Contacts of the strand formed by residues 208 - 220 (chain L) in PDB entry 6AHU
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 208 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123H LEU* 4.6 23.8 + - - +
66L TYR* 5.9 1.8 - - - +
206L GLN 3.6 5.4 + - - +
207L PRO* 1.3 71.8 - - - +
209L VAL* 1.3 59.4 + - - +
210L ALA* 5.7 0.2 - - - -
280L THR 3.2 5.0 - - - +
281L ILE* 3.4 2.4 - - - -
282L THR* 2.5 64.4 + - + +
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Residues in contact with VAL 209 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60L VAL* 3.8 37.5 - - + +
61L MET* 3.8 34.3 - - + -
207L PRO* 3.5 12.9 + - + +
208L LYS* 1.3 76.9 - - - +
210L ALA* 1.3 61.2 + - - +
211L LEU* 3.8 25.4 + - + +
279L CYS* 4.9 0.4 - - - -
280L THR 3.5 4.0 - - - +
281L ILE* 5.0 5.8 - - + -
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Residues in contact with ALA 210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208L LYS 4.1 0.6 - - - -
209L VAL* 1.3 72.2 - - - +
211L LEU* 1.3 63.7 + - - +
212L SER* 4.0 5.4 + - - +
278L LEU 4.5 0.2 - - - -
279L CYS* 3.4 5.5 - - - -
280L THR* 3.0 47.2 + - + +
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Residues in contact with LEU 211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L LEU* 5.5 1.8 - - + -
57L LYS* 4.2 19.1 - - + +
60L VAL* 4.9 5.6 - - + -
61L MET* 4.4 13.7 - - + -
209L VAL* 3.8 23.5 + - + +
210L ALA* 1.3 70.3 - - - +
212L SER* 1.3 63.8 + - - +
277L TYR* 3.3 27.6 - - + +
278L LEU 3.9 0.7 - - - -
279L CYS* 3.7 28.7 - - + -
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Residues in contact with SER 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210L ALA* 4.0 6.0 + - - +
211L LEU* 1.3 76.8 + - - +
213L THR* 1.3 63.7 + - - +
277L TYR* 3.7 5.7 - - - -
278L LEU* 2.8 58.4 + - - +
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Residues in contact with THR 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L CYS 4.8 9.9 - - - +
50L GLY* 5.3 8.7 + - - -
212L SER* 1.3 79.3 + - - +
214L LEU* 1.3 66.6 + - - +
215L ARG* 4.1 11.7 + - + +
275L LYS* 5.3 7.2 - - + -
276L ALA 3.5 14.1 - - - +
277L TYR* 3.9 14.0 - - - -
278L LEU* 4.5 0.7 - - - +
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Residues in contact with LEU 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212L SER 4.3 0.6 - - - -
213L THR* 1.3 74.7 - - - +
215L ARG* 1.3 75.5 + - - +
217L LEU* 3.9 21.8 - - + -
247L VAL* 3.8 34.8 - - + +
250L ASN* 5.5 7.9 - - - +
252L ASP* 5.0 13.9 - - + +
275L LYS* 3.5 1.4 - - - -
276L ALA* 2.6 51.2 + - + +
278L LEU* 3.9 18.5 - - + +
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Residues in contact with ARG 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213L THR* 4.1 13.2 + - + +
214L LEU* 1.3 89.6 - - - +
216L ASP* 1.3 80.8 + - - +
217L LEU 3.6 1.3 + - - -
252L ASP* 5.2 0.9 - - - +
274L ALA 3.4 11.0 + - - +
275L LYS* 5.1 8.7 - - + +
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Residues in contact with ASP 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215L ARG* 1.3 85.0 + - - +
217L LEU* 1.3 59.3 + - - +
218L GLN* 4.0 0.7 + - - +
252L ASP* 3.5 16.1 - - - +
272L VAL* 5.2 11.9 - - + +
273L VAL 3.4 7.4 - - - -
274L ALA* 2.8 25.9 + - - +
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Residues in contact with LEU 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L LEU* 4.7 8.1 - - + -
214L LEU* 3.9 20.2 - - + -
216L ASP* 1.3 75.8 - - - +
218L GLN* 1.3 61.4 + - - +
219L CYS* 3.8 20.6 - - - -
243L TRP* 3.8 16.4 - - + -
247L VAL* 3.8 36.8 - - + -
252L ASP* 3.6 21.5 - - + +
272L VAL* 4.1 1.1 - - - -
273L VAL* 2.8 39.8 + - + +
274L ALA 4.6 0.4 + - - -
276L ALA* 3.8 31.6 - - + -
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Residues in contact with GLN 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216L ASP 4.0 1.4 + - - +
217L LEU* 1.3 76.8 - - - +
219L CYS* 1.4 56.4 + - - +
243L TRP* 3.2 17.9 + - - +
252L ASP* 4.4 8.4 + - - +
254L ASN* 5.0 7.8 - - - +
266L CYS* 3.4 38.0 - - + +
268L GLU* 5.6 4.4 + - - +
270L SER* 2.8 29.5 + - - +
271L THR 3.8 9.0 - - - +
272L VAL* 4.7 12.4 - - + +
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Residues in contact with CYS 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45L LEU* 5.7 1.3 - - - -
47L PRO* 4.6 15.9 - - + -
217L LEU* 3.5 20.1 + - - -
218L GLN* 1.4 73.9 - - - +
220L PRO* 1.3 70.6 - - + +
243L TRP* 3.6 18.8 - - - -
270L SER* 3.3 1.3 - - - -
271L THR* 2.6 40.6 + - - +
273L VAL* 3.7 31.2 - - + -
309L TRP* 4.6 12.1 - - + +
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Residues in contact with PRO 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218L GLN 4.0 3.4 - - - +
219L CYS* 1.3 92.9 - - + +
221L VAL* 1.3 64.1 + - - +
222L LEU* 4.0 8.2 + - + +
235L CYS* 3.7 22.9 - - + -
240L LEU* 5.1 9.6 - - + -
243L TRP* 3.6 37.0 - - + -
266L CYS* 4.9 0.2 - - - -
267L PRO* 4.0 22.4 - - + +
269L PRO 3.7 6.1 - - - +
270L SER* 3.8 3.4 - - - -
271L THR* 4.9 2.3 + - - -
309L TRP* 4.2 20.7 + - + -
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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