Contacts of the helix formed by residues 390 - 407 (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 ASP 390 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D HIS* 3.1 31.0 + - + +
389D GLU* 1.3 75.7 - - - +
391D PRO* 1.3 74.5 - - - +
392D THR* 3.6 14.9 + - - +
393D HIS* 3.0 30.0 + - + +
394D LEU* 3.0 25.3 + - - +
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Residues in contact with PRO 391 (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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353D LEU* 3.7 29.8 - - + +
354D ILE 3.2 26.7 + - - +
389D GLU 2.8 10.0 - - - +
390D ASP* 1.3 87.8 - - - +
392D THR* 1.3 69.1 + - - +
393D HIS 3.1 0.5 + - - -
394D LEU* 3.1 4.2 + - + +
395D ARG* 2.7 26.1 + - - +
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Residues in contact with THR 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D LEU* 3.7 24.1 - - - +
390D ASP* 3.3 12.5 + - - +
391D PRO* 1.3 82.8 - - - +
393D HIS* 1.3 64.9 + - - +
395D ARG* 3.5 14.6 + - - +
396D ASP* 3.2 34.4 + - - +
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Residues in contact with HIS 393 (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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382D TYR 3.3 24.6 + - - -
383D THR* 4.5 0.9 - - - -
384D ASP* 3.8 33.5 + - + +
387D HIS* 5.0 4.5 - - + +
390D ASP* 3.0 30.9 + - + +
391D PRO 3.1 0.6 - - - -
392D THR* 1.3 73.9 - - - +
394D LEU* 1.3 59.9 + - + +
396D ASP* 3.1 9.9 + - + +
397D ALA* 2.7 40.5 + - + +
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Residues in contact with LEU 394 (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* 3.6 29.8 - - + +
355D SER 3.7 16.6 - - - -
356D ARG* 3.7 27.6 - - + +
359D PHE* 3.5 35.5 - - + -
383D THR* 6.1 2.7 - - - -
387D HIS 5.7 0.4 - - - +
388D PRO 4.3 2.2 - - - +
389D GLU* 3.5 23.3 - - - +
390D ASP 3.0 18.9 + - - +
391D PRO 3.2 6.3 - - - +
393D HIS* 1.3 78.7 - - + +
395D ARG* 1.3 64.3 + - - +
397D ALA* 2.8 16.6 + - - +
398D MET* 2.9 13.3 + - - +
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Residues in contact with ARG 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346D PHE* 3.8 18.1 - - + -
351D GLU* 3.1 32.5 + - - +
352D SER* 3.2 22.9 - - - +
353D LEU* 3.3 25.5 - - - +
354D ILE* 3.8 9.5 - - + +
391D PRO 2.7 20.3 + - - +
392D THR* 3.5 16.8 + - - +
394D LEU* 1.3 75.5 - - - +
396D ASP* 1.3 104.4 + - - +
397D ALA 3.0 0.2 + - - -
398D MET* 3.1 11.1 + - - +
399D SER* 3.2 11.8 + - - -
442D TRP* 3.7 42.1 + - + +
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Residues in contact with ASP 396 (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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392D THR* 3.2 19.3 + - - +
393D HIS* 3.1 10.7 + - + +
395D ARG* 1.3 110.9 + - - +
397D ALA* 1.3 62.0 + - - +
399D SER* 3.3 9.4 + - - -
400D ALA* 3.0 22.0 + - - +
442D TRP 4.8 4.3 - - - +
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Residues in contact with ALA 397 (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* 3.5 20.4 - - + -
382D TYR* 3.9 26.3 - - + +
393D HIS* 2.7 25.2 + - + +
394D LEU* 2.8 12.5 + - + +
396D ASP* 1.3 68.7 - - - +
398D MET* 1.3 56.6 - - - +
400D ALA* 2.9 10.5 + - - +
401D VAL* 2.7 36.8 + - - +
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Residues in contact with MET 398 (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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339D LEU* 4.0 13.2 - - + -
343D VAL* 4.4 3.6 - - + -
346D PHE* 3.4 35.9 - - + -
354D ILE* 4.5 2.2 - - + -
359D PHE* 2.9 48.4 - - + +
362D GLY* 3.4 18.2 - - - +
363D VAL* 3.0 30.1 - - + +
366D GLY* 5.8 1.6 - - - -
394D LEU 2.9 8.5 + - - +
395D ARG 3.3 9.2 - - - +
397D ALA* 1.3 75.9 - - - +
399D SER* 1.3 63.6 + - - +
401D VAL* 3.0 17.8 + - + +
402D VAL* 3.1 21.1 + - - +
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Residues in contact with SER 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333D ASP* 4.2 12.8 + - - +
335D GLY* 3.4 9.1 + - - -
336D SER* 3.3 25.5 + - - -
339D LEU* 3.5 22.5 - - - +
395D ARG* 3.2 8.1 + - - -
396D ASP* 3.6 11.2 - - - -
397D ALA 3.2 0.2 - - - -
398D MET* 1.3 78.9 - - - +
