Contacts of the helix formed by residues 332 - 345 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A PRO 3.8 2.0 + - - -
331A PRO* 1.3 74.6 - - - +
333A MET* 1.3 61.2 + - - +
334A LEU* 3.3 9.1 + - - +
335A GLY* 2.7 34.1 + - - -
336A ARG* 2.9 29.9 + - - +
446A ILE* 6.0 4.7 - - + -
589A LYS 3.9 7.7 - - - +
590A GLU* 3.7 9.6 - - + +
591A THR* 3.4 33.6 + - - +
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Residues in contact with MET 333 (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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332A ASP* 1.3 77.0 - - - +
334A LEU* 1.3 83.1 + - + +
336A ARG* 3.1 23.3 + - - +
337A LYS* 3.0 18.8 + - + -
356A GLU* 3.4 42.8 - - + +
359A ALA* 3.5 23.8 - - - +
360A LYS* 4.0 18.8 - - - -
588A GLU* 3.6 21.8 - - + +
589A LYS* 3.5 26.6 + - + +
590A GLU* 3.3 7.5 + - - +
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLU* 6.2 0.2 - - - +
332A ASP* 3.3 9.6 + - - +
333A MET* 1.3 100.9 - - + +
335A GLY* 1.3 65.1 + - - +
337A LYS* 2.8 32.6 + - + +
338A LYS* 3.0 31.8 + - - +
356A GLU* 5.0 2.5 - - - +
589A LYS* 4.6 26.6 + - + +
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Residues in contact with GLY 335 (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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165A GLY* 3.7 23.9 + - - -
167A GLU* 5.9 2.0 - - - -
331A PRO* 4.0 8.7 - - - -
332A ASP* 2.7 23.2 + - - -
334A LEU* 1.3 73.0 - - - +
336A ARG* 1.3 61.6 + - - +
338A LYS* 3.3 7.8 + - - +
339A ILE* 3.2 26.0 + - - +
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Residues in contact with ARG 336 (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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331A PRO* 2.9 36.7 + - + -
332A ASP 2.9 18.9 + - - +
333A MET* 3.6 18.8 - - - +
334A LEU 3.1 0.2 - - - -
335A GLY* 1.3 72.2 - - - +
337A LYS* 1.3 66.2 + - - +
339A ILE* 3.3 2.8 + - - +
340A LEU* 3.1 29.3 + - - +
359A ALA* 3.1 29.5 + - + -
360A LYS* 4.4 3.4 + - - +
362A THR* 3.1 32.0 + - - +
363A PRO* 3.8 11.6 - - - +
364A GLY 4.3 3.8 - - - +
365A PHE* 3.8 18.6 - - - +
370A LEU* 3.7 17.1 - - + +
590A GLU* 2.9 41.6 + - - -
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Residues in contact with LYS 337 (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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333A MET* 3.0 13.0 + - + +
334A LEU* 2.8 31.2 + - + +
336A ARG* 1.3 77.2 - - - +
338A LYS* 1.3 64.9 + - + +
340A LEU* 3.2 9.5 + - - +
341A GLU* 3.0 40.4 + - + +
355A LEU* 4.1 11.9 - - + +
356A GLU* 4.0 45.8 + - + +
359A ALA* 3.8 11.4 - - + +
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Residues in contact with LYS 338 (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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164A GLY* 4.2 14.4 - - - -
165A GLY* 4.5 2.9 - - - +
167A GLU* 5.7 4.7 - - - +
334A LEU* 3.0 41.5 + - - +
335A GLY* 3.6 9.4 - - - +
337A LYS* 1.3 85.9 - - + +
339A ILE* 1.3 61.2 + - - +
341A GLU* 3.0 32.6 + - - +
342A ILE* 2.9 35.6 + - + +
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Residues in contact with ILE 339 (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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164A GLY* 3.7 20.2 - - - +
