Contacts of the strand formed by residues 199 - 206 (chain E) in PDB entry 6D6Q
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 CYS 199 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150E ASP* 4.7 2.2 - - - +
153E SER* 3.2 6.7 - - - +
154E ILE* 5.0 3.8 - - + +
157E LYS* 5.9 2.0 - - + -
198E PRO* 1.3 73.6 - - - +
200E ILE* 1.3 65.0 + - - +
201E VAL* 4.2 10.7 - - - +
228E VAL 3.8 0.2 - - - +
229E SER* 3.4 2.2 - - - -
230E VAL* 2.9 33.5 + - - -
263E GLY* 3.9 17.7 - - - -
266E LEU* 3.7 24.9 - - + -
267E HIS* 2.7 42.4 - - + -
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Residues in contact with ILE 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E THR* 6.0 4.0 - - - -
109E LEU* 6.3 3.1 - - + -
112E ILE* 3.4 38.4 - - + -
149E PHE* 3.8 39.3 - - + +
150E ASP* 3.0 23.1 - - - +
153E SER* 3.1 21.9 + - - +
198E PRO 5.7 0.2 - - - +
199E CYS* 1.3 71.1 - - - +
201E VAL* 1.3 85.2 + - - +
202E THR* 4.3 0.4 - - - +
227E LEU* 4.1 20.2 - - + -
228E VAL 3.3 7.4 - - - +
229E SER* 3.9 10.8 - - - +
266E LEU* 4.7 0.2 - - - +
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Residues in contact with VAL 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E TYR* 4.0 17.9 - - - +
150E ASP* 4.8 1.6 - - - +
199E CYS* 4.2 19.5 - - - +
200E ILE* 1.3 84.5 - - - +
202E THR* 1.3 62.1 + - - +
203E LEU* 3.3 25.4 + - + +
212E VAL* 5.0 3.4 - - + -
226E LEU 3.4 2.6 - - - +
227E LEU* 3.4 4.0 - - - -
228E VAL* 2.9 39.4 + - + +
230E VAL* 5.1 4.7 - - + -
259E GLY* 4.2 24.0 - - - +
262E VAL* 4.4 15.7 - - + -
263E GLY* 4.8 1.3 - - - +
266E LEU* 5.3 1.8 - - + -
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Residues in contact with THR 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E TYR* 4.7 3.4 + - - -
147E ASN* 4.3 22.1 + - - -
149E PHE* 3.9 20.4 + - + +
150E ASP 4.5 0.5 + - - -
200E ILE* 4.3 0.9 - - - +
201E VAL* 1.3 73.8 - - - +
203E LEU* 1.3 62.2 + - - +
204E CYS* 3.6 22.7 + - - -
211E VAL 3.6 7.4 - - - +
212E VAL* 3.9 11.6 - - - +
213E ASP 4.1 5.4 + - - -
214E ALA* 4.8 3.6 + - + +
219E GLU* 5.8 2.7 - - - +
225E SER* 4.4 10.3 - - - +
226E LEU 3.7 2.5 - - - -
227E LEU* 2.8 29.7 - - + +
242E VAL* 5.8 0.4 - - + -
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Residues in contact with LEU 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E VAL* 3.3 36.1 - - + +
202E THR* 1.3 71.0 - - - +
204E CYS* 1.3 62.1 + - - +
205E LYS 3.9 0.7 + - - -
210E HIS* 3.8 22.2 - - + -
211E VAL 3.3 5.2 - - - +
212E VAL* 4.0 14.1 - - + -
225E SER* 3.2 1.2 - - - -
226E LEU* 2.9 40.2 + - - +
228E VAL* 5.2 4.9 - - + -
255E MET* 3.2 58.7 - - + +
258E THR* 3.9 9.6 - - + -
259E GLY* 4.5 4.9 - - - -
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Residues in contact with CYS 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E THR* 3.6 14.3 + - - -
203E LEU* 1.3 73.0 - - - +
205E LYS* 1.3 61.6 + - - +
206E ILE* 3.8 5.5 + - + +
210E HIS* 3.6 1.5 - - - -
211E VAL* 2.9 35.3 + - - +
214E ALA* 3.3 33.9 - - + -
218E GLU 5.6 0.2 - - - +
219E GLU* 4.5 12.1 - - - -
222E SER* 4.4 15.7 - - - -
224E ALA 3.5 6.5 - - - +
225E SER* 3.4 22.0 - - - -
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Residues in contact with LYS 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E LEU 3.9 1.2 + - - -
204E CYS* 1.3 71.1 - - - +
206E ILE* 1.3 61.3 + - - +
207E GLY 3.7 17.5 - - - +
208E TYR* 3.8 24.9 + - - +
209E ARG* 3.8 10.3 - - - +
210E HIS* 4.3 3.4 - - - +
222E SER* 3.3 21.8 - - - -
223E LEU* 3.6 26.1 + - + +
224E ALA 2.9 14.9 + - - +
247E LEU* 4.1 22.2 - - + -
248E ASP* 4.9 12.8 + - - +
251E SER* 4.1 20.9 - - - +
255E MET* 3.8 17.9 - - + +
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Residues in contact with ILE 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E ILE* 5.2 1.8 - - + -
15E VAL* 3.5 37.7 - - + +
18E VAL* 4.4 19.1 - - + +
19E GLN* 5.2 1.6 - - - +
204E CYS* 3.8 7.6 + - + +
205E LYS* 1.3 79.0 - - - +
207E GLY* 1.3 68.5 + - - +
208E TYR 3.1 0.2 + - - -
209E ARG* 2.7 35.0 + - - +
211E VAL* 4.4 16.6 - - + -
214E ALA* 5.7 0.2 - - + -
218E GLU* 3.7 44.0 - - + +
221E CYS* 4.5 6.7 - - + +
222E SER* 4.0 16.4 - - - +
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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