Contacts of the strand formed by residues 203 - 211 (chain E) in PDB entry 6XAV
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 VAL 203 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201E ASP 4.3 7.2 - - - +
202E CYS* 1.3 69.4 - - - +
204E LEU* 1.3 60.0 + - - +
205E MET* 3.8 24.0 + - + -
226E GLU* 6.0 0.4 - - + +
253E LEU* 4.8 13.9 - - + -
258E LYS* 4.9 15.0 - - + -
259E ASP 2.6 18.9 + - - +
260E VAL* 4.2 12.0 - - + +
261E ILE* 2.8 33.8 + - - +
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Residues in contact with LEU 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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192E ALA* 3.5 39.3 - - + +
195E ILE* 4.8 12.1 - - + -
196E ALA* 4.4 15.0 - - + +
202E CYS 3.2 7.5 + - - +
203E VAL* 1.3 74.7 - - - +
205E MET* 1.3 68.3 + - - +
206E VAL* 4.2 11.0 - - + -
223E VAL* 5.1 9.6 - - + -
224E LYS 5.2 9.0 - - - +
225E GLY* 4.8 4.0 - - - -
226E GLU* 3.7 20.3 + - - +
261E ILE* 3.8 13.9 - - + +
263E LEU* 3.8 31.2 - - + -
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Residues in contact with MET 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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72E TYR* 5.3 0.9 - - + +
203E VAL* 4.0 16.6 - - + -
204E LEU* 1.3 80.2 - - - +
206E VAL* 1.3 61.9 + - - +
207E LEU* 3.4 3.6 + - + +
226E GLU* 3.4 33.9 - - + +
228E VAL* 5.1 6.7 - - + -
246E VAL* 3.8 33.7 - - + +
249E LYS* 4.3 20.9 - - + -
250E ALA* 5.0 4.5 - - - -
253E LEU* 5.1 4.3 - - - -
260E VAL* 3.8 23.6 - - + -
261E ILE 2.9 15.0 + - - +
262E ILE* 3.3 11.2 - - + +
263E LEU* 3.0 23.9 + - - +
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Residues in contact with VAL 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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188E LEU* 4.2 11.0 - - + -
192E ALA* 4.6 4.9 - - + -
204E LEU* 4.3 17.3 - - + -
205E MET* 1.3 71.4 - - - +
207E LEU* 1.3 59.3 + - - +
208E LEU* 3.8 12.2 + - + -
219E MET* 3.7 31.9 - - + -
223E VAL* 4.6 18.8 - - + -
226E GLU 3.5 6.8 + - - +
227E VAL* 3.6 17.5 - - + +
228E VAL* 3.2 22.8 + - - +
263E LEU* 3.9 25.1 - - + +
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Residues in contact with LEU 207 (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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205E MET* 3.4 3.7 + - + +
206E VAL* 1.3 73.5 - - - +
208E LEU* 1.3 72.1 + - - +
209E ILE* 4.1 4.5 - - + -
228E VAL* 3.2 18.2 - - + +
242E VAL* 4.1 17.9 - - + -
243E ALA* 4.4 14.1 - - + +
246E VAL* 3.6 46.7 - - + -
262E ILE* 4.1 17.3 - - + -
263E LEU 3.0 18.9 + - - +
264E LEU* 3.2 44.8 - - + +
300E PHE* 4.9 3.4 - - + -
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Residues in contact with LEU 208 (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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188E LEU* 6.2 0.7 - - + -
206E VAL* 4.4 17.5 - - + +
207E LEU* 1.3 82.9 - - - +
209E ILE* 1.3 66.2 + - - +
211E GLU* 3.8 32.3 - - + +
215E GLU* 4.2 15.0 - - + +
216E VAL* 4.1 24.0 - - + -
219E MET* 4.7 16.2 - - + -
227E VAL* 4.9 3.4 - - + -
228E VAL 3.0 7.2 + - - +
229E ALA* 3.4 25.4 - - + -
230E SER 2.7 29.0 + - - +
263E LEU 4.9 1.8 - - - +
264E LEU* 4.2 0.7 - - - -
265E ASP* 5.1 11.2 - - - +
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Residues in contact with ILE 209 (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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207E LEU* 4.1 10.5 - - + -
208E LEU* 1.3 83.5 - - - +
210E ASP* 1.3 73.3 + - + +
211E GLU* 3.2 8.2 + - - +
230E SER* 3.7 9.4 - - - -
239E HIS* 3.7 39.9 - - + +
242E VAL* 3.8 27.6 - - + -
243E ALA* 4.2 8.3 - - + +
264E LEU* 3.7 19.7 - - + +
266E SER* 3.0 40.0 + - - +
269E ARG* 4.3 2.0 - - - +
270E LEU* 4.5 13.7 - - + +
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Residues in contact with ASP 210 (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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298D LYS* 4.4 8.0 + - - -
337D GLY 5.1 6.4 - - - +
209E ILE* 1.3 77.5 - - + +
211E GLU* 1.3 64.0 + - - +
230E SER 2.8 13.5 + - - -
232E PHE* 3.4 27.3 - - - +
239E HIS* 3.0 37.2 + - + +
269E ARG* 4.0 35.3 + - + +
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Residues in contact with GLU 211 (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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208E LEU* 3.8 30.4 - - + +
209E ILE 3.2 24.8 + - - +
210E ASP* 1.3 78.9 - - - +
212E ARG* 1.3 73.4 + - - +
215E GLU* 3.9 20.0 - - + +
216E VAL* 5.1 2.2 - - + -
230E SER 3.8 4.2 + - - +
231E THR* 3.3 8.3 - - - -
232E PHE* 3.1 29.1 + - - -
265E ASP* 3.0 36.5 - - - +
269E ARG* 6.2 1.8 - - - -
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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