Contacts of the helix formed by residues 1020 - 1028 (chain A) in PDB entry 5G04
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 ASN1020 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1018A ASP* 3.9 8.7 + - - +
1019A MET* 1.3 81.1 - - - +
1021A HIS* 1.3 58.3 + - - +
1022A GLU* 3.3 21.2 + - - +
1023A VAL* 3.5 27.5 + - - +
1024A MET* 3.1 20.7 + - - +
1091A SER* 5.7 2.7 - - - +
1571A ARG* 3.1 28.7 + - - +
1694A ASP* 6.0 2.4 - - - +
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Residues in contact with HIS1021 (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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1016A MET 4.6 5.8 - - - -
1017A ASN 4.7 5.7 + - - -
1019A MET* 3.3 32.4 + - + +
1020A ASN* 1.3 75.0 + - - +
1022A GLU* 1.3 56.6 + - - +
1023A VAL 3.4 0.2 - - - -
1024A MET* 3.5 25.5 - - + +
1025A SER* 2.4 41.6 + - - -
1034A VAL* 4.6 12.7 - - + +
1038A ARG* 4.7 13.6 - - - -
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Residues in contact with GLU1022 (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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1020A ASN* 3.3 15.6 - - - +
1021A HIS* 1.3 77.0 - - + +
1023A VAL* 1.3 62.2 + - - +
1025A SER* 3.9 3.9 - - - -
1026A LEU* 3.4 27.0 + - - +
1629A PRO* 4.1 26.6 - - + +
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Residues in contact with VAL1023 (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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1020A ASN* 3.5 30.0 + - - +
1021A HIS 3.4 0.2 - - - -
1022A GLU* 1.3 74.7 - - + +
1024A MET* 1.3 61.6 + - - +
1026A LEU* 3.1 30.0 - - - +
1027A ILE* 3.4 9.2 + - + +
1571A ARG* 4.0 10.8 - - - +
1618A LEU* 3.7 18.2 - - + -
1620A VAL* 3.7 34.1 - - + -
1629A PRO* 4.4 18.8 - - + -
1654A PRO* 5.1 1.0 - - + +
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Residues in contact with MET1024 (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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1019A MET* 3.6 44.0 - - + +
1020A ASN 3.1 14.3 + - - +
1021A HIS* 3.5 34.1 - - + +
1023A VAL* 1.3 77.0 - - - +
1025A SER* 1.3 63.3 + - - +
1027A ILE* 3.2 16.7 + - - +
1028A TRP* 3.3 44.2 + - + +
1034A VAL* 3.7 21.3 - - + +
1087A PHE* 4.5 2.5 - - + -
1569A GLY* 3.3 24.0 - - - +
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Residues in contact with SER1025 (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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1021A HIS* 2.4 35.5 + - - -
1022A GLU* 3.9 5.8 - - - -
1024A MET* 1.3 65.2 - - - +
1026A LEU* 1.3 68.3 + - - +
1028A TRP 3.4 6.9 + - - +
1029A SER* 3.4 27.4 + - - -
1034A VAL* 6.6 0.2 - - - -
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Residues in contact with LEU1026 (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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1022A GLU 3.4 16.8 + - - +
1023A VAL* 3.1 14.2 + - - +
1025A SER* 1.3 78.6 - - - +
1027A ILE* 1.3 64.3 + - - +
1029A SER* 4.2 2.9 + - - -
1620A VAL* 4.3 5.2 - - + -
1629A PRO* 3.7 44.9 - - + +
1630A CYS* 3.9 8.5 - - - +
1631A TYR* 3.5 41.3 - - + +
1654A PRO* 3.9 31.0 - - + +
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Residues in contact with ILE1027 (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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1023A VAL* 3.6 10.3 - - + +
1024A MET* 3.2 16.7 + - - +
1026A LEU* 1.3 78.9 - - - +
1028A TRP* 1.3 87.9 + - + +
1029A SER 3.7 2.3 + - - -
1530A SER* 5.8 1.6 - - - -
1569A GLY 3.9 9.0 - - - +
1570A GLY* 3.6 35.7 - - - +
1618A LEU* 4.1 14.6 - - + -
1654A PRO* 3.4 18.4 - - - +
1655A THR* 4.1 27.4 + - + +
1656A LEU* 5.5 2.9 - - + -
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Residues in contact with TRP1028 (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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1024A MET* 3.3 44.5 + - + +
1025A SER* 3.4 10.3 + - - +
1026A LEU 3.4 0.4 - - - -
1027A ILE* 1.3 99.2 - - + +
1029A SER* 1.3 62.1 + - - +
1030A GLU 5.0 0.2 - - - +
1031A ASP 3.2 12.1 - - - +
1032A LEU* 4.9 1.9 - - - -
1033A ARG* 2.9 47.8 - - + +
1034A VAL* 3.6 28.9 - - + -
1087A PHE* 5.4 0.2 - + - -
1529A GLY 3.9 10.1 - - - -
1530A SER* 4.8 1.0 - - - +
1531A GLY* 3.4 27.1 + - - +
1566A PHE* 3.5 28.7 - + - -
1569A GLY* 3.5 2.7 - - - -
1570A GLY* 3.5 26.5 - - - -
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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