Contacts of the strand formed by residues 127 - 133 (chain D) in PDB entry 5ZR1
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 PHE 127 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90D ILE* 3.9 24.9 - - + -
116D LEU* 4.1 41.7 - - + -
119D LEU* 3.9 12.1 - - + -
120D GLN* 4.3 10.3 - - + -
123D TYR 3.2 25.1 - - - -
124D LYS* 3.8 14.2 - - + +
125D GLU 3.4 0.8 - - - -
126D GLN* 1.3 79.8 - - - +
128D ILE* 1.3 64.8 + - - +
129D THR* 4.3 13.7 - - + -
153D GLN* 5.3 0.5 - - - +
157D ILE* 3.8 8.2 - - - +
210D ILE* 4.4 0.9 - - - -
211D THR* 3.2 25.6 - - + +
213D VAL* 3.7 22.4 - - + -
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Residues in contact with ILE 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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410A LEU* 4.9 1.8 - - + -
127D PHE* 1.3 74.1 - - - +
129D THR* 1.3 60.7 + - - +
130D ILE* 4.5 4.5 - - + -
150D LEU* 3.7 30.1 - - + +
153D GLN* 3.7 39.7 - - + +
154D LEU* 4.1 23.6 - - + -
157D ILE* 3.7 23.6 - - + -
210D ILE* 4.0 7.1 - - + +
211D THR 3.3 2.9 + - - +
212D VAL* 3.8 28.5 - - + -
213D VAL* 3.2 27.9 + - - +
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Residues in contact with THR 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D LEU* 4.0 15.8 - - + +
127D PHE* 4.3 13.0 - - + -
128D ILE* 1.3 77.2 - - - +
130D ILE* 1.3 69.1 + - - +
131D ARG* 4.3 14.2 + - - +
149D GLN* 4.5 2.8 - - - +
153D GLN* 3.4 36.3 + - - +
213D VAL* 3.5 18.8 + - - +
215D ILE* 4.2 6.4 - - - +
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Residues in contact with ILE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ILE* 4.5 6.5 - - + -
129D THR* 1.3 82.4 + - - +
131D ARG* 1.3 64.6 + - - +
132D LEU* 4.7 3.1 - - + -
146D ILE* 4.3 18.8 - - + +
149D GLN* 3.3 46.0 - - + +
150D LEU* 3.7 17.5 - - + +
153D GLN* 4.7 0.2 - - + -
212D VAL* 3.9 24.2 - - + -
213D VAL 2.8 9.9 + - - +
214D PHE* 3.7 32.3 - - + -
215D ILE* 2.9 24.4 + - - +
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Residues in contact with ARG 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D THR* 5.1 6.5 - - - +
113D ASP* 3.0 30.7 + - - -
116D LEU* 3.9 23.8 - - - +
129D THR* 4.2 14.3 + - - +
130D ILE* 1.3 75.9 - - - +
132D LEU* 1.3 66.1 + - - +
149D GLN* 3.0 34.3 + - - +
215D ILE* 3.4 32.8 - - + +
217D ASP* 5.9 3.8 - - - +
154E GLU* 3.5 22.2 + - - +
155E LEU* 3.6 18.1 - - + +
158E LYS* 3.1 25.3 - - - +
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Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ILE* 4.7 5.4 - - + -
131D ARG* 1.3 82.7 - - - +
133D ASN* 1.3 64.7 + - - +
137D HIS* 3.5 32.8 - - + +
142D ALA* 3.7 22.0 - - + +
145D GLY* 4.1 22.2 - - - +
146D ILE* 3.7 26.5 - - + +
149D GLN* 4.8 1.1 - - - +
215D ILE 2.8 16.6 + - - +
216D PHE* 3.5 37.6 - - + -
217D ASP* 3.4 16.3 + - - +
222D PHE* 4.4 5.8 - - + -
230D LEU* 4.5 1.1 - - + -
155E LEU* 4.8 2.2 - - - +
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Residues in contact with ASN 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LEU* 1.3 80.2 - - - +
134D GLY* 1.3 61.8 + - - +
135D PHE* 3.1 22.5 + - - +
136D ILE* 3.4 6.1 + - + +
137D HIS* 3.1 38.5 + - + +
217D ASP* 3.0 36.8 + - + +
218D GLU* 4.2 0.2 - - - +
222D PHE* 4.4 2.2 - - - -
151E LYS* 3.3 34.6 - - - +
154E GLU* 4.6 0.8 + - - -
155E LEU* 3.5 26.6 - - + +
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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