 + - - -
1079A THR 2.9 34.2 - - - +
1080A PHE 3.2 0.3 - - - -
1081A ARG* 2.7 36.8 + - - +
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Residues in contact with VAL1075 (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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311A LYS* 3.8 36.3 - - + +
1071A GLU 3.5 16.1 + - - +
1072A ASP* 3.6 7.3 + - - +
1073A ILE 3.4 0.6 - - - -
1074A ASP* 1.3 78.0 - - + +
1076A MET* 1.3 62.7 + - - +
1078A LEU 4.3 11.1 + - - +
1079A THR* 5.0 0.9 - - - -
1080A PHE* 3.8 25.4 - - + +
1081A ARG* 5.9 4.0 - - - +
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Residues in contact with MET1076 (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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310A ASN* 2.8 36.7 - - - +
311A LYS* 4.1 14.0 + - - +
312A GLN* 3.4 32.8 - - + +
313A PHE* 5.9 0.2 - - + -
1072A ASP 3.4 4.5 + - - +
1073A ILE 3.2 9.4 + - - +
1074A ASP 3.1 0.8 - - - -
1075A VAL* 1.3 80.6 - - - +
1077A GLY* 1.3 67.6 + - - +
1078A LEU* 3.5 0.5 + - - -
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Residues in contact with GLY1077 (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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135A ARG* 3.6 38.1 + - - -
257A TYR* 4.1 6.9 + - - -
310A ASN* 4.6 2.5 - - - -
1073A ILE 3.1 13.6 + - - -
1074A ASP* 3.7 3.2 + - - -
1075A VAL 3.5 0.8 - - - -
1076A MET* 1.3 79.1 - - - +
1078A LEU* 1.3 64.4 + - - +
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Residues in contact with LEU1078 (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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135A ARG* 5.3 7.9 - - + +
139A VAL* 5.7 6.3 - - + -
223A TYR* 5.2 6.7 - - + -
226A LEU* 3.4 42.4 - - + -
246A ALA* 4.9 1.4 - - - +
249A GLU* 5.0 8.5 - - - +
250A VAL* 3.5 49.4 + - + +
253A MET* 3.9 23.7 - - + +
254A VAL* 4.3 9.0 - - + -
257A TYR* 4.2 12.6 - - + +
1074A ASP 4.3 1.8 + - - -
1075A VAL 4.5 7.4 - - - +
1076A MET 3.5 1.7 + - - -
1077A GLY* 1.3 81.7 - - - +
1079A THR* 1.3 62.1 + - + +
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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