Contacts of the strand formed by residues 264 - 271 (chain H) in PDB entry 6IY6
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 264 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G ARG* 3.6 24.1 - - - +
213H LYS 3.2 19.3 + - - +
214H GLY 3.6 18.6 - - - +
215H PHE* 3.5 39.0 - - + -
216H VAL* 2.9 32.6 + - - +
262H PHE 5.0 0.3 - - - -
263H GLU* 1.3 92.3 - - + +
265H VAL* 1.3 59.5 + - - +
292H GLU 4.0 2.2 - - - -
293H MET* 4.1 29.6 - - + +
294H ALA 5.2 3.6 - - - +
305H GLU* 5.3 3.6 + - - -
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Residues in contact with VAL 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215H PHE* 3.5 10.9 - - - -
216H VAL* 3.3 11.4 - - + +
218H ILE* 3.9 26.0 - - + -
254H LYS* 3.9 24.7 - - + +
257H CYS* 4.0 4.0 - - + -
258H ILE* 4.5 3.6 - - + -
262H PHE* 3.6 32.8 - - + +
264H LYS* 1.3 77.9 - - - +
266H PHE* 1.3 59.8 + - - +
292H GLU* 3.0 55.2 + - + +
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Residues in contact with PHE 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207G ARG* 4.7 0.4 - - - -
206H PHE* 3.7 15.7 - + + -
207H ARG* 3.8 28.7 - - + -
210H LEU* 3.7 26.7 - - + -
211H ILE* 3.8 31.9 - - + -
215H PHE* 3.8 23.8 - - + -
216H VAL 3.5 2.1 + - - -
217H GLU* 3.5 43.3 - - + +
218H ILE* 3.1 27.5 + - - +
254H LYS* 5.6 1.8 - - - -
265H VAL* 1.3 72.4 - - - +
267H SER* 1.3 63.3 + - - +
268H ILE* 4.5 6.5 - - + -
290H ASP 3.1 16.6 - - - +
291H ILE* 4.4 0.9 - - + +
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Residues in contact with SER 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206H PHE* 5.5 0.2 - - - -
217H GLU* 5.1 0.7 - - - -
218H ILE* 3.8 27.8 - - - -
220H THR* 4.2 20.1 - - - +
250H PRO* 4.3 4.9 - - - +
254H LYS* 4.1 9.4 - - - +
266H PHE* 1.3 76.0 - - - +
268H ILE* 1.3 63.7 + - - +
269H GLY 3.7 0.9 + - - -
288H GLY 3.3 6.2 - - - +
290H ASP* 3.0 39.6 + - - +
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Residues in contact with ILE 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207G ARG* 5.2 3.8 + - - +
217G GLU* 4.6 0.7 - - - +
219G GLN* 4.6 7.9 - - - +
268G ILE* 5.0 8.2 - - - +
203H CYS* 3.9 21.3 - - + +
206H PHE* 3.8 28.5 - - + -
207H ARG* 3.3 44.1 + - + +
217H GLU* 5.0 8.9 + - - +
218H ILE 5.2 0.2 + - - -
219H GLN* 5.1 5.4 - - - +
266H PHE* 4.4 8.2 - - + -
267H SER* 1.3 70.8 - - - +
269H GLY* 1.3 57.9 + - - +
287H VAL* 4.4 9.9 - - + -
288H GLY 3.7 4.3 - - - -
289H LEU* 3.6 30.3 - - + -
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Residues in contact with GLY 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219G GLN* 6.1 0.9 - - - -
270G PRO* 5.9 0.9 - - - -
220H THR* 5.9 1.3 - - - -
222H LYS* 5.1 5.4 - - - -
267H SER* 3.7 2.8 + - - -
268H ILE* 1.3 77.0 - - - +
270H PRO* 1.4 75.3 - - - +
271H VAL* 3.5 4.4 + - - +
287H VAL* 4.5 5.8 - - - +
288H GLY 3.0 29.9 + - - +
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Residues in contact with PRO 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222G LYS* 3.7 33.4 - - + -
269G GLY* 5.9 0.2 - - - -
270G PRO* 4.4 19.3 - - + -
222H LYS* 3.2 41.3 + - + +
269H GLY* 1.4 82.4 - - - +
271H VAL* 1.3 58.4 + - - +
272H PHE* 4.0 7.7 - - + -
285H GLU* 3.8 24.7 - - + +
286H PHE 3.4 9.9 - - - +
287H VAL* 4.2 10.9 - - + -
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Residues in contact with VAL 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222H LYS* 4.8 3.6 - - - +
249H SER* 4.5 11.9 - - - +
250H PRO* 4.1 24.5 - - + -
269H GLY 3.5 11.9 - - - +
270H PRO* 1.3 76.8 - - - +
272H PHE* 1.3 72.2 + - - +
285H GLU* 3.6 4.3 - - - +
286H PHE* 2.6 54.8 + - + +
288H GLY* 3.8 20.2 - - - +
290H ASP* 4.2 13.9 - - - +
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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