Contacts of the strand formed by residues 199 - 207 (chain A) in PDB entry 2IAU
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 LYS 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A LYS* 6.0 2.4 - - - +
193A ALA* 3.7 2.3 - - - +
194A GLU* 3.0 30.4 + - - +
197A THR* 3.2 35.3 - - - +
198A LYS* 1.3 80.5 - - - +
200A LEU* 1.3 63.1 + - - +
201A TRP* 3.7 42.8 - - + +
216A VAL* 4.2 23.3 - - + +
218A GLY 3.6 4.5 - - - +
219A HIS* 5.0 5.2 - - - +
220A ILE* 3.8 5.6 - - - +
228A ALA* 4.6 0.3 - - - +
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Residues in contact with LEU 200 (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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191A ILE* 4.3 4.0 - - + -
192A VAL 3.4 3.4 - - - -
193A ALA* 3.9 2.7 - - + -
199A LYS* 1.3 72.0 - - - +
201A TRP* 1.3 60.9 + - - +
216A VAL* 3.7 3.6 - - - +
217A TRP* 2.8 51.9 + - + -
218A GLY 3.0 16.9 + - - +
220A ILE* 3.2 26.2 - - + -
228A ALA* 3.7 18.6 - - + -
231A MET* 3.7 24.7 - - + -
239A LEU* 4.1 2.5 - - + -
241A VAL* 4.0 9.9 - - + -
252A PHE* 3.4 37.5 - - + -
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Residues in contact with TRP 201 (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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171A PHE* 3.8 30.3 - + + -
191A ILE* 3.2 5.7 - - - +
192A VAL* 2.6 47.0 + - + +
194A GLU* 2.9 36.2 + - + -
199A LYS* 3.7 36.6 - - + +
200A LEU* 1.3 78.6 - - - +
202A SER* 1.3 61.8 + - - +
203A TYR* 4.9 5.4 - - + -
214A LYS* 3.7 33.9 - - + -
215A LYS* 3.2 22.9 - - - -
216A VAL* 3.6 25.4 - - + -
217A TRP* 4.1 1.1 - - - -
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Residues in contact with SER 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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189A GLN* 3.6 22.2 + - - -
190A LEU 3.0 9.6 - - - -
191A ILE* 4.5 2.5 - - - -
201A TRP* 1.3 74.4 - - - +
203A TYR* 1.3 64.6 + - - +
213A ASN 3.4 1.7 + - - +
214A LYS* 3.4 4.9 - - - +
215A LYS* 2.8 64.3 + - - +
217A TRP* 3.5 16.9 - - - +
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Residues in contact with TYR 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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155A ILE* 5.2 1.8 - - + -
168A ASP* 2.6 32.3 + - + +
171A PHE* 2.9 27.7 - + - -
189A GLN* 3.2 10.3 - - - +
190A LEU* 2.9 43.7 + - + -
192A VAL* 4.0 22.2 - - + -
201A TRP* 4.9 4.0 - - + -
202A SER* 1.3 77.8 - - - +
204A ASP* 1.3 62.5 + - - +
211A ILE* 3.7 48.5 - - + -
212A GLU* 3.3 15.9 - - - +
213A ASN 3.9 2.5 - - - -
214A LYS* 3.7 31.0 - - + -
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Residues in contact with ASP 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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188A TYR* 3.4 10.6 - - - +
189A GLN* 5.0 7.8 + - - +
203A TYR* 1.3 74.4 - - - +
205A ILE* 1.3 61.2 + - - +
206A LYS* 3.4 26.4 + - - +
211A ILE* 3.3 3.8 - - - -
212A GLU 2.8 33.2 + - - +
213A ASN* 2.7 33.8 - - - +
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Residues in contact with ILE 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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125A ASP* 5.2 0.7 - - - +
131A TRP* 3.9 24.9 - - + +
179A VAL* 3.7 31.0 - - + -
186A ARG* 4.8 5.4 + - - -
187A PRO* 3.9 27.1 - - + +
188A TYR* 2.9 20.6 + - - +
189A GLN 3.7 15.3 - - - +
190A LEU* 3.9 17.3 - - + +
204A ASP* 1.3 71.2 - - - +
206A LYS* 1.3 60.9 + - - +
207A GLY* 3.5 26.7 - - - +
210A LYS 3.6 4.0 - - - +
211A ILE* 3.9 16.6 - - + -
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Residues in contact with LYS 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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204A ASP* 3.9 20.7 + - - +
205A ILE* 1.3 74.9 - - - +
207A GLY* 1.3 56.5 + - - +
210A LYS* 2.8 20.1 + - + +
212A GLU* 2.7 53.2 + - + +
213A ASN* 3.7 16.0 + - - -
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Residues in contact with GLY 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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131A TRP* 4.0 0.2 - - - -
205A ILE* 3.4 17.8 - - - +
206A LYS* 1.3 78.5 - - - +
208A PRO* 1.3 75.2 - - - +
209A ALA 3.2 1.0 + - - -
210A LYS* 3.0 22.4 + - - +
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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