Contacts of the helix formed by residues 1071 - 1080 (chain A) in PDB entry 5DSG
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 PHE1071 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1059A MET* 3.9 22.0 - - + -
1063A MET* 4.0 13.9 - - - -
1067A GLY 3.3 22.7 - - - -
1068A VAL* 3.1 18.5 + - - +
1070A GLY* 1.3 73.4 - - - +
1072A THR* 1.3 59.0 + - - +
1073A ASN 3.4 2.0 - - - -
1074A SER* 4.0 15.7 - - - -
1075A LEU* 2.9 36.7 + - + +
1089A ASN* 5.8 0.9 - - - -
1090A LEU* 3.6 23.3 - - + -
1093A SER* 3.5 29.6 - - - -
1095A TRP* 4.0 23.1 - + + -
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Residues in contact with THR1072 (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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1040A LYS* 3.3 35.2 + - + +
1069A ALA 3.8 4.9 + - - -
1070A GLY* 2.9 13.6 + - - -
1071A PHE* 1.3 72.7 - - - +
1073A ASN* 1.3 62.8 + - - +
1075A LEU* 3.7 4.1 - - - +
1076A ARG* 2.9 71.1 + - + +
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Residues in contact with ASN1073 (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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1071A PHE 3.4 0.2 - - - -
1072A THR* 1.3 83.2 - - - +
1074A SER* 1.3 58.1 + - - +
1076A ARG* 3.4 8.7 + - - +
1077A MET* 2.9 41.2 + - + +
1089A ASN* 3.6 25.6 + - - +
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Residues in contact with SER1074 (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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1071A PHE* 3.4 15.8 + - - +
1072A THR 3.3 0.4 - - - -
1073A ASN* 1.3 77.6 - - - +
1075A LEU* 1.3 58.9 + - - +
1077A MET* 3.3 10.1 + - - +
1078A LEU* 2.9 34.7 + - - +
1086A ALA* 4.2 3.5 - - - +
1089A ASN* 2.4 32.5 + - - +
1090A LEU* 3.4 41.5 - - - +
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Residues in contact with LEU1075 (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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1040A LYS* 4.3 26.7 - - + +
1041A LEU* 3.6 18.6 - - + -
1044A VAL* 3.6 34.0 - - + +
1056A LEU* 3.8 24.2 - - + -
1059A MET* 6.1 1.3 - - + -
1068A VAL* 3.4 25.6 - - + +
1069A ALA* 4.3 0.2 - - - -
1071A PHE* 2.9 26.5 + - + +
1072A THR* 3.7 3.4 - - - +
1074A SER* 1.3 78.3 - - - +
1076A ARG* 1.3 59.1 + - + +
1078A LEU* 3.0 13.2 + - + +
1079A GLN* 2.9 29.1 + - - +
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Residues in contact with ARG1076 (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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1040A LYS* 6.4 0.2 - - - +
1072A THR* 2.9 42.8 + - + +
1073A ASN* 3.7 8.8 + - - +
1075A LEU* 1.3 76.8 - - + +
1077A MET* 1.3 61.4 + - + +
1079A GLN* 3.4 20.9 + - - +
1080A GLN* 2.8 31.1 - - - +
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Residues in contact with MET1077 (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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1073A ASN* 2.9 30.6 + - + +
1074A SER* 3.5 5.6 - - - +
1076A ARG* 1.3 77.4 - - + +
1078A LEU* 1.3 60.4 + - - +
1080A GLN* 3.4 7.5 + - - +
1081A LYS 3.4 3.1 + - - -
1082A ARG* 3.2 27.3 + - - +
1085A GLU* 3.3 58.8 - - + +
1086A ALA* 3.8 15.7 - - + +
1089A ASN* 3.5 31.4 - - + +
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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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1044A VAL* 3.9 13.2 - - + -
1047A SER 4.6 0.3 - - - +
1048A LEU* 3.8 13.9 - - + +
1056A LEU* 5.0 3.1 - - + -
1059A MET* 5.7 2.5 - - - -
1074A SER* 2.9 24.2 + - - +
1075A LEU* 3.0 27.3 + - + +
1077A MET* 1.3 75.2 - - - +
1079A GLN* 1.3 64.1 + - - +
1081A LYS* 3.0 15.1 + - - +
1083A TRP* 3.6 35.6 - - + -
1086A ALA* 4.0 14.8 - - + -
1090A LEU* 5.3 7.4 - - + -
1110A PHE* 3.6 44.2 - - + -
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Residues in contact with GLN1079 (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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1040A LYS 4.9 0.8 + - - -
1043A PRO* 3.4 34.2 - - - +
1044A VAL* 3.5 28.4 - - + +
1047A SER* 4.6 19.2 - - - +
1075A LEU 2.9 15.7 + - - +
1076A ARG* 3.4 17.3 - - - +
1077A MET 3.3 0.2 - - - -
1078A LEU* 1.3 77.7 - - - +
1080A GLN* 1.3 76.2 + - - +
1081A LYS* 3.3 12.1 + - - +
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Residues in contact with GLN1080 (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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1076A ARG* 2.8 20.0 + - - +
1077A MET* 3.4 9.0 + - - +
1078A LEU 3.3 0.6 - - - -
1079A GLN* 1.3 96.2 + - - +
1081A LYS* 1.3 70.2 + - - +
1082A ARG* 3.1 31.0 + - + +
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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