Contacts of the helix formed by residues 354 - 364 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266C TYR* 3.3 41.7 - - + +
352C ASP 4.5 1.8 - - - +
353C TYR* 1.3 86.3 - - + +
355C VAL* 1.3 65.8 + - - +
356C GLU 3.2 3.1 - - - -
357C ARG* 3.0 29.5 + - + +
358C TYR* 2.9 46.4 + - + +
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Residues in contact with VAL 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C TYR* 3.7 34.8 - - + -
337C CYS 4.5 2.1 - - - +
340C ALA* 4.1 24.0 - - + -
341C ILE* 3.7 23.2 - - + +
344C LEU* 4.3 11.7 - - + -
347C TYR 4.8 2.0 - - - +
348C GLY* 3.6 32.8 - - - +
353C TYR* 4.8 5.2 - - + +
354C PRO* 1.3 76.8 - - - +
356C GLU* 1.3 64.0 + - - +
358C TYR* 3.4 16.1 + - + +
359C TRP* 3.2 16.8 + - - +
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Residues in contact with GLU 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ASP* 4.4 0.7 - - - +
341C ILE* 4.2 9.4 - - - -
348C GLY 3.7 14.4 - - - +
350C VAL 4.1 13.7 - - - +
351C LYS* 2.9 37.4 + - - +
353C TYR 3.9 13.7 + - - +
355C VAL* 1.3 79.9 - - - +
357C ARG* 1.3 69.1 + - - +
359C TRP* 3.4 3.8 + - - +
360C ARG* 2.7 70.2 + - - +
208D LEU* 3.2 30.3 - - + +
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Residues in contact with ARG 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ALA* 3.7 18.4 + - - +
31C ALA* 4.1 19.9 - - - +
34C ASP* 3.5 31.9 - - - +
81C TYR* 3.5 24.0 + - - +
82C ASP* 5.1 2.4 + - - +
83C GLY 5.6 0.8 - - - +
259C LEU* 6.3 0.2 - - - +
353C TYR 5.5 0.2 - - - +
354C PRO* 3.0 29.3 + - + +
356C GLU* 1.3 82.6 - - - +
358C TYR* 1.3 81.0 + - - +
360C ARG* 3.1 26.9 + - - +
361C ASP* 2.7 56.7 + - - +
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Residues in contact with TYR 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C TYR 4.8 7.2 + - - -
81C TYR 6.1 0.2 - - - -
259C LEU* 4.3 22.2 - - + +
262C ALA* 3.9 21.8 + - + +
263C ALA* 3.5 33.9 - - + -
266C TYR* 4.3 11.9 - - + -
337C CYS* 3.9 16.6 - - - -
354C PRO* 2.9 45.8 + - + +
355C VAL* 3.6 14.4 - - - +
357C ARG* 1.3 103.3 + - - +
359C TRP* 1.3 58.1 + - - +
361C ASP* 3.7 1.3 - - - +
362C ALA* 2.8 33.6 + - - +
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Residues in contact with TRP 359 (chain C).
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* 3.8 25.4 - - + -
334C VAL* 3.4 37.4 + - + +
337C CYS* 3.7 10.7 - - + +
338C ASP* 3.8 21.4 - - + +
341C ILE* 3.6 24.0 - - + -
355C VAL 3.2 3.2 + - - +
356C GLU 3.7 4.0 - - - +
357C ARG 3.2 0.4 - - - -
358C TYR* 1.3 80.6 - - - +
360C ARG* 1.3 70.0 + - + +
362C ALA* 4.6 0.2 - - - -
363C ARG* 2.8 61.0 + - + +
338D ASP* 3.6 12.3 - - - -
341D ILE* 4.3 2.7 - - + -
359D TRP* 3.3 62.4 - + - -
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Residues in contact with ARG 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ASP* 2.8 39.6 + - - -
208C LEU* 3.1 49.6 + - + +
209C GLY* 3.9 4.8 - - - -
211C THR* 4.7 0.8 + - - -
351C LYS* 3.4 15.7 - - - +
356C GLU* 2.7 56.9 + - - +
357C ARG* 3.4 15.5 - - - +
359C TRP* 1.3 91.3 - - + +
361C ASP* 1.3 57.4 + - - +
363C ARG* 3.6 2.3 + - - +
208D LEU* 4.0 13.2 - - + -
349D TYR* 2.7 34.0 + - - -
351D LYS* 6.0 0.4 - - - +
360D ARG* 4.6 3.1 - - - +
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Residues in contact with ASP 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ASP* 4.8 1.4 - - - +
83C GLY* 3.6 19.2 + - - -
84C ALA* 4.3 1.4 + - - +
209C GLY* 3.8 2.1 - - - -
210C LEU* 2.8 61.2 + - + +
259C LEU* 3.9 20.3 - - + +
357C ARG* 2.7 47.3 + - - +
358C TYR 3.7 2.9 - - - +
360C ARG* 1.3 74.1 - - - +
362C ALA* 1.3 62.7 + - - +
363C ARG 3.3 0.7 + - - -
364C LEU* 3.5 8.1 + - - +
365C THR* 4.6 2.4 + - - +
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Residues in contact with ALA 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C ALA* 5.6 0.2 - - - -
259C LEU* 3.5 28.0 - - + +
333C ALA* 4.8 4.3 - - + -
334C VAL* 3.5 18.2 - - + +
337C CYS* 4.0 14.4 - - - -
358C TYR 2.8 21.2 + - - +
359C TRP 4.0 1.6 - - - +
361C ASP* 1.3 73.8 - - - +
363C ARG* 1.3 61.4 + - - +
365C THR* 2.6 33.5 + - + +
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Residues in contact with ARG 363 (chain C).
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* 4.3 10.3 - - + -
334C VAL* 3.8 18.6 - - - +
359C TRP* 2.8 52.3 + - + +
360C ARG 3.7 8.5 - - - +
361C ASP 3.2 0.6 - - - -
362C ALA* 1.3 72.9 - - - +
364C LEU* 1.3 61.0 + - - +
365C THR 3.4 0.5 + - - -
366C ARG* 3.5 28.9 + - - +
367C ILE* 3.8 12.2 + - - +
338D ASP* 2.7 43.4 + - - -
341D ILE* 3.7 10.4 - - + +
342D GLN* 3.0 36.1 + - - +
349D TYR* 4.2 8.1 - - + -
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Residues in contact with LEU 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LEU* 4.0 22.0 - - + -
207C LYS* 5.8 2.9 - - + -
210C LEU* 3.2 31.2 - - + -
255C MET* 6.4 0.7 - - - -
361C ASP 3.5 2.7 + - - +
362C ALA 3.0 1.4 + - - -
363C ARG* 1.3 74.6 - - - +
365C THR* 1.3 59.8 + - + +
366C ARG 3.1 3.1 - - - -
367C ILE* 2.9 17.2 + - + +
368C GLY* 2.9 45.7 + - - +
346D GLY* 6.0 1.8 - - - -
349D TYR* 3.7 45.3 - - + -
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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