Contacts of the strand formed by residues 206 - 214 (chain A) in PDB entry 3AIH
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 TYR 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A LEU* 3.9 11.4 - - - -
197A ASP* 3.0 37.4 + - + -
198A GLU 4.7 1.2 + - - -
199A GLY* 4.8 1.9 + - - -
203A SER* 5.8 2.5 - - - -
204A GLY 3.7 13.9 - - - -
205A ASP* 1.3 74.7 - - - +
207A ILE* 1.3 75.3 + - - +
208A ASP* 3.3 8.0 + - + -
222A ILE* 3.4 2.8 - - - -
223A ARG* 2.9 67.4 + - + +
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Residues in contact with ILE 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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111A LEU* 3.4 42.4 - - + +
112A LEU 3.7 10.0 + - - +
113A LYS* 3.6 38.4 + - + +
120A TYR* 3.6 22.9 - - + +
122A PHE* 4.0 12.3 - - + +
206A TYR* 1.3 79.4 - - - +
208A ASP* 1.3 61.4 + - - +
209A ARG 4.3 5.8 - - - +
210A VAL* 4.2 21.5 - - + -
220A LEU* 5.0 6.3 - - + -
221A THR 4.4 1.8 - - - +
222A ILE* 3.8 20.4 - - + -
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Residues in contact with ASP 208 (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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113A LYS* 3.6 22.3 + - - -
206A TYR* 3.3 8.7 + - + -
207A ILE* 1.3 73.4 - - - +
209A ARG* 1.3 73.8 + - - +
221A THR* 2.9 25.8 + - - +
223A ARG* 2.8 52.8 + - + +
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Residues in contact with ARG 209 (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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113A LYS* 5.0 2.7 - - - +
115A LYS* 5.2 5.7 - - - +
207A ILE* 4.3 2.7 - - - +
208A ASP* 1.3 98.2 - - - +
210A VAL* 1.3 69.9 + - - +
211A ASP* 2.7 40.0 + - - +
220A LEU* 3.5 2.9 - - - +
221A THR* 2.9 38.9 + - - +
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Residues in contact with VAL 210 (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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113A LYS* 5.4 5.6 - - + +
115A LYS* 3.2 32.6 + - + +
120A TYR* 3.9 54.3 - - + +
145A LEU* 4.8 0.2 - - + -
207A ILE* 4.2 12.8 - - + -
209A ARG* 1.3 80.4 + - - +
211A ASP* 1.3 67.2 + - - +
212A GLU* 6.1 0.2 - - + -
218A TYR* 4.1 21.3 - - + -
219A VAL 3.7 2.2 - - - -
220A LEU* 4.2 24.5 - - + +
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Residues in contact with ASP 211 (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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115A LYS* 5.3 0.8 + - - +
209A ARG* 2.7 53.5 + - - +
210A VAL* 1.3 75.8 - - - +
212A GLU* 1.3 60.9 + - - +
213A PRO* 3.6 8.7 - - + -
218A TYR* 3.2 8.1 - - - +
219A VAL* 2.7 46.6 + - + +
221A THR* 5.1 3.1 + - - -
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Residues in contact with GLU 212 (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 TYR* 5.7 0.2 + - - -
210A VAL* 6.1 0.2 - - + -
211A ASP* 1.3 75.6 - - - +
213A PRO* 1.4 65.0 - - - +
214A LEU 3.3 16.3 + - - +
215A SER* 3.6 4.5 - - - -
216A CYS* 2.7 21.5 + - - +
217A SER 3.4 7.4 - - - +
218A TYR* 3.4 17.1 - - + -
3C MAN 2.7 46.9 + - - -
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Residues in contact with PRO 213 (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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211A ASP* 3.6 11.7 - - + +
212A GLU* 1.4 88.3 - - - +
214A LEU* 1.3 63.2 + - + +
217A SER 3.3 8.3 - - - +
219A VAL* 4.0 12.1 - - + -
193B ARG* 3.0 35.8 + - - +
213B PRO* 3.7 38.6 - - + -
214B LEU* 3.8 14.1 - - + -
219B VAL* 3.8 4.3 - - + +
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Residues in contact with LEU 214 (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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212A GLU* 3.4 7.7 - - - +
213A PRO* 1.3 86.7 - - + +
215A SER* 1.3 68.8 + - - +
216A CYS 3.0 1.0 + - - -
217A SER* 2.8 32.8 + - - +
189B GLU* 3.6 36.1 - - + +
190B ALA 4.2 0.4 - - - -
191B GLU* 3.5 30.3 - - + +
213B PRO* 4.1 12.6 - - + -
214B LEU* 5.0 0.2 - - + -
217B SER* 4.0 19.7 - - - -
218B TYR 3.6 17.7 - - - +
219B VAL* 3.6 18.6 - - + -
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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