Contacts of the helix formed by residues 132 - 138 (chain B) in PDB entry 5Z7R
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 GLN 132 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B GLY 4.0 1.5 - - - +
113B CYS* 3.3 29.5 - - - +
114B GLU* 3.8 16.1 - - - +
117B MET* 3.3 23.4 - - - +
131B GLY* 1.3 74.3 - - - -
133B PRO* 1.3 63.0 - - - +
134B GLU* 3.1 33.6 + - - +
135B VAL 4.6 0.9 + - - -
141B PRO* 3.9 10.3 - - + +
145B GLY* 4.4 3.3 - - - -
149B LEU* 4.4 10.5 - - + +
161B LEU* 3.9 11.5 + - + +
162B ILE* 4.0 33.7 - - + +
165B ALA* 3.3 21.3 - - - +
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Residues in contact with PRO 133 (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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109B LEU* 4.4 13.5 - - + -
110B GLY* 3.6 22.9 - - - +
131B GLY 3.9 2.0 - - - +
132B GLN* 1.3 83.9 - - - +
134B GLU* 1.3 70.2 + - + +
135B VAL 3.1 2.5 - - - -
136B GLY* 2.9 19.6 + - - -
137B LEU* 3.8 19.0 + - + +
165B ALA* 3.7 19.9 - - + +
167B ASN* 5.7 3.8 - - - +
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Residues in contact with GLU 134 (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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110B GLY* 3.0 32.1 - - - -
111B GLY 3.7 1.2 + - - -
114B GLU* 3.5 8.1 - - - +
132B GLN* 3.1 38.3 + - - +
133B PRO* 1.3 72.7 - - + +
135B VAL* 1.3 57.5 + - - +
137B LEU* 3.0 23.5 + - + +
139B ILE* 2.8 47.5 + - + +
140B THR 3.5 21.5 - - - +
141B PRO* 3.7 11.2 - - + +
142B GLY 4.7 1.2 + - - +
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Residues in contact with VAL 135 (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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132B GLN 4.6 0.8 + - - -
133B PRO 2.9 1.8 + - - -
134B GLU* 1.3 78.0 - - - +
136B GLY* 1.3 59.5 + - - +
137B LEU 3.2 0.7 - - - -
138B GLY 3.5 0.6 + - - -
139B ILE 3.2 8.0 + - - +
141B PRO* 5.5 1.3 - - + +
162B ILE* 3.5 26.2 - - + +
163B PHE* 3.7 3.8 - - - +
165B ALA* 4.1 6.1 - - + -
202C ASN* 3.5 28.5 - - + +
203C ALA* 3.0 35.9 + - - +
206C ALA* 3.4 14.6 - - + +
207C VAL* 3.3 43.1 - - + +
210C SER* 4.2 5.8 - - - +
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Residues in contact with GLY 136 (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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133B PRO 2.9 9.8 + - - -
135B VAL* 1.3 83.2 - - - +
137B LEU* 1.3 64.7 + - - +
138B GLY 3.4 2.2 - - - -
165B ALA* 4.5 1.7 - - - +
202C ASN* 3.2 19.5 + - - -
203C ALA* 4.7 2.9 - - - -
245C ALA* 3.6 13.0 - - - +
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Residues in contact with LEU 137 (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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68B ILE* 3.8 31.9 - - + -
133B PRO* 4.1 19.3 - - + +
134B GLU* 3.0 20.0 + - + +
136B GLY* 1.3 84.8 - - - +
138B GLY* 1.3 61.3 + - - +
139B ILE* 3.4 10.9 + - + -
242C GLN* 3.7 13.2 - - - +
245C ALA* 3.6 19.9 - - - +
246C MET* 3.7 18.0 - - + +
249C PHE* 4.3 34.8 - - + -
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Residues in contact with GLY 138 (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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134B GLU 3.3 0.8 + - - -
135B VAL 3.5 2.2 + - - -
136B GLY 3.4 4.0 - - - -
137B LEU* 1.3 80.6 - - - +
139B ILE* 1.3 63.1 + - - +
203C ALA* 3.4 24.5 - - - +
205C VAL* 6.0 1.0 - - - +
206C ALA* 3.6 9.7 + - - +
236C CYS* 3.5 13.0 - - - +
239C THR* 4.2 3.8 + - - -
241C ASP* 4.3 2.0 - - - +
242C GLN* 3.6 21.1 - - - +
245C ALA* 4.2 0.4 - - - +
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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