Contacts of the strand formed by residues 206 - 215 (chain A) in PDB entry 1D8V
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
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Residue Dist Surf HB Arom Phob DC
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200A ALA* 4.0 1.9 - - - -
203A GLN* 2.4 50.2 + - + +
204A GLY 3.7 0.2 - - - -
205A GLY* 1.3 80.4 - - - +
207A PHE* 1.3 83.1 + - - +
208A ARG 5.5 1.0 + - - -
210A PRO* 5.9 3.8 - - - -
224A THR* 2.5 36.1 - - - +
225A ASN* 4.2 5.8 - - + -
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Residues in contact with PHE 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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193A LEU* 4.1 26.9 - - + -
196A GLN* 3.4 51.4 - - + +
197A ILE* 3.9 6.1 - - + -
199A LEU* 5.9 0.7 - - - -
200A ALA* 3.9 14.8 - - + -
203A GLN* 4.6 1.1 - - - -
206A LYS* 1.3 99.0 + - - +
208A ARG* 1.3 67.4 + - - +
209A ASN 3.2 20.3 + - - +
210A PRO* 4.2 2.2 - - + +
211A VAL* 4.3 4.9 - - + -
223A VAL* 4.3 3.6 - - + -
224A THR* 2.9 32.6 + - - +
225A ASN* 3.8 22.9 - - - -
226A VAL* 4.6 1.1 - - + -
231A VAL* 4.0 20.0 - - + -
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Residues in contact with ARG 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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196A GLN* 5.7 1.0 - - - +
199A LEU* 4.5 35.9 + - + +
202A ASN* 5.1 13.1 - - - +
203A GLN* 2.7 37.8 - - + +
206A LYS* 4.0 2.7 + - - +
207A PHE* 1.3 74.1 - - - +
209A ASN* 1.3 73.9 + - - +
210A PRO* 3.6 7.1 - - - +
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Residues in contact with ASN 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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195A LYS* 5.9 2.4 - - - -
196A GLN* 2.8 45.6 + - - +
199A LEU* 5.7 3.8 - - - +
207A PHE* 3.4 6.7 - - - +
208A ARG* 1.3 92.0 + - - +
210A PRO* 1.3 71.7 - - + +
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Residues in contact with PRO 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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196A GLN* 4.3 1.7 + - - -
206A LYS* 5.9 3.1 - - - +
207A PHE* 4.2 3.6 - - + +
208A ARG 3.6 8.5 - - - +
209A ASN* 1.3 92.1 - - + +
211A VAL* 1.3 62.6 + - + +
212A ASP* 4.2 7.3 + - - +
222A GLN* 6.2 2.9 - - + -
223A VAL 4.1 3.8 - - - +
224A THR* 4.2 22.9 - - + -
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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
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189A GLN* 3.0 30.5 - - + +
192A ALA* 4.8 2.9 - - + -
193A LEU* 4.2 25.6 - - + +
196A GLN* 2.4 38.4 - - - +
207A PHE* 4.3 8.1 - - + -
209A ASN 3.8 0.4 - - - +
210A PRO* 1.3 74.2 - - - +
212A ASP* 1.3 63.8 + - - +
213A LEU* 4.0 19.3 - - + -
223A VAL* 2.8 48.6 + - - +
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Residues in contact with ASP 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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185A SER* 5.4 0.3 - - - -
189A GLN* 2.9 27.9 + - - +
210A PRO* 4.2 6.2 + - - +
211A VAL* 1.3 80.4 + - - +
213A LEU* 1.3 61.3 + - - +
220A ARG* 4.1 25.9 + - - +
221A PHE 4.0 5.2 - - - +
222A GLN* 3.2 38.4 + - + +
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Residues in contact with LEU 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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185A SER* 4.5 4.7 - - - -
186A LEU* 4.4 16.8 - - + -
189A GLN* 3.8 18.4 - - + -
193A LEU* 4.4 8.1 - - + -
211A VAL* 4.0 20.4 - - + -
212A ASP* 1.3 74.3 - - - +
214A ILE* 1.3 89.4 + - - +
215A LYS* 4.3 4.3 - - + +
220A ARG* 3.2 9.6 - - - +
221A PHE* 3.2 32.0 + - + +
223A VAL* 4.1 28.3 - - + -
230A VAL* 4.3 26.5 - - + -
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Residues in contact with ILE 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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164A TYR* 5.9 0.7 - - - -
181A LEU* 3.5 21.8 - - + +
182A ALA* 3.8 30.4 - - - +
185A SER* 2.6 35.1 - - - +
186A LEU* 4.6 4.1 - - - +
213A LEU* 1.3 94.6 - - - +
215A LYS* 1.3 72.0 + - - +
216A PRO* 3.7 2.1 - - - +
218A GLY* 4.3 4.7 - - - -
219A GLU 2.9 27.8 - - - +
220A ARG* 4.1 16.8 - - + -
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Residues in contact with LYS 215 (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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182A ALA* 3.5 1.8 - - - +
213A LEU* 4.3 6.5 + - + +
214A ILE* 1.3 82.9 - - - +
216A PRO* 1.3 74.6 - - + +
217A THR* 2.9 36.2 + - + +
218A GLY 3.0 11.8 + - - -
219A GLU* 3.0 20.9 + - + +
221A PHE* 3.5 44.8 - - + +
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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