Contacts of the helix formed by residues 390 - 403 (chain D) in PDB entry 2CEA
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 390 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350D ALA* 3.8 15.9 - - + -
352D ASP* 4.2 8.7 - - - +
353D VAL* 3.5 3.6 - - - -
386D ARG* 3.8 22.7 + - - +
388D LYS* 3.9 4.7 - - + +
389D ILE* 1.3 75.4 - - - +
391D MET* 1.3 67.4 + - - +
392D LYS* 3.5 11.3 + - - +
393D ASP* 3.0 42.0 + - - +
394D PHE* 3.3 8.3 + - - -
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Residues in contact with MET 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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352D ASP* 3.2 35.5 + - + +
353D VAL* 3.3 7.4 - - - +
354D ASN* 3.6 32.1 - - + +
357D ILE* 3.6 42.0 - - + -
358D ILE* 4.1 20.9 - - + -
390D THR* 1.3 71.2 - - - +
392D LYS* 1.3 64.7 + - - +
394D PHE* 2.9 18.1 + - - +
395D GLU* 3.0 32.1 + - - +
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Residues in contact with LYS 392 (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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352D ASP* 4.9 0.6 + - - -
384D GLU* 5.2 8.1 + - - -
386D ARG* 5.8 2.0 - - - +
390D THR* 3.2 11.2 + - - +
391D MET* 1.3 78.8 - - - +
393D ASP* 1.3 62.6 + - - +
395D GLU* 3.7 14.1 - - + +
396D GLU* 2.9 57.9 + - + +
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Residues in contact with ASP 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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377D ALA* 3.8 23.3 - - - +
380D LEU* 3.6 14.3 - - + +
381D ALA* 3.5 12.0 - - - +
386D ARG* 3.0 41.7 + - - -
389D ILE* 3.8 5.8 - - + -
390D THR* 3.0 29.8 + - - +
392D LYS* 1.3 77.9 + - - +
394D PHE* 1.3 52.4 + - - +
396D GLU* 3.2 15.0 + - - +
397D ALA* 2.8 33.4 + - - +
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Residues in contact with PHE 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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340D LEU* 4.6 1.1 - - + -
344D THR* 4.4 5.2 - - - -
349D LEU* 4.1 16.6 - - + -
353D VAL* 4.0 24.9 - - + -
355D LEU* 4.1 19.1 - - + -
358D ILE* 3.6 37.5 - - + -
373D LEU* 4.1 9.3 - - + +
374D VAL* 4.2 24.7 - - + -
377D ALA* 3.9 11.6 - - + +
389D ILE* 3.5 27.4 - - + -
390D THR 3.4 12.6 - - - -
391D MET* 2.9 11.1 + - - +
393D ASP* 1.3 72.0 - - - +
395D GLU* 1.3 68.8 + - - +
397D ALA* 3.0 16.0 + - - +
398D ILE* 3.1 16.3 + - - +
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Residues in contact with GLU 395 (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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358D ILE* 4.7 2.7 - - + -
361D ARG* 2.3 41.7 + - - +
391D MET* 3.0 41.1 + - + +
392D LYS* 3.7 16.6 + - + +
394D PHE* 1.3 77.6 - - - +
396D GLU* 1.3 62.4 + - + +
398D ILE* 3.3 24.5 + - - +
399D ASP* 3.7 10.3 + - - +
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Residues in contact with GLU 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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380D LEU* 3.8 18.4 - - + +
392D LYS* 2.9 53.4 + - + +
393D ASP* 3.5 15.8 - - - +
395D GLU* 1.3 74.2 - - + +
397D ALA* 1.3 65.9 + - - +
398D ILE 3.3 0.2 - - - -
399D ASP* 3.6 10.7 + - - +
400D ARG* 3.3 24.1 + - + +
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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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373D LEU* 3.4 32.5 - - + +
376D GLU* 4.1 6.1 - - + -
377D ALA 3.9 11.9 - - - +
380D LEU* 4.1 4.5 - - - +
393D ASP 2.8 17.4 + - - +
394D PHE* 3.0 13.9 + - - +
396D GLU* 1.3 70.2 - - - +
398D ILE* 1.3 69.3 + - - +
400D ARG* 2.8 18.2 + - - +
401D VAL* 3.0 14.6 + - - +
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Residues in contact with ILE 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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358D ILE* 4.2 13.9 - - + -
361D ARG* 4.1 30.5 - - + +
362D THR* 4.2 20.6 - - + -
365D PHE* 4.6 7.0 - - + -
373D LEU* 3.5 20.0 - - + -
394D PHE 3.1 14.3 + - - +
395D GLU* 3.5 11.2 - - - +
397D ALA* 1.3 76.3 - - - +
399D ASP* 1.3 71.6 + - - +
401D VAL* 2.9 20.0 - - - +
402D ILE* 3.0 16.5 + - + +
411D LEU* 3.8 28.9 - - + -
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Residues in contact with ASP 399 (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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395D GLU 3.7 12.4 + - - +
396D GLU* 3.6 10.6 + - - +
397D ALA 3.2 0.6 - - - -
398D ILE* 1.3 83.6 - - - +
400D ARG* 1.3 64.3 + - + +
402D ILE* 3.4 9.8 - - - +
403D ALA* 3.2 24.1 + - - +
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Residues in contact with ARG 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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376D GLU* 3.7 25.8 + - + +
380D LEU* 4.1 31.9 - - - +
383D ARG* 3.9 20.6 - - - +
396D GLU* 3.3 14.3 + - + +
397D ALA* 2.8 11.6 + - - +
399D ASP* 1.3 73.6 - - + +
401D VAL* 1.3 56.1 + - + +
402D ILE 2.7 14.5 + - - +
403D ALA 2.6 26.1 - - - +
172E GLU* 5.7 4.9 + - - -
175E GLU* 4.7 5.5 + - - -
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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
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365D PHE* 3.9 24.9 - - + -
369D ASP 5.0 1.3 - - - +
372D ASN* 3.0 33.4 - - + +
373D LEU* 4.0 16.4 - - + +
376D GLU* 3.7 19.0 - - + +
397D ALA 3.0 8.7 + - - +
398D ILE* 2.9 24.2 - - - +
400D ARG* 1.3 74.5 - - - +
402D ILE* 1.3 61.6 + - - +
408D LYS* 3.4 7.7 - - - +
409D SER* 2.9 30.3 + - - +
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Residues in contact with ILE 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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365D PHE* 4.5 8.3 - - + -
398D ILE* 3.0 26.0 + - + +
399D ASP* 3.4 11.2 - - - +
400D ARG 2.7 4.7 + - - +
401D VAL* 1.3 81.0 - - - +
403D ALA* 1.3 92.0 + - + +
408D LYS* 3.3 24.2 - - - +
409D SER 4.0 16.8 - - - +
411D LEU* 3.6 39.5 - - + +
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Residues in contact with ALA 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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399D ASP 3.2 10.4 + - - +
400D ARG* 2.6 24.1 - - - +
402D ILE* 1.3 92.0 - - + +
408D LYS* 4.8 9.6 - - - +
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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