Contacts of the helix formed by residues 131 - 139 (chain A) in PDB entry 1ZEB
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 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A LEU* 3.3 15.0 - - - -
101A CYS* 3.7 4.5 - - - -
129A VAL 3.8 2.6 + - - -
130A ILE* 1.3 75.7 - - - +
132A VAL* 1.3 62.9 + - - +
133A MET* 3.2 4.9 + - - +
134A ASN* 2.9 19.6 + - - +
135A ARG* 3.0 24.1 + - - +
158A GLY 3.7 18.2 - - - -
159A THR* 2.6 32.0 + - - -
160A TYR* 5.4 0.2 - - - -
162A HIS* 5.0 1.6 + - - -
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Residues in contact with VAL 132 (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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36A LEU* 4.0 15.5 - - + -
99A TYR 5.0 0.7 - - - +
100A LEU* 2.8 27.8 + - - +
131A SER* 1.3 72.8 - - - +
133A MET* 1.3 51.7 + - - +
135A ARG* 3.2 24.8 + - - +
136A ALA* 2.7 32.4 + - - +
307A PHE* 3.6 26.7 - - + -
459A ALA* 3.6 34.3 - - + +
462A MET* 4.4 4.9 - - + -
463A ALA* 4.3 11.4 - - + +
468A LEU* 4.1 8.4 - - + +
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Residues in contact with MET 133 (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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131A SER* 3.2 7.9 + - - +
132A VAL* 1.3 75.4 - - - +
134A ASN* 1.3 66.3 + - - +
136A ALA* 3.2 2.9 + - - +
137A LYS* 2.9 19.9 + - - +
143A VAL* 3.5 24.4 - - + +
144A GLY 4.0 5.2 - - - +
145A VAL* 3.7 22.0 - - + -
159A THR* 3.3 45.8 - - - +
194A MET* 3.8 20.8 - - + +
196A ILE* 4.1 14.6 - - + -
307A PHE* 3.4 44.4 - - + -
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Residues in contact with ASN 134 (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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130A ILE* 3.1 23.0 - - + +
131A SER* 2.9 22.4 + - - +
133A MET* 1.3 75.3 - - - +
135A ARG* 1.3 57.0 + - - +
137A LYS* 3.2 5.2 + - - +
138A LYS* 2.6 66.3 + - - +
159A THR 4.7 0.4 - - - +
160A TYR* 5.8 0.8 - - - +
162A HIS* 5.8 2.6 - - - -
193A ASN* 4.9 3.5 - - - +
194A MET* 3.7 36.1 - - - +
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Residues in contact with ARG 135 (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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101A CYS 3.1 24.5 + - - -
130A ILE* 2.7 43.1 + - + +
131A SER 3.0 6.5 + - - +
132A VAL* 3.4 29.0 - - - +
133A MET 3.2 0.2 - - - -
134A ASN* 1.3 80.8 - - - +
136A ALA* 1.3 60.9 + - - +
138A LYS* 3.4 12.2 + - + +
139A ALA* 3.1 22.5 + - - +
459A ALA* 5.1 1.8 + - - +
460A HIS* 6.0 4.2 - - - +
463A ALA* 3.9 12.9 - - - +
468A LEU* 4.0 6.9 - - + +
469A GLU* 2.9 49.2 - - + +
470A PRO* 3.9 8.4 - - - +
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Residues in contact with ALA 136 (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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36A LEU* 5.3 0.4 - - + -
132A VAL 2.7 19.9 + - - +
133A MET 3.2 5.6 + - - +
135A ARG* 1.3 70.3 - - - +
137A LYS* 1.3 63.8 + - - +
139A ALA* 3.2 9.0 + - - +
140A GLY 3.4 0.2 + - - -
141A LYS* 3.1 35.2 + - + +
143A VAL* 4.2 2.9 - - + -
307A PHE* 3.8 26.9 - - + -
468A LEU* 3.8 22.1 - - + +
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Residues in contact with LYS 137 (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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133A MET 2.9 13.1 + - - +
134A ASN 3.4 8.3 - - - +
136A ALA* 1.3 76.3 - - - +
138A LYS* 1.3 59.6 + - + +
140A GLY* 2.9 20.5 + - - -
141A LYS 3.5 20.7 + - - +
142A SER* 4.4 0.6 - - - +
143A VAL* 3.9 6.8 - - + +
194A MET* 3.8 14.8 - - + -
195A ASP* 2.7 56.5 + - + +
197A ASP* 2.8 31.6 + - - -
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Residues in contact with LYS 138 (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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130A ILE* 4.0 14.8 - - - +
134A ASN* 2.6 49.3 + - - +
135A ARG* 3.6 15.7 - - + +
136A ALA 3.3 0.2 - - - -
137A LYS* 1.3 79.0 - - + +
139A ALA* 1.3 56.3 + - - +
140A GLY 3.4 3.1 + - - -
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Residues in contact with ALA 139 (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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135A ARG 3.1 6.5 + - - +
136A ALA 3.6 5.4 - - - +
137A LYS 3.1 1.6 - - - -
138A LYS* 1.3 77.4 - - - +
140A GLY* 1.3 57.7 + - - +
141A LYS* 3.4 8.6 + - + +
304A ARG* 4.3 12.7 + - - +
468A LEU* 3.5 31.2 - - + -
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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