Contacts of the helix formed by residues 354 - 364 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A TYR* 3.6 34.3 - - + +
352A ASP 4.6 0.9 - - - +
353A TYR* 1.3 85.6 - - + +
355A VAL* 1.3 66.7 + - - +
356A GLU 3.2 2.7 - - - -
357A ARG* 3.0 35.6 + - + +
358A TYR* 3.0 45.4 + - + +
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Residues in contact with VAL 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A ALA* 5.6 0.2 - - + -
266A TYR* 3.4 36.6 - - + -
337A CYS 4.6 1.9 - - - +
340A ALA* 4.1 30.7 - - + +
341A ILE* 3.8 22.0 - - + +
344A LEU* 4.4 5.6 - - + -
348A GLY* 3.7 30.1 - - - -
353A TYR* 3.5 6.5 - - + +
354A PRO* 1.3 75.7 - - - +
356A GLU* 1.3 64.7 + - - +
358A TYR* 3.3 16.6 + - + +
359A TRP* 3.2 18.0 + - - +
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Residues in contact with GLU 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ASP* 4.4 1.6 - - - +
341A ILE* 4.1 8.2 - - - +
348A GLY 3.5 19.1 - - - +
350A VAL 3.9 14.1 - - - +
351A LYS* 2.9 36.2 + - + +
353A TYR 3.8 15.3 + - - +
355A VAL* 1.3 82.5 - - - +
357A ARG* 1.3 68.1 + - - +
359A TRP* 3.7 2.6 + - - +
360A ARG* 2.7 67.9 + - - +
208B LEU* 3.4 26.6 - - + +
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Residues in contact with ARG 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA* 3.7 13.9 + - - +
31A ALA* 3.8 26.2 - - - +
34A ASP* 3.5 39.5 - - - +
81A TYR* 3.3 25.5 + - - +
82A ASP* 5.0 1.0 - - - +
83A GLY 5.5 1.6 - - - +
354A PRO* 3.0 28.2 + - + +
356A GLU* 1.3 85.2 - - - +
358A TYR* 1.3 85.3 + - - +
359A TRP 3.2 0.2 - - - -
360A ARG* 3.3 16.6 + - - +
361A ASP* 2.8 48.9 + - - +
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Residues in contact with TYR 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A TYR 4.6 6.5 + - - -
259A LEU* 4.3 20.3 - - + +
262A ALA* 3.7 35.9 + - + +
263A ALA* 3.3 26.0 - - + -
266A TYR* 4.2 12.4 - - + -
337A CYS* 3.7 16.7 - - - -
354A PRO* 3.0 39.6 + - + +
355A VAL* 3.6 17.3 - - + +
357A ARG* 1.3 103.7 + - - +
359A TRP* 1.3 58.5 + - - +
361A ASP* 3.7 1.6 - - - +
362A ALA* 2.9 31.9 + - - +
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Residues in contact with TRP 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LEU* 3.8 23.6 - - + -
334A VAL* 3.4 38.5 + - + +
337A CYS* 3.6 11.2 - - + +
338A ASP* 3.7 22.4 - - + +
341A ILE* 3.6 24.2 - - + -
355A VAL 3.2 4.1 + - - +
356A GLU 3.9 1.6 - - - +
357A ARG 3.2 0.6 - - - -
358A TYR* 1.3 77.7 - - - +
360A ARG* 1.3 74.0 + - + +
362A ALA* 4.5 0.4 - - - +
363A ARG* 2.9 60.6 + - + +
208B LEU* 5.5 0.2 - - + -
338B ASP* 3.7 10.5 - - - -
341B ILE* 4.4 3.6 - - + -
359B TRP* 3.3 61.3 - + - -
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Residues in contact with ARG 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ASP* 3.0 38.6 + - - -
208A LEU* 2.9 51.1 + - + +
209A GLY* 3.7 6.6 - - - -
211A THR* 4.5 2.0 + - - -
351A LYS* 3.6 12.1 - - - +
356A GLU* 2.7 50.3 + - - +
357A ARG* 3.3 11.5 + - - +
359A TRP* 1.3 94.0 - - + +
361A ASP* 1.3 57.3 + - - +
363A ARG* 3.7 2.1 + - - +
208B LEU* 3.8 16.4 - - + -
349B TYR* 2.8 35.8 + - - -
351B LYS* 6.0 0.4 - - - +
360B ARG* 4.3 4.7 - - - +
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Residues in contact with ASP 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ASP* 4.6 1.6 - - - +
83A GLY* 3.6 19.4 + - - -
84A ALA* 4.3 1.2 + - - +
209A GLY* 3.8 2.1 - - - -
210A LEU* 2.8 65.3 + - + +
255A MET* 4.5 2.3 - - - +
259A LEU* 3.9 19.3 - - + +
357A ARG* 2.8 43.6 + - - +
358A TYR 3.7 3.8 - - - +
360A ARG* 1.3 77.2 - - - +
362A ALA* 1.3 62.5 + - - +
363A ARG 3.4 0.3 + - - -
364A LEU* 3.5 9.9 + - - +
365A THR 4.5 1.0 + - - -
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Residues in contact with ALA 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A ALA 5.4 0.2 - - - +
259A LEU* 3.7 26.0 - - + +
333A ALA* 4.8 4.9 - - + -
334A VAL* 3.5 19.5 - - + +
337A CYS* 4.1 13.2 - - - -
358A TYR 2.9 20.8 + - - +
359A TRP 4.1 1.6 - - - +
361A ASP* 1.3 69.8 - - - +
363A ARG* 1.3 64.4 + - - +
364A LEU 3.0 2.7 - - - -
365A THR* 2.7 33.9 + - + +
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Residues in contact with ARG 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LEU* 4.1 10.5 - - + -
334A VAL* 3.9 9.1 - - - +
359A TRP* 2.9 51.9 + - + +
360A ARG 3.8 8.5 - - - +
361A ASP 3.3 0.2 - - - -
362A ALA* 1.3 76.3 - - - +
364A LEU* 1.3 63.5 + - - +
365A THR 3.3 0.5 + - - -
366A ARG* 3.3 32.1 + - - +
367A ILE* 3.7 13.3 - - + +
338B ASP* 2.8 42.7 + - - -
341B ILE* 3.5 14.7 - - + +
342B GLN* 3.0 39.8 + - - +
349B TYR* 4.2 6.1 - - + -
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Residues in contact with LEU 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 4.3 15.9 - - + -
207A LYS* 5.7 3.6 - - + -
210A LEU* 3.3 30.7 - - + -
255A MET* 5.8 0.7 - - + -
361A ASP 3.5 3.2 + - - +
362A ALA 3.0 1.2 + - - -
363A ARG* 1.3 80.0 - - - +
365A THR* 1.3 56.1 + - + +
366A ARG 3.1 0.4 - - - -
367A ILE* 2.9 36.9 + - + +
368A GLY* 2.9 25.1 + - - +
346B GLY* 5.8 1.8 - - - -
349B TYR* 3.7 48.4 - - + -
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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