Contacts of the helix formed by residues 354 - 363 (chain D) in PDB entry 2CX9
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 PRO 354 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266D TYR* 3.6 36.6 - - + +
352D ASP 4.5 1.6 - - - +
353D TYR* 1.3 85.7 - - + +
355D VAL* 1.3 66.5 + - - +
356D GLU 3.2 3.1 - - - -
357D ARG* 2.9 35.9 + - + +
358D TYR* 2.9 42.3 + - + +
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Residues in contact with VAL 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D TYR* 3.4 34.3 - - + -
267D ALA 5.4 0.2 - - - +
337D CYS 4.5 1.9 - - - +
340D ALA* 4.0 22.9 - - + -
341D ILE* 3.7 20.8 - - + +
344D LEU* 3.2 29.2 - - + -
347D TYR 4.8 1.3 - - - +
348D GLY* 3.8 21.8 - - - +
350D VAL 6.0 0.2 - - - +
353D TYR* 4.8 2.5 - - + -
354D PRO* 1.3 76.6 - - - +
356D GLU* 1.3 64.7 + - - +
358D TYR* 3.3 16.4 + - + +
359D TRP* 3.2 17.2 + - - +
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Residues in contact with GLU 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C LEU* 3.3 29.4 - - + +
34D ASP* 4.5 0.9 - - - +
341D ILE* 4.1 10.3 - - + -
348D GLY 3.5 16.6 - - - +
350D VAL 4.1 6.3 - - - +
351D LYS* 2.8 52.5 + - + +
353D TYR 3.8 14.8 - - - +
355D VAL* 1.3 80.1 - - - +
357D ARG* 1.3 68.8 + - - +
359D TRP* 3.5 3.6 + - - +
360D ARG* 2.8 55.5 + - - +
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Residues in contact with ARG 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ALA* 3.5 15.7 + - - +
31D ALA* 3.7 25.4 - - - +
34D ASP* 3.5 31.0 - - - +
81D TYR 3.4 24.4 + - - -
82D ASP* 4.9 1.8 - - - +
83D GLY 5.6 1.0 - - - +
354D PRO* 2.9 26.1 + - + +
356D GLU* 1.3 83.0 - - - +
358D TYR* 1.3 84.9 + - - +
360D ARG* 3.1 26.0 + - - +
361D ASP* 2.8 52.4 + - - +
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Residues in contact with TYR 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D TYR* 4.4 8.8 + - - -
81D TYR* 5.8 0.4 - - - -
259D LEU* 4.2 19.9 - - + +
262D ALA* 3.8 37.2 + - + +
263D ALA* 3.6 21.5 - - + -
266D TYR* 4.3 11.1 - - + +
337D CYS* 3.7 16.6 - - - -
354D PRO* 2.9 38.3 + - + +
355D VAL* 3.5 20.6 - - - +
357D ARG* 1.3 103.2 + - - +
359D TRP* 1.3 57.1 + - - +
361D ASP* 3.9 1.7 - - - +
362D ALA* 2.9 31.5 + - - +
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Residues in contact with TRP 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C LEU* 6.0 0.2 - - + -
338C ASP* 3.7 11.6 - - - -
341C ILE* 4.4 2.7 - - + -
359C TRP* 3.3 60.8 - + - -
208D LEU* 3.8 26.2 - - + -
334D VAL* 3.4 35.5 + - + +
337D CYS* 3.6 10.5 - - + +
338D ASP* 3.7 23.7 - - + +
341D ILE* 3.7 24.7 - - + -
355D VAL 3.2 2.8 + - - +
356D GLU 3.7 3.4 - - - +
357D ARG 3.1 0.6 - - - -
358D TYR* 1.3 78.4 - - - +
360D ARG* 1.3 72.8 + - + +
362D ALA* 3.4 1.5 + - - +
363D ARG* 2.8 58.9 + - + -
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Residues in contact with ARG 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C LEU* 3.9 17.9 - - + -
349C TYR* 2.8 35.1 + - - -
351C LYS* 5.7 1.3 - - - +
360C ARG* 4.6 4.3 - - - +
34D ASP* 2.8 43.2 + - - -
208D LEU* 3.1 46.9 + - + +
209D GLY* 3.8 5.6 - - - -
211D THR* 4.5 2.0 + - - -
351D LYS* 3.3 13.2 - - - +
356D GLU* 2.8 46.4 + - - +
357D ARG* 3.1 14.2 + - - +
359D TRP* 1.3 94.9 - - + +
361D ASP* 1.3 55.6 + - - +
363D ARG* 3.5 2.4 + - - +
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Residues in contact with ASP 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ASP* 4.7 2.1 - - - +
83D GLY* 3.8 14.9 + - - -
84D ALA 4.5 0.9 + - - -
209D GLY* 3.7 2.1 - - - -
210D LEU* 2.7 67.4 + - + +
255D MET* 4.4 2.9 - - - +
259D LEU* 3.9 20.0 - - + +
357D ARG* 2.8 48.7 + - - +
358D TYR 3.9 2.9 - - - +
360D ARG* 1.3 73.4 - - - +
362D ALA* 1.3 63.6 + - - +
363D ARG 3.3 0.7 + - - -
364D LEU* 3.5 8.3 + - - +
365D THR 4.5 0.3 + - - -
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Residues in contact with ALA 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D ALA* 5.7 0.2 - - - -
259D LEU* 3.8 21.5 - - + +
333D ALA* 4.8 4.9 - - + -
334D VAL* 3.4 18.7 - - + +
337D CYS* 3.9 17.5 - - - -
358D TYR 2.9 20.2 + - - +
359D TRP* 3.9 3.1 - - - +
361D ASP* 1.3 77.4 - - - +
363D ARG* 1.3 62.6 + - - +
365D THR* 2.8 31.4 + - + +
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Residues in contact with ARG 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C ASP* 2.7 43.8 + - - -
341C ILE* 3.7 12.8 - - + +
342C GLN* 3.0 37.2 + - - +
349C TYR* 4.2 6.7 - - + -
208D LEU* 4.2 9.9 - - + -
334D VAL* 3.9 10.5 - - - +
359D TRP* 2.8 52.2 + - + +
360D ARG 3.6 8.5 - - - +
361D ASP 3.2 0.6 - - - -
362D ALA* 1.3 76.4 - - - +
364D LEU* 1.3 60.1 + - - +
365D THR 3.5 0.3 + - - -
366D ARG* 3.2 35.9 + - - +
367D ILE* 3.8 12.3 - - + +
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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