331A PRO* 4.1 21.5 - - + -
335A GLY 3.2 14.0 + - - +
336A ARG 3.3 6.0 + - - +
338A LYS* 1.3 76.4 - - - +
340A LEU* 1.3 62.2 + - - +
342A ILE* 3.4 7.7 + - - +
343A HIS* 3.1 43.2 + - + +
367A GLY* 3.9 18.2 - - - +
370A LEU* 4.0 22.2 - - + -
1604A ADP 3.6 33.2 - - + +
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Residues in contact with LEU 340 (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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336A ARG 3.1 21.2 + - - +
337A LYS* 3.4 6.1 - - - +
338A LYS 3.1 0.2 - - - -
339A ILE* 1.3 73.8 - - - +
341A GLU* 1.3 71.7 + - - +
342A ILE 3.1 0.2 + - - -
343A HIS 3.2 1.9 + - - -
344A THR* 2.9 23.9 + - - +
355A LEU* 3.7 42.8 - - + +
358A ILE* 4.1 18.8 - - + -
359A ALA* 3.9 15.0 - - - +
370A LEU* 4.0 29.2 - - + +
373A LEU* 4.9 2.7 - - + -
374A VAL* 4.0 25.9 - - + +
394A PHE* 4.9 2.9 - - + -
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Residues in contact with GLU 341 (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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337A LYS* 3.0 24.1 + - + +
338A LYS* 3.0 47.5 + - - +
340A LEU* 1.3 78.7 - - - +
342A ILE* 1.3 67.3 + - + +
344A THR* 2.9 14.2 + - - +
345A ARG* 3.0 25.7 + - - +
355A LEU* 3.8 17.8 - - + +
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Residues in contact with ILE 342 (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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161A LYS 3.6 7.4 - - - +
162A ASP* 3.3 49.1 - - + +
163A VAL 3.5 3.6 - - - +
164A GLY* 3.5 24.7 - - - +
338A LYS* 2.9 19.0 + - + +
339A ILE* 3.6 6.3 - - - +
340A LEU 3.1 0.2 - - - -
341A GLU* 1.3 75.9 - - + +
343A HIS* 1.3 71.5 + - + +
344A THR 3.0 2.9 + - - -
345A ARG* 2.9 51.0 + - + +
346A ASN* 5.5 0.9 + - - -
1604A ADP 4.4 2.7 - - + -
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Residues in contact with HIS 343 (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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162A ASP 5.5 0.9 - - - -
209A LEU* 6.2 0.4 - - + -
339A ILE* 3.1 37.3 + - + +
340A LEU 3.2 2.0 + - - +
342A ILE* 1.3 84.7 - - + +
344A THR* 1.3 58.3 + - - +
346A ASN 5.2 0.7 - - - -
347A LYS* 4.0 11.6 - - - +
370A LEU 5.2 0.2 - - - -
371A GLU* 3.5 36.6 + - + +
374A VAL* 3.5 33.4 - - + +
1604A ADP 2.8 53.5 + + - -
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Residues in contact with THR 344 (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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340A LEU 2.9 17.4 + - - +
341A GLU* 2.9 11.2 + - - +
343A HIS* 1.3 78.8 + - - +
345A ARG* 1.3 71.1 + - - +
346A ASN 3.0 3.4 - - - -
347A LYS* 2.7 26.7 + - - +
349A LEU* 3.8 38.0 - - + +
355A LEU* 4.5 9.0 - - + +
374A VAL* 4.4 5.9 - - - +
394A PHE* 4.2 11.6 - - - -
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Residues in contact with ARG 345 (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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161A LYS* 3.3 35.7 + - - +
162A ASP* 4.3 8.1 + - - -
341A GLU* 3.0 23.8 + - - +
342A ILE* 2.9 50.7 - - - +
344A THR* 1.3 79.1 - - - +
346A ASN* 1.3 75.2 + - - +
347A LYS 3.6 3.5 + - - +
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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