Contacts of the strand formed by residues 163 - 170 (chain A) in PDB entry 2PZI
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 GLY 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A SER 5.3 7.0 - - - -
159A HIS* 3.5 15.6 - - - -
160A GLY* 2.9 31.4 + - - -
161A GLY 3.3 2.0 + - - -
162A LEU* 1.3 80.3 + - - +
164A TRP* 1.3 67.5 - - - -
165A ILE* 3.8 6.5 + - - +
181A LYS* 5.8 0.2 - - - -
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Residues in contact with TRP 164 (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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93A MET* 4.0 22.9 - - + -
96A PRO* 3.6 15.3 - - + -
97A VAL* 3.4 38.8 - - - -
98A VAL* 3.7 18.8 - - + -
136A SER 5.6 0.9 - - - -
137A PHE 3.0 23.7 + - - -
138A LEU 3.7 4.9 - - - -
139A PRO* 3.5 29.1 - - + +
156A CYS* 3.6 19.7 - - + -
158A ALA 3.2 24.2 - - - -
159A HIS* 3.5 26.4 - + + -
162A LEU 5.0 0.7 - - - +
163A GLY* 1.3 75.5 - - - +
165A ILE* 1.3 63.4 + - - +
166A TYR* 3.3 43.1 + - + +
180A LEU 4.2 1.7 - - - +
181A LYS* 4.5 5.4 - - - +
182A GLY 5.0 1.0 + - - -
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Residues in contact with ILE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A CYS* 3.2 5.5 - - - -
157A ILE* 2.9 40.3 + - + -
158A ALA* 2.7 39.1 + - + +
159A HIS* 4.2 3.1 - - - +
160A GLY* 5.1 2.5 - - - +
163A GLY 3.9 8.3 - - - +
164A TRP* 1.3 76.1 - - - +
166A TYR* 1.3 60.3 + - - +
179A VAL* 3.2 33.2 - - + -
180A LEU 3.8 3.4 - - - +
181A LYS* 3.7 38.6 - - + +
753A AXX 3.9 26.7 - - + -
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Residues in contact with TYR 166 (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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138A LEU 4.6 0.2 + - - -
139A PRO* 3.6 4.7 - - + +
140A GLN* 2.7 34.2 + - + +
141A LEU* 3.5 55.2 - - + -
153A VAL* 4.7 6.7 - - + -
155A GLY 3.2 9.9 - - - +
156A CYS* 3.8 17.0 - - - -
157A ILE* 4.8 1.6 - - - -
164A TRP* 3.3 36.5 + - + +
165A ILE* 1.3 73.9 - - - +
167A LEU* 1.3 62.2 + - - +
179A VAL* 3.2 11.4 - - - +
180A LEU* 2.9 53.7 + - + +
181A LYS* 5.2 1.3 - - - -
229A TYR* 4.1 13.9 - + - -
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Residues in contact with LEU 167 (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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88A PRO* 3.8 31.2 - - + +
89A LEU 4.8 0.2 - - - +
92A LEU* 3.8 27.6 - - + -
153A VAL* 3.6 3.5 - - - +
154A LYS* 2.9 36.2 + - + -
155A GLY 2.8 10.2 + - - +
157A ILE* 3.9 16.5 - - + +
165A ILE 4.2 0.6 + - - -
166A TYR* 1.3 72.0 - - - +
168A ALA* 1.3 64.6 + - - +
169A LEU* 5.0 5.2 - - + -
177A PRO* 4.0 17.7 - - + -
178A VAL 3.6 11.9 - - - +
179A VAL* 4.6 2.2 - - + -
234A TYR* 3.8 31.4 - - + -
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Residues in contact with ALA 168 (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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151A TYR* 3.9 15.7 - - + -
152A GLU 3.1 19.1 - - - +
153A VAL* 4.1 7.2 - - + -
154A LYS* 4.7 0.4 - - - -
166A TYR* 3.9 0.6 + - + -
167A LEU* 1.3 76.5 - - - +
169A LEU* 1.3 65.6 - - - +
177A PRO* 3.4 5.4 - - - +
178A VAL* 2.8 36.1 + - + -
180A LEU* 3.8 26.0 - - + -
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Residues in contact with LEU 169 (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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88A PRO* 5.7 2.2 - - + -
150A GLN 3.5 1.7 - - - +
151A TYR* 3.6 0.6 - - - -
152A GLU* 2.8 52.4 + - - +
154A LYS* 3.6 32.5 - - + +
167A LEU* 5.0 7.0 - - + -
168A ALA* 1.3 81.1 - - - +
170A ASP* 1.3 62.9 - - - +
171A ARG 3.5 2.6 + - - -
175A GLY* 3.2 25.6 - - - +
176A ARG 3.6 0.7 - - - -
177A PRO* 4.0 17.0 - - + -
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Residues in contact with ASP 170 (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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150A GLN* 3.0 29.6 + - - +
151A TYR* 3.7 20.4 + - + -
168A ALA 3.9 0.8 + - - -
169A LEU* 1.3 69.3 - - - +
171A ARG* 1.3 59.1 + - - +
172A ASN* 3.0 8.8 + - - -
173A VAL* 3.4 11.9 + - - +
175A GLY* 2.6 30.7 + - - -
176A ARG* 2.7 58.1 + - + +
178A VAL* 3.8 10.7 - - + +
214A PHE* 5.5 0.9 - - - +
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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