Contacts of the helix formed by residues 332 - 345 (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 ASP 332 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330D PRO 3.9 1.8 + - - +
331D PRO* 1.3 73.3 - - - +
333D MET* 1.3 68.5 + - - +
334D LEU* 3.7 9.8 + - - +
335D GLY* 2.7 24.8 + - - +
336D ARG* 2.9 18.7 + - - +
446D ILE* 4.2 11.9 - - + -
589D LYS 5.6 0.7 - - - -
590D GLU* 3.6 10.1 - - + +
591D THR* 2.6 36.2 + - + +
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Residues in contact with MET 333 (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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332D ASP* 1.3 73.7 - - - +
334D LEU* 1.3 87.6 + - + +
336D ARG* 3.2 21.3 + - - +
337D LYS* 3.0 21.1 + - + +
356D GLU* 3.6 33.2 - - + +
359D ALA* 3.7 19.7 - - - +
360D LYS* 4.2 30.5 - - + +
588D GLU 5.9 2.5 - - - +
589D LYS 5.5 4.9 + - - +
590D GLU* 2.5 24.7 + - + +
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Residues in contact with LEU 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D ASP* 3.3 8.8 + - - +
333D MET* 1.3 103.2 - - + +
335D GLY* 1.3 57.2 + - - +
337D LYS* 3.1 12.0 + - + +
338D LYS* 2.9 55.6 + - - +
356D GLU* 5.8 1.1 - - - +
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Residues in contact with GLY 335 (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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165D GLY* 4.1 18.8 + - - -
167D GLU* 5.6 1.6 - - - -
331D PRO* 4.1 11.2 - - - -
332D ASP* 2.7 21.2 + - - -
334D LEU* 1.3 71.0 - - - +
336D ARG* 1.3 58.3 + - - -
337D LYS 3.1 1.3 - - - -
338D LYS* 3.1 10.7 + - - +
339D ILE* 2.9 32.4 + - - +
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Residues in contact with ARG 336 (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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331D PRO* 3.0 31.0 + - + +
332D ASP* 2.9 21.7 + - - +
333D MET* 3.6 16.0 - - - +
335D GLY* 1.3 72.9 - - - +
337D LYS* 1.3 65.3 + - - +
339D ILE* 3.8 1.5 - - - +
340D LEU* 3.1 29.8 + - - +
359D ALA* 3.1 34.7 + - + -
360D LYS* 4.6 3.4 + - - +
362D THR* 2.9 26.0 + - - +
363D PRO* 3.5 24.0 - - - +
364D GLY 4.3 0.4 - - - +
365D PHE* 3.8 14.1 - - - -
370D LEU* 3.6 25.2 - - + +
446D ILE* 4.0 4.9 - - - +
590D GLU* 2.9 30.5 + - - -
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Residues in contact with LYS 337 (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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333D MET* 3.0 15.1 + - - +
334D LEU* 3.2 20.2 - - + +
335D GLY 3.1 0.2 - - - -
336D ARG* 1.3 77.1 - - - +
338D LYS* 1.3 74.7 + - + +
340D LEU* 3.0 8.5 + - - +
341D GLU* 3.0 52.1 + - + +
355D LEU* 4.5 4.7 - - + +
356D GLU* 4.2 48.7 + - + +
359D ALA* 4.0 9.1 - - + +
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Residues in contact with LYS 338 (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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164D GLY* 4.4 13.2 - - - -
165D GLY* 4.4 5.6 - - - +
167D GLU* 5.1 10.3 - - - +
334D LEU* 2.9 45.3 + - - +
335D GLY* 3.1 10.5 + - - +
337D LYS* 1.3 83.4 - - + +
339D ILE* 1.3 62.7 + - - +
341D GLU* 3.3 20.0 + - - +
342D ILE* 3.0 30.0 + - + +
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Residues in contact with ILE 339 (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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164D GLY 3.9 17.0 - - - +
331D PRO* 4.0 21.5 - - + -
335D GLY 2.9 21.0 + - - +
336D ARG 3.8 4.5 - - - +
337D LYS 3.2 0.2 - - - -
338D LYS* 1.3 78.1 - - - +
340D LEU* 1.3 62.1 + - - +
342D ILE* 3.2 7.9 + - - +
343D HIS* 3.1 41.9 + - + -
367D GLY* 4.1 15.9 - - - +
370D LEU* 3.7 35.9 - - + -
1608D ADP 3.7 26.2 - - + +
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Residues in contact with LEU 340 (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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336D ARG 3.1 20.4 + - - +
337D LYS* 3.0 7.1 + - - +
339D ILE* 1.3 73.9 - - - +
341D GLU* 1.3 68.0 + - - +
343D HIS* 3.4 1.4 + - - +
344D THR* 3.0 28.2 + - - -
355D LEU* 3.9 37.9 - - + +
358D ILE* 3.7 26.2 - - + -
359D ALA* 4.0 7.6 - - - +
370D LEU* 4.4 19.5 - - + +
373D LEU* 4.1 19.1 - - + -
374D VAL* 3.5 28.3 - - + -
394D PHE* 4.6 2.0 - - + -
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Residues in contact with GLU 341 (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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337D LYS* 3.0 45.0 + - + +
338D LYS* 3.6 25.5 + - - +
340D LEU* 1.3 76.7 - - - +
342D ILE* 1.3 61.9 + - + +
344D THR* 3.1 3.3 + - - +
345D ARG* 3.0 27.7 + - - +
355D LEU* 4.0 19.8 - - + +
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Residues in contact with ILE 342 (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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161D LYS 3.4 14.8 - - - +
162D ASP* 3.5 24.7 - - + +
163D VAL 3.5 6.7 - - - +
164D GLY* 3.4 35.7 - - - +
338D LYS* 3.0 15.9 + - + +
339D ILE 3.2 7.4 + - - +
341D GLU* 1.3 78.0 - - + +
343D HIS* 1.3 75.2 + - + +
344D THR 3.0 3.3 + - - -
345D ARG* 3.5 45.8 + - - +
1608D ADP 4.4 2.5 - - + -
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Residues in contact with HIS 343 (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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162D ASP 5.1 1.6 - - - -
339D ILE* 3.1 36.9 + - + +
340D LEU 3.7 0.7 - - - +
342D ILE* 1.3 87.9 - - + +
344D THR* 1.3 59.7 + - - +
346D ASN 5.3 0.8 + - - -
347D LYS* 3.8 13.9 + - - +
371D GLU* 4.1 27.4 + - + +
374D VAL* 3.5 34.1 - - + +
1608D ADP 2.9 53.2 + + - -
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Residues in contact with THR 344 (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 3.0 18.8 + - - -
341D GLU* 3.7 3.8 - - - +
342D ILE 3.0 0.2 - - - -
343D HIS* 1.3 81.4 + - - +
345D ARG* 1.3 67.3 + - - +
346D ASN 3.1 2.7 - - - -
347D LYS* 2.8 22.3 + - - +
349D LEU* 3.1 47.9 - - + +
355D LEU* 4.3 8.8 - - + +
374D VAL* 4.1 15.2 - - - +
394D PHE* 4.4 5.7 - - - -
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Residues in contact with ARG 345 (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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161D LYS* 2.4 48.3 + - - +
162D ASP* 3.4 19.0 + - - -
341D GLU 3.0 15.8 + - - +
342D ILE* 3.5 33.2 + - - +
343D HIS 3.6 0.2 - - - -
344D THR* 1.3 77.2 - - - +
346D ASN* 1.3 77.4 + - - +
347D LYS 3.6 2.9 + - - +
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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