Contacts of the strand formed by residues 178 - 184 (chain D) in PDB entry 2PZX
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 ILE 178 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D ILE* 3.4 23.3 - - + -
86D MET* 4.1 14.8 - - - -
90D GLU* 4.2 26.0 - - + +
93D GLU* 4.1 8.0 + - + +
94D LEU* 3.8 21.5 - - + -
95D ASP* 3.4 23.7 + - - +
167D HIS* 4.1 14.1 - - + -
168D LEU 3.5 22.4 - - - +
169D THR* 3.7 18.2 - - + +
176D THR* 5.8 0.4 - - - +
177D SER* 1.3 77.6 - - - +
179D ARG* 1.3 66.0 + - - +
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Residues in contact with ARG 179 (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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95D ASP* 4.5 24.0 - - + -
97D PHE 5.8 2.7 - - - +
132D LEU 4.8 0.8 + - - -
133D ASP* 3.8 5.5 + - - -
134D ASN* 3.2 33.5 + - - +
135D ARG* 3.8 21.5 - - - +
167D HIS* 5.2 0.4 - - - -
168D LEU 3.3 22.8 + - - +
170D PHE* 3.0 56.4 - - + +
177D SER* 4.1 3.5 + - - +
178D ILE* 1.3 78.6 - - - +
180D ILE* 1.3 78.6 + - - +
181D ALA* 3.2 6.5 + - - +
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Residues in contact with ILE 180 (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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69D PHE* 4.3 9.0 - - + -
95D ASP 4.1 10.9 + - - +
96D PRO 4.3 5.6 - - - +
97D PHE 5.8 1.8 - - - +
98D LEU* 3.4 39.4 - - + +
112D PHE* 3.4 39.0 - - + -
134D ASN* 5.5 1.0 + - - -
141D TYR* 4.6 2.9 + - - -
165D LEU* 3.5 25.1 - - + -
166D GLN* 3.4 16.2 - - - +
167D HIS* 3.5 24.9 - - + +
179D ARG* 1.3 85.3 + - - +
181D ALA* 1.3 61.6 + - - +
182D PRO* 4.4 2.8 - - - +
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Residues in contact with ALA 181 (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 3.4 15.3 - - - +
165D LEU* 4.1 3.1 - - - -
166D GLN 3.0 21.2 + - - +
168D LEU* 4.3 13.0 - - + -
170D PHE* 3.4 35.4 - - + -
179D ARG* 3.2 3.7 + - - +
180D ILE* 1.3 74.1 - - - +
182D PRO* 1.3 72.6 - - + +
183D HIS* 3.1 13.5 - - - -
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Residues in contact with PRO 182 (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* 3.0 52.1 + - + +
134D ASN* 5.2 2.2 - - - +
141D TYR* 3.3 41.3 - - + +
149D PHE* 3.4 20.4 - - + -
163D TYR* 5.3 0.7 - - + -
164D CYS 3.9 0.2 - - - +
165D LEU* 3.2 25.8 - - + -
180D ILE 4.4 0.2 - - - +
181D ALA* 1.3 85.9 - - + +
183D HIS* 1.3 69.4 + - - +
184D ASN* 4.5 0.7 - - - +
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Residues in contact with HIS 183 (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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70D CYS* 4.6 1.8 - - - -
77D MET* 3.1 40.8 - - + +
80D GLY* 4.6 4.6 - - - -
125D PRO* 4.7 3.8 - - - +
129D MET* 4.0 33.7 + - + +
130D PHE 3.7 4.5 - - - -
131D TYR* 3.4 16.4 + + + +
162D GLU 4.3 0.2 - - - +
163D TYR* 3.6 5.7 - - - -
164D CYS* 3.1 34.1 + - - +
166D GLN* 4.6 7.0 - - + +
168D LEU* 3.1 30.5 - - + +
181D ALA 3.1 17.7 + - - -
182D PRO* 1.3 91.8 - - - +
184D ASN* 1.3 66.0 + - - +
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Residues in contact with ASN 184 (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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126D CYS* 4.5 0.7 - - - -
129D MET* 3.7 4.6 - - - +
130D PHE* 3.1 53.7 + - + -
132D LEU* 4.1 7.5 - - - +
149D PHE* 3.6 16.1 - - - -
151D ARG* 2.8 44.1 - - - +
158D LEU* 3.1 28.4 - - + +
162D GLU 4.4 4.0 - - - -
163D TYR* 4.0 3.8 - - - +
182D PRO 4.3 0.2 - - - -
183D HIS* 1.3 82.9 + - - +
185D CYS* 1.3 64.0 + - - +
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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