Contacts of the helix formed by residues 1031 - 1038 (chain B) in PDB entry 5ZCS
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 MET1031 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1027B ILE* 3.4 11.2 - - + +
1028B ARG* 3.3 58.3 + - - +
1029B PRO 3.8 1.2 - - - -
1030B TYR* 1.3 74.9 - - - +
1032B ASP* 1.3 78.1 + - - +
1033B GLU* 3.3 4.3 - - - -
1034B ILE* 3.5 30.9 + - + +
1035B VAL* 3.9 10.6 + - + +
1069B LEU* 4.7 13.9 - - + -
1070B TYR* 3.6 39.0 - - + -
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Residues in contact with ASP1032 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028B ARG 5.3 2.8 - - - +
1029B PRO 5.1 5.8 - - - +
1030B TYR* 4.6 0.2 - - - +
1031B MET* 1.3 93.9 - - - +
1033B GLU* 1.3 60.7 + - - +
1035B VAL* 3.4 7.3 + - - +
1036B THR* 2.7 39.6 + - - +
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Residues in contact with GLU1033 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994B MET 4.5 4.9 - - - +
995B PRO* 5.1 6.1 - - - +
998B LEU* 3.4 41.1 - - + +
1030B TYR* 3.0 34.1 - - - +
1031B MET* 4.5 0.9 - - - -
1032B ASP* 1.3 81.8 + - - +
1034B ILE* 1.3 62.6 + - + +
1036B THR* 3.7 2.9 - - - -
1037B LEU* 2.9 51.4 + - + +
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Residues in contact with ILE1034 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998B LEU* 5.0 9.2 - - + -
1016B LEU* 6.4 2.0 - - + -
1019B LEU* 6.2 2.9 - - + -
1020B VAL* 5.1 15.9 - - + -
1027B ILE* 5.6 7.4 - - + -
1028B ARG* 6.1 0.4 - - - +
1030B TYR 5.0 2.5 - - - +
1031B MET* 3.5 25.3 + - + +
1032B ASP 3.2 0.6 - - - -
1033B GLU* 1.3 88.9 - - + +
1035B VAL* 1.3 63.8 + - + +
1037B LEU* 5.1 0.6 - - - +
1038B MET* 3.3 23.2 + - - +
1055B LEU* 5.7 8.1 - - + -
1059B ILE* 5.4 13.2 - - + -
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Residues in contact with VAL1035 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031B MET* 3.9 17.7 + - + +
1032B ASP* 3.4 7.9 + - - +
1034B ILE* 1.3 82.0 - - + +
1036B THR* 1.3 62.1 + - - +
1038B MET* 3.3 22.8 - - + +
1039B ARG* 3.9 10.2 - - - +
1070B TYR* 4.1 29.2 - - + +
1073B GLN* 3.8 37.2 - - + +
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Residues in contact with THR1036 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032B ASP* 2.7 26.5 + - - +
1033B GLU* 4.1 7.4 - - - -
1034B ILE 3.3 0.2 - - - -
1035B VAL* 1.3 78.7 - - - +
1037B LEU* 1.3 73.0 + - + +
1038B MET 3.3 1.0 + - - -
1039B ARG* 3.4 20.5 + - - +
1040B GLU* 4.5 5.9 + - - +
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Residues in contact with LEU1037 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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998B LEU* 4.9 13.9 - - + +
1001B ILE* 5.1 19.8 - - + +
1002B ARG* 3.6 35.4 - - + +
1033B GLU* 2.9 43.5 + - + +
1034B ILE 5.1 0.2 - - - +
1036B THR* 1.3 83.0 - - + +
1038B MET* 1.3 60.7 + - - +
1039B ARG 3.3 0.6 + - - -
1040B GLU* 3.8 8.3 + - + +
1041B PHE* 3.3 40.8 - - + -
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Residues in contact with MET1038 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034B ILE 3.3 21.5 + - - +
1035B VAL* 3.3 13.7 - - - +
1037B LEU* 1.3 77.6 - - - +
1039B ARG* 1.3 71.7 + - - +
1040B GLU 3.3 0.9 + - - -
1041B PHE* 3.6 19.3 + - - +
1042B TRP* 4.0 12.8 + - + +
1052B ILE* 4.9 24.8 - - + +
1056B ILE* 6.5 0.9 - - + -
1073B GLN 4.8 3.6 - - - +
1074B LEU* 4.7 14.6 - - + -
1077B HIS* 3.7 42.0 - - + +
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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