Contacts of the strand formed by residues 201 - 207 (chain A) in PDB entry 1I43
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 VAL 201 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A HIS* 4.1 13.2 - - + +
157A VAL* 3.5 36.3 - - + -
192A LEU* 6.3 0.2 - - + -
195A ALA 3.7 22.0 - - - +
196A LEU* 3.7 29.1 + - + +
199A LYS 3.4 1.6 + - - +
200A LYS* 1.3 79.4 - - - +
202A ASN* 1.3 63.7 + - - +
203A LEU 3.6 19.5 - - - +
204A PHE* 4.4 2.5 - - + +
229A LYS 4.7 4.1 + - - +
230A GLY 4.5 2.8 - - - +
231A ALA* 3.7 26.0 + - + +
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Residues in contact with ASN 202 (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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149A LEU 5.5 1.1 + - - +
150A VAL* 4.5 9.0 - - + -
151A PRO* 3.8 29.7 - - + +
154A GLY* 3.1 11.7 - - - -
155A HIS 2.9 39.2 + - - +
200A LYS* 4.0 17.2 - - - +
201A VAL* 1.3 75.0 - - - +
203A LEU* 1.3 65.8 + - + +
230A GLY 4.5 2.5 - - - +
231A ALA* 3.8 1.7 - - - -
232A LEU* 3.1 24.3 + - - +
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Residues in contact with LEU 203 (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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145A MET* 3.7 32.5 - - + -
146A LEU* 4.1 0.9 - - + -
149A LEU* 4.5 16.2 - - + -
150A VAL* 4.1 10.8 - - + -
155A HIS 3.8 1.2 + - - -
156A ILE* 3.3 38.5 - - + +
157A VAL 3.1 21.5 + - - -
201A VAL* 3.6 5.9 - - - +
202A ASN* 1.3 83.1 - - + +
204A PHE* 1.3 63.2 + - - +
205A PHE* 3.9 10.3 - - + -
232A LEU* 3.2 28.7 - - + +
233A VAL 4.8 0.4 - - - +
234A CYS* 4.1 16.6 - - + +
254A LEU* 5.0 2.2 - - + -
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Residues in contact with PHE 204 (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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157A VAL* 3.1 48.9 - - + -
158A THR* 4.1 15.0 - - - -
159A THR* 4.3 7.4 - - + -
184A ILE* 4.5 8.5 - - + -
186A PRO 6.1 0.2 - - - -
192A LEU* 3.8 14.4 - - + -
201A VAL* 4.4 2.8 - - + +
203A LEU* 1.3 71.6 - - - +
205A PHE* 1.3 60.4 + - - +
206A THR* 3.4 30.5 - - + -
217A VAL* 4.6 5.4 - - + -
222A VAL* 3.3 41.7 - - + -
226A CYS* 3.6 22.0 - - - -
232A LEU 2.5 10.3 + - - +
233A VAL* 3.4 8.1 - - + -
234A CYS 2.9 27.2 + - - +
235A ILE* 5.2 0.4 - - + -
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Residues in contact with PHE 205 (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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142A SER* 4.7 8.3 - - - -
145A MET* 4.4 10.1 - - + -
146A LEU* 5.1 6.3 - - + -
156A ILE* 4.6 2.9 - - + -
157A VAL 2.8 8.9 + - - -
158A THR* 2.9 46.3 - - + +
162A CYS* 4.0 12.8 - - - -
166A THR* 3.9 29.4 - - + -
170A ILE* 4.9 3.4 - - + -
203A LEU* 3.8 18.7 + - + -
204A PHE* 1.3 75.3 - - - +
206A THR* 1.3 72.4 + - - +
207A GLU* 4.3 8.5 - - - -
234A CYS* 3.6 21.5 - - + -
236A ASP* 4.5 20.6 - - + -
256A LEU* 3.7 29.6 - - + -
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Residues in contact with THR 206 (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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158A THR* 5.4 0.2 - - - -
159A THR* 3.0 33.2 + - + +
162A CYS* 5.8 1.8 - - - -
204A PHE* 3.4 32.5 - - + -
205A PHE* 1.3 86.2 - - - +
207A GLU* 1.3 79.1 + - - +
210A THR* 5.0 0.2 + - - -
217A VAL* 4.2 11.5 - - + +
234A CYS 3.2 4.4 + - - +
235A ILE* 3.1 27.4 - - + +
236A ASP* 2.9 21.0 + - - -
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Residues in contact with GLU 207 (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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159A THR* 5.7 0.4 - - - +
161A ASP 3.6 7.7 - - - +
162A CYS* 4.1 15.7 - - - -
163A TYR* 3.1 32.4 + - - +
205A PHE* 4.3 7.1 - - - -
206A THR* 1.3 86.4 + - - +
208A SER* 1.3 64.6 + - - +
209A PRO 3.5 11.6 - - - +
210A THR* 3.8 21.5 + - - +
211A ASN* 4.0 7.2 + - - +
215A ARG 4.2 1.9 - - - +
217A VAL* 4.7 2.6 - - - +
236A ASP* 3.3 34.4 - - + +
239A PHE* 5.9 0.2 - - + -
500A PLP 3.7 22.0 - - + +
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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