Contacts of the strand formed by residues 206 - 212 (chain A) in PDB entry 4TZ1
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 206 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A MET 2.9 8.9 + - - +
182A HIS* 3.3 17.7 + - + +
183A VAL 2.9 25.5 + - - -
205A SER* 1.3 73.4 - - - +
207A ILE* 1.3 64.9 + - - +
208A ASP* 3.6 28.1 + - - +
225A SER* 3.3 22.4 - - - +
290A THR* 4.5 5.8 - - + +
292A TRP* 3.7 24.8 - - + -
293A GLY* 6.5 1.1 - - - -
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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
----------------------------------------------------------
178A PHE* 5.2 0.7 - - + -
183A VAL* 3.7 13.9 - - + -
185A GLY 3.5 19.1 - - - +
186A GLY 4.4 0.2 - - - -
187A LEU* 4.1 33.2 - - + +
202A ILE* 4.6 12.1 - - + -
205A SER* 4.4 18.8 - - - +
206A LYS* 1.3 77.8 - - - +
208A ASP* 1.3 58.0 + - - +
209A GLY 3.7 14.6 - - - +
211A VAL* 4.0 23.1 - - + -
221A THR* 6.0 0.2 - - + -
224A SER* 5.6 0.9 - - - -
225A SER* 2.7 12.4 + - - +
226A VAL* 3.3 24.0 - - + -
227A GLY 3.0 26.0 + - - -
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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
----------------------------------------------------------
182A HIS* 2.8 31.8 + - - -
183A VAL 2.9 16.5 + - - +
184A LYS* 3.4 19.9 - - - +
185A GLY* 4.1 6.5 - - - +
206A LYS* 3.6 21.4 + - - +
207A ILE* 1.3 73.2 - - - +
209A GLY* 1.3 59.9 + - - +
227A GLY* 3.6 12.5 - - - -
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Residues in contact with GLY 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLY* 3.0 20.4 + - - -
186A GLY* 4.4 0.2 - - - -
207A ILE* 3.4 9.0 - - - +
208A ASP* 1.3 77.8 - - - +
210A GLU* 1.3 62.8 + - - -
211A VAL 3.8 0.3 + - - -
226A VAL* 4.4 0.2 - - - -
227A GLY* 3.0 25.5 + - - -
228A GLY 3.4 3.3 + - - +
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Residues in contact with GLU 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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186A GLY* 3.4 6.7 - - - -
187A LEU 3.0 23.4 + - - +
207A ILE* 4.4 0.7 - - - -
209A GLY* 1.3 72.6 - - - -
211A VAL* 1.3 75.2 + - - +
212A GLY* 3.8 7.5 + - - -
214A TYR* 5.0 6.8 + - - -
228A GLY* 3.5 12.8 - - - +
229A TRP 3.9 4.3 + - - +
230A GLY* 3.5 28.1 - - - +
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Residues in contact with VAL 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A LEU* 3.3 13.7 - - + +
189A LEU* 3.7 28.3 - - + -
202A ILE* 4.8 2.9 - - + -
207A ILE* 4.0 25.4 - - + -
209A GLY 3.8 0.2 + - - -
210A GLU* 1.3 76.5 - - - +
212A GLY* 1.3 62.1 + - - +
213A PRO* 3.7 2.3 - - + +
226A VAL* 3.6 30.5 - - + -
228A GLY 2.9 5.7 + - - -
229A TRP* 3.5 33.6 - - + -
230A GLY 2.8 27.2 + - - -
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Residues in contact with GLY 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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187A LEU 2.9 12.2 + - - -
188A ASN* 3.4 2.1 - - - +
189A LEU* 3.0 24.8 + - - -
210A GLU* 3.8 11.1 + - - -
211A VAL* 1.3 75.2 - - - +
213A PRO* 1.4 65.3 - - - +
214A TYR* 3.3 25.7 - - - -
230A GLY* 4.7 1.3 - - - -
231A ASN* 4.8 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