400D ALA* 1.3 58.1 + - - +
402D VAL 3.5 0.2 + - - -
403D GLY* 2.9 25.5 + - - -
442D TRP* 5.3 4.5 - - - -
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Residues in contact with ALA 400 (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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382D TYR* 3.6 18.6 - - + -
396D ASP 3.0 12.1 + - - +
397D ALA* 2.9 10.9 + - - +
399D SER* 1.3 75.0 + - - +
401D VAL* 1.3 58.5 + - - +
403D GLY* 4.4 1.1 - - - +
404D ASP* 2.6 50.3 + - - +
525D ARG* 5.1 9.9 - - - +
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Residues in contact with VAL 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359D PHE* 4.7 1.1 - - + -
363D VAL* 4.5 16.8 - - + -
366D GLY* 5.4 1.3 - - - -
367D VAL* 3.7 29.8 - - + -
378D VAL* 3.8 17.3 - - + -
382D TYR* 3.6 38.8 - - + -
397D ALA 2.7 25.6 + - - +
398D MET* 3.0 11.2 + - - +
400D ALA* 1.3 71.3 - - - +
402D VAL* 1.3 63.4 + - + +
405D HIS* 2.9 34.7 + - - +
532D TRP* 3.9 6.0 - - + -
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Residues in contact with VAL 402 (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 15.5 - - + -
295D PHE* 4.0 15.0 - - + -
335D GLY* 3.9 19.5 - - - +
338D PHE* 4.3 8.3 - - + -
339D LEU* 3.6 26.7 - - + -
366D GLY* 4.4 14.1 - - - +
398D MET* 3.1 11.5 + - - +
399D SER 3.9 4.7 - - - +
401D VAL* 1.3 79.9 - - + +
403D GLY* 1.3 63.2 + - - +
405D HIS* 4.6 0.9 - - - -
406D ASN* 2.9 49.4 + - - +
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Residues in contact with GLY 403 (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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295D PHE* 6.0 0.4 - - - -
334D GLU* 3.8 9.2 - - - -
335D GLY* 3.3 24.3 - - - -
399D SER 2.9 16.6 + - - -
400D ALA* 3.8 0.7 - - - -
402D VAL* 1.3 73.9 - - - +
404D ASP* 1.4 62.3 + - - +
407D VAL* 3.0 11.6 + - - +
408D VAL* 3.0 27.8 + - - +
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Residues in contact with ASP 404 (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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382D TYR* 2.6 35.7 + - - +
400D ALA* 2.6 29.2 + - - +
403D GLY* 1.4 75.0 - - - +
405D HIS* 1.3 62.2 + - - +
408D VAL* 4.1 11.0 - - - +
409D CYS* 2.9 39.2 + - - +
410D PRO* 3.3 3.8 - - - +
525D ARG* 3.3 36.3 + - - -
528D THR* 3.4 11.1 - - - +
532D TRP* 3.7 6.3 - - - +
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Residues in contact with HIS 405 (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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235D PRO* 3.7 19.4 - - + +
296D ARG* 3.9 11.8 + - - -
366D GLY 3.9 20.9 - - - -
367D VAL* 4.3 6.2 - - + +
369D GLN* 2.9 35.8 + - - -
401D VAL* 2.9 21.7 + - + +
402D VAL* 3.9 2.2 - - - +
404D ASP* 1.3 78.7 - - - +
406D ASN* 1.3 60.9 + - - +
409D CYS* 5.4 0.2 - - - +
410D PRO* 3.5 14.6 - - - +
532D TRP* 3.3 44.9 - + + +
536D LEU* 5.4 2.5 - - + -
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Residues in contact with ASN 406 (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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230D GLY* 5.8 0.3 - - - -
231D THR* 5.2 2.6 + - - -
234D GLY* 5.1 0.3 - - - -
235D PRO* 3.5 5.2 - - - +
236D TRP* 3.2 34.9 + - + +
295D PHE* 3.2 46.0 - - + +
296D ARG* 3.0 27.1 + - - +
366D GLY 4.8 2.8 + - - -
402D VAL* 2.9 33.6 + - - +
405D HIS* 1.3 82.4 - - - +
407D VAL* 1.3 59.3 + - + +
410D PRO* 3.2 17.6 - - - +
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Residues in contact with VAL 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D SER* 3.3 34.5 - - - +
230D GLY* 4.0 3.1 - - - +
231D THR* 5.0 0.3 - - - +
236D TRP* 5.0 1.1 - - + +
295D PHE* 3.7 31.2 - - + -
330D VAL* 4.2 0.2 - - + -
334D GLU* 3.2 47.6 - - + +
403D GLY* 3.0 7.3 + - - +
405D HIS 3.8 0.2 - - - -
406D ASN* 1.3 81.9 - - + +
408D VAL* 1.3 60.3 + - - +
410D PRO* 3.0 5.9 - - - +
411D VAL* 2.9 36.6 + - + +
447D HIS* 4.3 2.0 - - - +
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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
------------------------------------------------------------
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