Contacts of the strand formed by residues 383 - 390 (chain N) in PDB entry 4G7H
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 GLY 383 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213N VAL* 4.5 1.3 - - - -
214N GLU 3.0 15.5 - - - -
215N TYR* 3.9 4.7 - - - -
216N VAL* 4.1 4.5 - - - -
360N ARG* 3.4 4.2 - - - +
361N VAL* 2.8 46.8 + - - +
381N ALA 3.4 1.6 + - - -
382N GLU* 1.3 81.2 - - - +
384N VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 384 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212N ARG 3.8 0.5 - - - +
213N VAL* 3.4 3.9 - - - -
214N GLU* 2.9 46.2 + - + +
216N VAL* 5.1 6.5 - - + -
340N THR* 6.0 2.0 - - + -
358N GLY* 4.7 5.8 - - - +
359N ALA 3.1 10.5 - - - +
360N ARG* 3.5 41.7 - - + +
383N GLY* 1.3 80.8 - - - +
385N VAL* 1.3 61.9 + - - +
386N HIS* 3.4 24.7 - - + +
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Residues in contact with VAL 385 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211N VAL* 3.8 26.7 - - + -
212N ARG 3.8 2.5 - - - +
213N VAL* 4.4 9.9 - - + +
355N VAL* 3.8 27.1 - - + -
356N PRO 4.3 2.9 - - - +
357N GLU* 3.8 0.6 - - - -
358N GLY* 2.7 33.6 + - - -
359N ALA 2.8 12.4 + - - +
361N VAL* 3.5 35.9 - - + -
367N ILE* 4.2 7.4 - - + -
384N VAL* 1.3 75.8 - - - +
386N HIS* 1.3 68.1 + - - +
387N LEU* 4.4 9.9 - - + -
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Residues in contact with HIS 386 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180N LYS* 4.6 6.2 + - - -
211N VAL* 3.5 4.9 - - - +
212N ARG* 2.9 46.6 + - + +
214N GLU* 4.1 15.7 - - + +
357N GLU* 3.2 22.5 + - - +
358N GLY* 5.3 4.7 - - - -
384N VAL* 3.4 29.8 - - + +
385N VAL* 1.3 80.3 + - - +
387N LEU* 1.3 65.4 + - - +
388N HIS* 3.8 21.9 + - + +
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Residues in contact with LEU 387 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180N LYS* 6.0 0.9 - - - +
181N ASP* 5.4 4.5 - - - +
205N TYR* 3.4 34.1 + - + -
208N PRO* 4.0 23.8 - - + -
210N ARG 4.1 0.9 - - - -
211N VAL* 3.9 18.6 - - + -
353N VAL* 4.0 19.5 - - + -
355N VAL 4.0 6.1 - - - +
356N PRO* 3.8 5.2 - - + -
357N GLU* 3.2 55.4 + - + +
385N VAL* 4.4 8.1 - - + -
386N HIS* 1.3 79.3 - - - +
388N HIS* 1.3 68.0 + - - +
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Residues in contact with HIS 388 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176N ASP* 3.2 21.9 + - - +
180N LYS* 6.5 1.1 - - + -
205N TYR* 5.0 0.4 - - - -
208N PRO* 3.5 4.6 - - - +
209N ARG 3.3 2.8 + - - -
210N ARG* 2.9 69.4 + - - +
212N ARG* 3.8 27.2 - - + +
386N HIS* 3.8 21.4 + - + +
387N LEU* 1.3 80.8 + - - +
389N GLU* 1.3 70.7 + - - +
390N PRO* 3.5 4.3 - - - -
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Residues in contact with GLU 389 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174N GLY* 3.3 40.3 + - - +
175N VAL 4.2 6.7 - - - +
176N ASP* 2.8 24.8 + - + +
209N ARG* 2.6 45.4 + - + +
210N ARG* 3.2 32.4 + - - +
346N ARG* 3.4 31.4 + - - -
388N HIS* 1.3 73.3 - - - +
390N PRO* 1.3 64.5 - - - +
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Residues in contact with PRO 390 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171N LEU* 3.5 36.1 - - + +
175N VAL 4.8 1.6 - - - +
176N ASP* 4.1 6.1 - - - +
177N ALA* 4.3 6.5 - - + +
205N TYR* 3.9 43.7 - - + -
206N ARG 4.2 2.7 - - - +
207N PHE 3.3 7.4 - - - +
208N PRO* 3.7 4.9 - - + -
209N ARG* 4.7 2.5 + - - -
388N HIS 3.5 2.7 - - - -
389N GLU* 1.3 93.3 - - - +
391N ALA* 1.3 65.7 + - - +
392N SER 3.8 13.7 - - - +
393N ILE* 4.1 4.0 - - + -
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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