Contacts of the strand formed by residues 130 - 137 (chain A) in PDB entry 2IZW
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 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A THR 5.2 0.5 - - - +
129A ASN* 1.3 77.9 - - - +
131A GLU* 1.3 62.5 + - - +
161A PRO* 3.8 5.2 - - - +
162A ILE* 3.0 22.0 + - - +
163A TRP* 5.5 0.3 - - - -
206A GLN* 3.0 32.3 - - - -
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Residues in contact with GLU 131 (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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130A GLY* 1.3 75.7 - - - +
132A VAL* 1.3 62.9 + - - +
148A ILE* 4.0 29.9 - - + +
152A MET* 3.7 19.5 - - - +
159A TRP* 5.4 0.9 - - - -
160A GLY* 3.4 19.0 + - - +
161A PRO* 4.6 1.1 - - + -
162A ILE* 3.1 11.8 - - - +
205A ALA* 3.3 4.5 - - - +
206A GLN* 3.1 38.8 + - + +
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Residues in contact with VAL 132 (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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120A TRP* 3.6 66.2 - - + +
131A GLU* 1.3 82.0 - - - +
133A ALA* 1.3 66.3 + - - +
134A MET* 6.0 2.9 - - + -
148A ILE* 4.2 1.1 - - - -
159A TRP* 3.3 26.6 - - - +
160A GLY 3.1 18.2 + - - +
161A PRO 4.6 0.7 - - - +
162A ILE* 4.2 8.7 - - + -
164A SER 5.6 0.2 - - - +
166A THR* 5.0 3.4 - - + -
204A ALA 3.5 6.3 - - - +
205A ALA* 3.8 16.8 - - + -
214A LEU* 5.6 0.2 - - + -
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Residues in contact with ALA 133 (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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132A VAL* 1.3 80.8 - - - +
134A MET* 1.3 66.9 + - - +
148A ILE* 3.8 32.1 - - + +
151A LEU* 3.7 17.7 - - + -
152A MET* 4.7 3.1 - - + -
158A THR 3.2 12.3 - - - +
159A TRP* 4.3 4.0 - - + +
203A TRP* 3.1 24.3 - - - +
204A ALA 3.0 9.9 + - - +
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Residues in contact with MET 134 (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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118A PHE* 3.4 35.7 - - + +
119A THR* 4.3 21.8 - - - +
120A TRP* 4.6 7.9 - - + -
132A VAL* 6.0 2.9 - - + -
133A ALA* 1.3 81.0 - - - +
135A ALA* 1.3 61.5 + - - +
151A LEU* 4.1 4.6 - - - +
156A GLY 3.9 0.3 - - - +
157A GLY* 3.0 7.1 - - - -
158A THR* 3.0 38.1 + - - +
166A THR* 5.4 6.1 - - - -
170A LEU* 3.9 11.4 - - + -
201A ILE* 3.6 13.2 - - + -
202A ALA 3.2 8.7 - - - +
203A TRP* 4.1 12.3 - - + -
217A ILE* 3.6 27.1 - - + -
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Residues in contact with ALA 135 (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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134A MET* 1.3 78.6 - - - +
136A MET* 1.3 62.0 + - - +
151A LEU* 3.6 32.1 - - + +
154A THR* 3.6 22.7 - - + +
155A ARG 3.8 8.3 - - - +
157A GLY* 4.3 0.7 - - - +
170A LEU* 3.7 13.3 - - - +
201A ILE* 3.6 5.4 - - - -
202A ALA* 3.0 29.1 + - + +
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Residues in contact with MET 136 (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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118A PHE* 5.1 1.1 - - - -
135A ALA* 1.3 74.6 - - - +
137A LEU* 1.3 69.1 + - - +
138A TYR* 3.1 51.2 - - + +
154A THR* 3.7 10.2 - - - +
155A ARG* 3.2 32.5 + - - +
170A LEU* 3.9 16.6 - - + -
171A SER 3.7 11.7 - - - +
172A TYR* 3.7 15.3 - - + -
199A PHE* 3.2 38.1 - - + -
200A GLN 3.5 1.3 - - - +
201A ILE* 4.0 17.5 - - + -
109B SER* 4.8 1.4 + - - -
228B PRO 5.2 0.2 - - - +
229B VAL* 5.5 0.2 - - - +
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Residues in contact with LEU 137 (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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87A THR* 5.5 3.1 - - - +
135A ALA* 5.6 0.4 - - + -
136A MET* 1.3 83.3 - - - +
138A TYR* 1.3 65.9 + - - +
139A ASP 3.6 2.5 - - - +
142A ASP* 3.6 30.7 - - + +
146A ILE* 4.8 4.9 - - + -
151A LEU* 5.8 0.2 - - + -
154A THR* 4.2 15.7 - - + -
199A PHE* 3.3 6.9 - - - +
200A GLN* 2.8 50.6 + - + +
202A ALA* 3.9 26.0 - - + -
109B SER* 5.2 1.8 - - - +
229B VAL* 4.3 11.4 - - + -
233B ILE* 3.8 32.1 - - + -
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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