Contacts of the helix formed by residues 348 - 359 (chain A) in PDB entry 2CI9
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 THR 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A TYR* 3.6 12.6 - - - -
346A PHE* 3.2 9.8 - - - +
347A SER* 1.3 96.1 + - - +
349A MET* 1.3 64.3 + - - +
350A GLU* 3.4 19.2 + - - +
351A GLU* 3.1 27.6 + - + +
352A LEU* 3.2 15.6 + - - +
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Residues in contact with MET 349 (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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282A TRP* 3.6 56.0 - - + +
307A ILE* 3.8 24.0 - - + -
317A PHE* 4.0 18.6 - - + -
332A VAL* 3.9 22.7 - - + -
339A TYR* 3.6 39.7 - - + -
348A THR* 1.3 73.9 - - - +
350A GLU* 1.3 63.5 + - - +
352A LEU* 3.2 19.0 + - - +
353A VAL* 3.0 22.1 + - - +
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Residues in contact with GLU 350 (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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280A SER* 5.3 1.0 + - - -
281A PRO* 4.5 16.2 - - + +
282A TRP* 3.5 31.9 + - + -
348A THR* 3.1 21.0 - - - +
349A MET* 1.3 81.9 + - - +
351A GLU* 1.3 58.0 + - + +
353A VAL* 3.4 7.1 + - - +
354A GLU* 3.0 34.5 + - + +
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Residues in contact with GLU 351 (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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346A PHE* 3.8 10.1 - - + -
347A SER* 4.6 1.1 - - - +
348A THR* 3.1 22.7 + - + +
350A GLU* 1.3 75.5 - - + +
352A LEU* 1.3 66.1 + - - +
354A GLU* 3.8 13.5 - - - +
355A HIS* 3.1 23.4 + - - +
298B GLU* 3.5 58.4 - - + +
299B ARG* 5.7 1.7 - - - +
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Residues in contact with LEU 352 (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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319A VAL* 4.8 7.6 - - + -
332A VAL* 3.8 31.0 - - + -
339A TYR* 4.1 8.7 - - + +
341A ILE* 3.6 33.9 - - + -
346A PHE* 3.6 29.2 - - + -
348A THR 3.2 8.1 + - - +
349A MET* 3.2 23.7 + - - +
351A GLU* 1.3 77.9 - - - +
353A VAL* 1.3 72.4 + - + +
355A HIS* 3.3 10.2 + - - +
356A TYR* 3.3 33.3 + - + -
361A ILE* 5.7 0.7 - - + -
372A LEU* 5.2 3.6 - - + -
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Residues in contact with VAL 353 (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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282A TRP* 5.2 1.3 - - + -
305A PHE* 3.7 29.8 - - + -
307A ILE* 3.8 27.8 - - + -
349A MET* 3.0 18.1 + - + +
350A GLU* 3.7 9.4 - - - +
351A GLU 3.3 0.2 - - - -
352A LEU* 1.3 83.9 - - + +
354A GLU* 1.3 67.5 + - - +
356A TYR* 3.2 3.6 + - - +
357A LYS* 3.1 41.3 + - - +
372A LEU* 4.2 9.5 - - + +
375A HIS* 4.1 13.0 - - + +
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Residues in contact with GLU 354 (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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350A GLU* 3.0 23.4 + - + +
351A GLU* 3.8 16.6 - - - +
352A LEU 3.3 0.2 - - - -
353A VAL* 1.3 79.3 - - - +
355A HIS* 1.3 62.8 + - - +
357A LYS* 3.0 51.7 + - - +
358A LYS* 3.9 6.4 + - - +
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Residues in contact with HIS 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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344A ARG* 3.4 42.0 + - - -
346A PHE* 3.6 27.3 - + + -
351A GLU 3.1 6.8 + - - +
352A LEU 3.5 8.7 - - - +
353A VAL 3.2 0.2 - - - -
354A GLU* 1.3 77.0 - - - +
356A TYR* 1.3 92.1 + + - +
358A LYS* 3.2 6.8 + - - +
359A ALA* 3.0 47.3 + - + +
480L ASP* 4.1 6.9 + - - -
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Residues in contact with TYR 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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341A ILE* 3.7 34.3 + - + +
344A ARG* 4.0 17.3 - - - +
346A PHE* 4.2 5.6 - + - -
352A LEU* 3.3 27.3 + - + +
353A VAL 3.2 3.9 + - - -
355A HIS* 1.3 96.4 + + - +
357A LYS* 1.3 61.1 + - - +
358A LYS 3.3 0.4 - - - -
359A ALA 3.3 14.1 - - - +
360A PRO 3.5 25.8 - - - -
361A ILE* 3.5 25.4 - - + -
371A TYR* 3.7 2.9 - - - -
372A LEU* 2.9 46.6 + - + -
477L VAL* 3.5 24.6 - - + +
478L ALA 5.1 2.8 + - - -
480L ASP* 6.0 0.6 - - - +
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Residues in contact with LYS 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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305A PHE* 5.3 1.1 - - - -
353A VAL* 3.1 29.3 + - + +
354A GLU* 3.0 43.7 + - - +
355A HIS 3.3 0.6 - - - -
356A TYR* 1.3 77.3 - - - +
358A LYS* 1.3 66.1 + - + +
371A TYR* 3.8 15.8 - - - +
372A LEU* 3.4 23.4 - - + +
373A VAL 3.7 21.2 + - - +
374A LYS* 5.1 4.6 - - - +
375A HIS* 5.8 4.3 - - - -
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Residues in contact with LYS 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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354A GLU 3.9 5.1 + - - +
355A HIS 3.2 6.6 + - - +
357A LYS* 1.3 87.7 - - + +
359A ALA* 1.3 57.8 + - - +
360A PRO* 4.6 0.5 - - - +
371A TYR* 3.6 13.0 - - - -
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Residues in contact with ALA 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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355A HIS* 3.0 40.2 + - + +
356A TYR* 3.3 24.4 - - - +
358A LYS* 1.3 77.5 - - - +
360A PRO* 1.3 76.2 - - + +
371A TYR* 3.6 3.0 - - - -
480L ASP* 5.9 0.7 - - - +
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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