Contacts of the helix formed by residues 127 - 135 (chain F) in PDB entry 5ZX2
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 SER 127 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046C THR* 3.6 10.1 - - - -
1047C GLY* 3.4 39.2 + - - -
1049C TYR* 4.2 0.2 - - - -
125F LEU 3.8 2.6 + - - -
126F ARG* 1.3 77.1 - - - +
128F ALA* 1.3 66.5 + - - +
129F GLU* 3.7 9.5 + - - +
130F VAL* 3.2 35.9 + - - +
131F GLU* 3.2 12.8 + - - +
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Residues in contact with ALA 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046C THR* 4.1 11.3 - - + -
1049C TYR* 3.5 28.3 + - - +
1099C ARG* 3.7 39.0 - - + +
1100C VAL* 4.0 12.3 - - + +
1103C TYR* 4.7 2.7 - - + -
127F SER* 1.3 73.7 - - - +
129F GLU* 1.3 55.8 + - - +
131F GLU* 3.8 1.8 - - - +
132F ALA* 2.9 31.8 + - - +
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Residues in contact with GLU 129 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1045C SER* 5.1 1.1 + - - -
1046C THR* 3.4 20.5 + - - +
1103C TYR* 2.3 50.1 + - + +
453D LYS* 2.7 35.9 + - - +
457D MET* 3.6 8.7 - - - +
473D LYS* 3.4 24.2 - - - +
127F SER* 3.0 8.2 + - - +
128F ALA* 1.3 75.9 - - - +
130F VAL* 1.3 65.7 + - - +
132F ALA* 3.2 2.1 + - - +
133F LEU* 2.9 35.3 + - + +
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Residues in contact with VAL 130 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473D LYS* 4.9 15.3 - - - +
126F ARG* 3.7 32.8 - - + +
127F SER* 3.2 27.6 + - - +
129F GLU* 1.3 76.0 - - - +
131F GLU* 1.3 65.3 + - - +
133F LEU* 3.2 6.0 + - - +
134F GLU* 2.9 28.1 + - + +
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Residues in contact with GLU 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100C VAL* 3.8 23.9 - - + +
126F ARG* 3.1 58.3 + - - +
127F SER 3.2 8.3 + - - +
128F ALA* 3.8 7.6 - - - +
130F VAL* 1.3 78.3 - - - +
132F ALA* 1.3 61.9 + - - +
134F GLU* 4.1 3.1 - - - +
135F ALA* 3.2 24.6 + - - +
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Residues in contact with ALA 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100C VAL* 3.8 28.0 - - + +
1103C TYR* 4.2 11.2 - - + -
1104C GLU* 4.1 22.3 - - + +
128F ALA 2.9 19.0 + - - +
129F GLU 3.2 4.0 + - - +
131F GLU* 1.3 77.8 - - - +
133F LEU* 1.3 64.6 + - + +
135F ALA* 3.5 6.4 + - - +
136F LEU* 3.4 23.2 + - - +
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Residues in contact with LEU 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1103C TYR* 4.8 11.4 - - + -
1107C VAL* 4.9 3.8 - - + -
457D MET* 4.6 4.3 - - + -
469D ILE* 3.9 31.4 - - + -
470D LYS* 4.1 34.1 + - + -
473D LYS* 3.6 37.2 - - + -
129F GLU* 2.9 28.1 + - + +
130F VAL* 3.9 4.7 - - - +
132F ALA* 1.3 76.9 - - + +
134F GLU* 1.3 66.6 + - - +
136F LEU* 3.0 29.1 + - + +
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Residues in contact with GLU 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813C GLU 5.7 0.3 - - - +
815C THR* 3.3 34.9 - - + +
817C GLU* 5.5 5.0 - - - +
1161C ASN* 5.3 1.0 + - - -
470D LYS* 5.2 6.5 - - - +
126F ARG* 2.4 37.4 + - - +
130F VAL* 2.9 19.6 + - + +
131F GLU* 4.1 3.5 - - - +
133F LEU* 1.3 76.0 - - - +
135F ALA* 1.3 61.4 + - - +
136F LEU 3.2 9.0 + - - +
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Residues in contact with ALA 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100C VAL* 5.7 3.1 - - + -
1104C GLU* 5.0 9.0 - - - +
1154C ASP* 5.4 7.9 - - - +
1157C ARG* 3.8 23.8 - - - +
1161C ASN* 3.2 16.1 + - - +
131F GLU 3.2 19.7 + - - +
132F ALA* 3.8 7.6 - - - +
133F LEU 3.2 0.4 - - - -
134F GLU* 1.3 73.9 - - - +
136F LEU* 1.3 64.2 + - - +
137F PRO* 3.7 1.2 - - - +
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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