Contacts of the strand formed by residues 178 - 184 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B ILE* 3.4 23.3 - - + -
86B MET* 4.1 14.6 - - - -
90B GLU* 4.2 26.0 - - + +
93B GLU* 4.1 8.6 + - + +
94B LEU* 3.8 21.4 - - + -
95B ASP* 3.4 23.4 + - - +
167B HIS* 4.1 13.9 - - + -
168B LEU 3.5 22.7 - - - +
169B THR* 3.7 18.6 - - + +
176B THR* 5.8 0.4 - - - +
177B SER* 1.3 78.0 - - - +
179B ARG* 1.3 66.9 + - - +
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Residues in contact with ARG 179 (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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95B ASP* 4.5 24.0 - - + -
97B PHE 5.8 2.7 - - - +
132B LEU 4.8 0.6 + - - -
133B ASP* 3.8 5.5 + - - -
134B ASN* 3.2 32.9 + - - +
135B ARG* 3.8 21.5 - - - +
167B HIS* 5.2 0.4 - - - -
168B LEU 3.3 22.8 + - - +
170B PHE* 3.0 56.4 - - + +
177B SER* 4.1 3.3 + - - +
178B ILE* 1.3 78.8 - - - +
180B ILE* 1.3 77.4 + - + +
181B ALA* 3.2 6.6 + - - +
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Residues in contact with ILE 180 (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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69B PHE* 4.3 9.0 - - + -
95B ASP 4.1 10.7 + - - +
96B PRO 4.3 5.6 - - - +
97B PHE 5.8 1.8 - - - +
98B LEU* 3.4 39.2 - - + +
112B PHE* 3.4 38.6 - - + -
134B ASN* 5.5 1.2 + - - -
141B TYR* 4.6 2.8 + - - -
165B LEU* 3.5 25.4 - - + -
166B GLN* 3.4 15.9 - - - +
167B HIS* 3.5 24.7 - - + +
179B ARG* 1.3 85.9 + - + +
181B ALA* 1.3 62.0 + - - +
182B PRO* 4.4 2.8 - - - +
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Residues in contact with ALA 181 (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 LEU 3.4 15.5 - - - +
165B LEU* 4.1 2.9 - - - -
166B GLN 3.0 20.8 + - - +
168B LEU* 4.3 13.0 - - + -
170B PHE* 3.4 35.7 - - + -
179B ARG* 3.2 3.7 + - - +
180B ILE* 1.3 73.9 - - - +
182B PRO* 1.3 72.4 - - + +
183B HIS* 3.1 13.7 - - - -
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Residues in contact with PRO 182 (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 LEU* 3.0 52.2 + - + +
134B ASN* 5.2 2.2 - - - +
141B TYR* 3.3 40.8 - - + +
149B PHE* 3.4 20.6 - - + -
163B TYR* 5.3 0.7 - - + -
164B CYS 3.9 0.2 - - - +
165B LEU* 3.2 25.6 - - + -
180B ILE 4.4 0.2 - - - +
181B ALA* 1.3 86.5 - - + +
183B HIS* 1.3 68.8 + - - +
184B ASN* 4.5 0.9 - - - +
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Residues in contact with HIS 183 (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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70B CYS* 4.6 1.8 - - - -
77B MET* 3.1 41.2 - - + +
80B GLY* 4.6 4.4 - - - -
125B PRO* 4.7 3.8 - - - +
129B MET* 4.0 33.7 + - + +
130B PHE 3.7 4.7 - - - -
131B TYR* 3.4 16.4 + + + +
163B TYR* 3.6 5.9 - - - -
164B CYS* 3.1 33.5 + - - +
166B GLN* 4.6 6.8 - - + +
168B LEU* 3.1 30.7 - - + +
181B ALA 3.1 17.7 + - - -
182B PRO* 1.3 91.8 - - - +
184B ASN* 1.3 66.4 + - - +
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Residues in contact with ASN 184 (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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126B CYS* 4.5 0.7 - - - -
129B MET* 3.7 4.6 - - - +
130B PHE* 3.1 54.7 + - + -
132B LEU* 4.1 7.5 - - - +
149B PHE* 3.6 16.3 - - - -
151B ARG* 2.8 44.7 - - - +
158B LEU* 3.1 27.7 - - + +
162B GLU 4.4 3.8 - - - -
163B TYR* 4.0 3.6 - - - +
182B PRO 4.3 0.2 - - - -
183B HIS* 1.3 82.7 + - - +
185B 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