Contacts of the helix formed by residues 1032 - 1042 (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 LEU1032 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1028A TRP 4.9 2.0 - - - -
1030A GLU 4.9 1.3 - - - +
1031A ASP* 1.3 77.6 + - - +
1033A ARG* 1.3 62.3 + - - +
1034A VAL* 4.3 10.1 - - + +
1035A GLN* 3.2 32.5 - - + +
1036A ASP* 2.9 23.0 + - - +
489N PRO* 3.5 22.2 - - + +
490N GLY 4.0 7.6 - - - +
491N LYS* 4.0 22.0 - - - +
492N SER* 4.8 2.2 - - - +
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Residues in contact with ARG1033 (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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1028A TRP* 2.9 44.0 - - + +
1031A ASP* 3.3 23.9 + - - +
1032A LEU* 1.3 70.5 - - - +
1034A VAL* 1.3 58.2 + - - +
1036A ASP* 3.1 13.6 + - - +
1037A VAL* 2.9 29.0 + - - +
1531A GLY 2.7 27.1 + - - -
1532A ASN* 4.2 4.0 + - - +
1533A LEU* 3.3 48.9 - - - +
1536A LEU* 4.5 12.9 - - + +
1566A PHE* 3.8 26.0 - - + -
488N ASP* 5.2 0.9 - - + -
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Residues in contact with VAL1034 (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* 4.6 11.7 - - + +
1024A MET* 3.7 30.3 - - + +
1025A SER* 6.6 0.2 - - - -
1028A TRP* 3.6 38.4 - - + -
1032A LEU* 4.7 12.6 - - + -
1033A ARG* 1.3 73.1 - - - +
1035A GLN* 1.3 61.8 - - + +
1037A VAL* 3.6 7.5 - - - +
1038A ARG* 2.9 38.0 + - + +
1087A PHE* 4.5 12.1 - - + -
1566A PHE* 4.9 2.7 - - + -
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Residues in contact with GLN1035 (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 LEU* 3.2 36.7 + - + +
1033A ARG 3.4 0.4 - - - -
1034A VAL* 1.3 80.1 - - + +
1036A ASP* 1.3 70.6 + - - +
1038A ARG* 3.9 11.9 + - - +
1039A ARG* 3.2 55.9 + - - +
489N PRO* 5.3 4.0 - - + -
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Residues in contact with ASP1036 (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 LEU 2.9 19.1 - - - +
1033A ARG* 3.1 9.1 + - - +
1035A GLN* 1.3 82.9 + - - +
1037A VAL* 1.3 51.8 + - - +
1039A ARG* 3.2 15.1 + - - +
1040A LEU* 2.8 50.2 + - + +
1536A LEU* 5.0 11.1 - - + +
1540A ARG* 4.6 12.0 + - - +
488N ASP* 3.3 38.1 - - - +
489N PRO* 3.8 3.1 - - - +
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Residues in contact with VAL1037 (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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1033A ARG 2.9 20.8 + - - +
1034A VAL* 3.6 10.3 - - - +
1035A GLN 3.3 0.2 - - - -
1036A ASP* 1.3 73.8 - - - +
1038A ARG* 1.3 56.5 + - - +
1040A LEU* 3.0 9.7 + - - +
1041A LEU* 2.9 51.7 + - + +
1087A PHE* 3.7 27.4 - - + -
1536A LEU* 4.8 4.7 - - + -
1562A LEU* 4.1 13.2 - - + -
1563A GLY* 6.2 0.4 - - - -
1566A PHE* 3.6 40.2 - - + -
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Residues in contact with ARG1038 (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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1013A ASP 4.9 0.8 + - - -
1014A ASP* 3.7 17.6 + - - +
1015A GLY 3.4 20.8 + - - -
1016A MET* 3.4 45.1 + - + +
1017A ASN* 3.7 15.6 + - - -
1019A MET* 5.2 1.6 - - - -
1021A HIS* 4.7 15.5 + - - -
1034A VAL* 2.9 26.2 + - - +
1035A GLN* 3.9 11.4 + - - +
1037A VAL* 1.3 71.6 - - - +
1039A ARG* 1.3 56.3 + - - +
1042A GLN* 3.1 31.4 + - - +
1087A PHE* 4.2 9.2 - - + -
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Residues in contact with ARG1039 (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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1035A GLN* 3.2 39.8 + - - +
1036A ASP* 3.3 18.3 + - - +
1038A ARG* 1.3 73.1 - - - +
1040A LEU* 1.3 71.1 + - + +
1042A GLN* 3.1 31.4 + - + +
1543A HIS* 5.1 2.1 - - - -
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Residues in contact with LEU1040 (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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1036A ASP* 2.8 39.7 + - + +
1037A VAL* 3.0 8.0 + - - +
1039A ARG* 1.3 81.4 - - + +
1041A LEU* 1.3 59.6 + - - +
1042A GLN 3.8 0.3 + - - -
1080A LEU* 3.5 22.5 - - - +
1536A LEU* 4.2 16.4 - - + -
1539A CYS 5.1 0.4 - - - -
1540A ARG* 4.3 27.4 - - + +
1543A HIS* 3.3 44.7 + - + +
1544A MET* 6.1 1.8 - - + -
1559A HIS* 4.0 3.5 - - + -
1562A LEU* 3.8 32.1 - - + -
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Residues in contact with LEU1041 (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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1016A MET* 3.5 15.6 - - + +
1037A VAL* 2.9 34.6 + - + +
1040A LEU* 1.3 74.9 - - - +
1042A GLN* 1.3 65.0 + - - +
1043A SER* 3.3 4.7 + - - -
1080A LEU* 3.8 23.5 - - - +
1083A GLY* 3.8 10.8 - - - +
1084A ARG* 3.6 44.2 - - + +
1087A PHE* 3.8 20.2 - - + -
1559A HIS* 4.2 17.7 - - + +
1562A LEU* 3.7 23.8 - - + -
1563A GLY* 5.1 1.6 - - - +
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Residues in contact with GLN1042 (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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1014A ASP* 3.1 26.5 - - - +
1016A MET* 3.7 0.4 - - - -
1038A ARG 3.1 16.7 + - - +
1039A ARG* 3.1 30.9 + - + +
1040A LEU 3.5 0.8 - - - -
1041A LEU* 1.3 73.8 - - - +
1043A SER* 1.3 59.1 - - - +
1044A ALA 2.7 28.6 - - - +
1045A HIS* 3.3 19.9 + - + +
1046A PRO 5.5 3.5 + - - +
1047A VAL* 6.2 1.4 - - - +
1077A THR* 5.7 1.2 - - - +
1080A LEU* 3.4 14.8 - - - +
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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