Contacts of the helix formed by residues 355 - 367 (chain D) in PDB entry 1C2O
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 SER 355 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353D LEU 4.0 0.2 + - - -
354D ILE* 1.3 81.0 - - - +
356D ARG* 1.3 64.5 + - - +
357D ALA* 2.9 10.2 + - - +
358D GLN* 2.8 38.6 + - - +
359D PHE* 3.2 15.2 + - - +
389D GLU 5.8 0.4 - - - -
394D LEU* 3.7 3.3 - - - +
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Residues in contact with ARG 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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355D SER* 1.3 71.7 + - - +
357D ALA* 1.3 52.5 + - - +
359D PHE* 2.7 11.9 + - + +
360D LEU* 2.7 54.6 + - + +
379D VAL* 3.4 17.7 - - - +
383D THR* 2.8 43.7 + - - +
385D TRP* 4.1 11.3 - - - -
388D PRO* 2.6 52.5 + - - +
389D GLU* 4.2 24.7 + - - +
394D LEU* 3.7 26.8 - - + +
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Residues in contact with ALA 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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355D SER* 2.9 6.7 + - - +
356D ARG* 1.3 78.3 - - - +
358D GLN* 1.3 63.4 + - + +
360D LEU* 3.2 16.2 + - + +
361D ALA* 3.0 22.5 + - - +
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Residues in contact with GLN 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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343D VAL* 5.2 2.1 - - - +
344D PRO* 4.0 20.3 + - + +
345D GLY* 3.6 26.2 - - - +
353D LEU 4.7 0.2 - - - +
354D ILE* 3.1 19.4 - - + +
355D SER* 2.8 45.3 + - - +
357D ALA* 1.3 75.8 - - + +
359D PHE* 1.3 53.0 + - - +
361D ALA* 2.8 10.2 + - - +
362D GLY* 2.7 33.1 + - - -
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Residues in contact with PHE 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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354D ILE* 3.3 20.0 - - + +
355D SER 3.2 2.8 + - - +
356D ARG* 2.7 15.9 + - - +
358D GLN* 1.3 74.6 - - - +
360D LEU* 1.3 71.7 + - + -
363D VAL* 3.0 23.1 + - + +
379D VAL* 3.8 26.7 - - + -
382D TYR* 4.2 24.2 - - + -
383D THR* 4.5 5.2 - - - -
394D LEU* 3.5 43.3 - - + -
397D ALA* 3.5 25.6 - - + -
398D MET* 2.9 46.8 - - + +
401D VAL* 4.7 0.9 - - + -
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Residues in contact with LEU 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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356D ARG* 2.7 58.6 + - + +
357D ALA* 3.5 13.2 - - + +
359D PHE* 1.3 80.5 - - + +
361D ALA* 1.3 61.1 + - - +
363D VAL* 3.6 9.4 + - - +
364D ARG* 3.4 18.9 - - - +
379D VAL* 3.7 39.5 - - + +
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Residues in contact with ALA 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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344D PRO* 5.6 8.3 - - + -
357D ALA 3.0 11.6 + - - +
358D GLN* 2.8 14.8 + - - +
360D LEU* 1.3 71.0 - - - +
362D GLY* 1.3 69.5 + - - +
364D ARG* 2.8 21.1 + - - +
365D ILE* 3.1 19.7 + - + +
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Residues in contact with GLY 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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343D VAL* 3.8 20.5 - - - +
344D PRO* 6.1 0.2 - - - +
358D GLN 2.7 16.5 + - - -
359D PHE 3.2 0.4 + - - -
361D ALA* 1.3 72.4 - - - +
363D VAL* 1.3 64.7 + - - +
365D ILE* 2.7 19.5 + - - +
366D GLY* 2.7 13.3 + - - -
398D MET* 3.4 25.1 - - - +
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Residues in contact with VAL 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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359D PHE* 3.0 29.2 + - + +
360D LEU 3.7 9.4 - - - +
361D ALA 3.1 0.2 - - - -
362D GLY* 1.3 75.2 - - - +
364D ARG* 1.3 58.1 + - - +
366D GLY* 4.7 0.9 - - - +
367D VAL* 3.0 35.4 + - + +
370D ALA* 5.7 0.2 - - - +
375D ALA* 4.2 23.1 - - + +
378D VAL* 4.1 33.9 - - + -
379D VAL* 4.2 9.4 - - + -
398D MET* 3.0 25.3 - - + +
401D VAL* 4.5 6.7 - - + -
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Residues in contact with ARG 364 (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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292D GLU 4.5 1.6 - - - +
360D LEU 3.4 18.4 - - - +
361D ALA* 2.8 14.8 + - - +
363D VAL* 1.3 73.2 + - - +
365D ILE* 1.3 61.1 + - + +
367D VAL 3.7 4.6 + - - +
368D PRO* 3.3 23.0 - - - +
370D ALA 3.0 26.7 + - - -
371D SER* 3.5 8.7 + - - +
372D ASP* 2.9 28.9 + - - +
375D ALA* 3.4 30.6 - - - +
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Residues in contact with ILE 365 (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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292D GLU* 3.7 35.9 - - + +
293D SER* 3.4 24.8 - - - +
294D ILE* 3.4 25.5 + - + -
342D GLY 3.3 22.9 - - - +
343D VAL* 3.9 12.3 - - + -
344D PRO* 3.7 18.2 - - + -
361D ALA* 3.1 16.5 + - + +
362D GLY* 2.7 15.2 + - - +
364D ARG* 1.3 74.3 - - + +
366D GLY* 1.3 58.5 + - - +
368D PRO* 2.9 21.0 - - - +
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Residues in contact with GLY 366 (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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294D ILE* 3.8 22.2 - - - +
296D ARG* 4.1 5.4 + - - -
362D GLY 2.7 13.4 + - - -
363D VAL* 4.0 1.3 - - - -
365D ILE* 1.3 80.3 - - - +
367D VAL* 1.3 63.2 + - - +
368D PRO* 3.3 5.2 - - - +
398D MET* 5.8 1.1 - - - -
401D VAL* 5.4 2.0 - - - +
402D VAL* 4.4 13.6 - - - +
405D HIS* 3.9 14.4 - - - +
406D ASN* 4.8 5.2 + - - -
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Residues in contact with VAL 367 (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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363D VAL* 3.0 26.3 + - + +
364D ARG* 3.6 8.1 + - - +
366D GLY* 1.3 81.1 - - - +
368D PRO* 1.3 61.4 - - - +
369D GLN* 3.1 17.9 - - - +
370D ALA* 2.9 43.2 + - + +
378D VAL* 4.7 6.3 - - + -
401D VAL* 3.7 27.8 - - + -
405D HIS* 4.3 9.9 - - + +
532D TRP* 4.2 19.5 - - + -
536D LEU* 5.1 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