Contacts of the helix formed by residues 332 - 345 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330E PRO 3.8 1.6 + - - -
331E PRO* 1.3 69.8 - - - +
333E MET* 1.3 66.4 + - - +
334E LEU* 3.4 8.5 + - - +
335E GLY* 2.7 34.7 + - - -
336E ARG* 2.8 32.6 + - - +
446E ILE* 4.7 8.0 - - + +
589E LYS 3.9 12.6 - - - +
590E GLU* 3.7 8.5 - - + +
591E THR* 3.7 31.8 - - - +
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Residues in contact with MET 333 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332E ASP* 1.3 78.9 - - - +
334E LEU* 1.3 89.8 + - + +
336E ARG* 3.2 28.3 + - - +
337E LYS* 3.0 18.5 + - - +
356E GLU* 4.1 31.6 - - + +
359E ALA* 3.5 16.4 - - + +
360E LYS* 4.0 19.1 - - + -
588E GLU* 3.5 26.0 - - + +
589E LYS* 3.4 27.6 + - + +
590E GLU* 3.8 3.0 + - - +
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Residues in contact with LEU 334 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332E ASP* 3.4 7.8 + - - +
333E MET* 1.3 100.9 - - + +
335E GLY* 1.3 63.1 + - - +
337E LYS* 3.0 30.7 + - + +
338E LYS* 3.0 33.6 + - + +
356E GLU* 4.6 4.9 - - - +
589E LYS* 4.8 24.5 + - + +
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Residues in contact with GLY 335 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E GLY 4.4 1.0 - - - -
165E GLY* 3.9 23.8 - - - -
167E GLU* 6.1 0.4 - - - -
331E PRO* 4.0 11.7 - - - -
332E ASP* 2.7 24.0 + - - -
334E LEU* 1.3 73.6 - - - +
336E ARG* 1.3 61.7 + - - +
338E LYS* 3.1 6.9 + - - +
339E ILE* 3.1 24.5 + - - +
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Residues in contact with ARG 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331E PRO* 3.2 28.4 + - + +
332E ASP 2.8 33.8 + - - +
333E MET* 3.4 17.0 - - - +
335E GLY* 1.3 71.6 - - - +
337E LYS* 1.3 63.0 + - - +
339E ILE* 3.2 4.1 + - - +
340E LEU* 3.0 28.3 + - - +
359E ALA* 2.9 39.2 + - + -
360E LYS* 4.2 5.5 + - - +
362E THR* 3.0 27.6 + - - +
363E PRO* 3.7 11.8 - - - +
364E GLY 4.5 2.6 - - - +
365E PHE* 3.9 18.6 - - - -
370E LEU* 3.8 17.7 - - + +
590E GLU* 2.4 45.8 + - - -
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Residues in contact with LYS 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333E MET* 3.0 12.2 + - - +
334E LEU* 3.0 31.9 + - + +
336E ARG* 1.3 77.5 - - - +
338E LYS* 1.3 76.2 + - - +
340E LEU* 3.3 6.5 + - - +
341E GLU* 3.0 27.7 + - + +
355E LEU* 4.5 10.9 - - + +
356E GLU* 3.7 44.4 + - + +
359E ALA* 3.9 10.7 - - + +
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Residues in contact with LYS 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164E GLY* 4.2 15.9 - - - -
165E GLY* 4.5 4.7 - - - +
167E GLU* 6.1 0.4 - - - +
334E LEU* 3.0 27.5 + - + +
335E GLY* 3.1 6.9 + - - +
337E LYS* 1.3 97.0 - - - +
339E ILE* 1.3 62.3 + - - +
341E GLU* 3.2 26.7 + - - +
342E ILE* 2.9 34.3 + - + +
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Residues in contact with ILE 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E GLY* 3.7 19.7 - - - +
331E PRO* 3.9 19.5 - - + -
335E GLY 3.1 14.4 + - - +
336E ARG 3.5 6.3 - - - +
338E LYS* 1.3 77.6 - - - +
340E LEU* 1.3 63.4 + - - +
342E ILE* 3.0 9.7 + - - +
343E HIS* 3.0 40.4 + - + -
367E GLY* 4.1 10.5 - - - -
370E LEU* 3.7 37.7 - - + -
1604E ADP 3.7 32.1 - - + +
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Residues in contact with LEU 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336E ARG 3.0 22.7 + - - +
337E LYS* 3.8 4.0 - - - +
339E ILE* 1.3 76.5 - - - +
341E GLU* 1.3 53.8 + - - +
343E HIS* 4.5 0.9 - - - +
344E THR* 2.6 41.1 + - - +
355E LEU* 3.5 29.4 - - + +
358E ILE* 3.7 23.8 - - + -
359E ALA* 4.0 17.3 - - + +
370E LEU* 4.2 19.7 - - + +
373E LEU* 4.0 21.1 - - + -
374E VAL* 3.8 26.9 - - + -
394E PHE* 4.5 4.9 - - + -
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Residues in contact with GLU 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337E LYS* 3.0 15.1 + - + +
338E LYS* 3.3 40.8 + - - +
339E ILE 3.1 0.2 - - - -
340E LEU* 1.3 74.1 - - - +
342E ILE* 1.3 65.8 + - + +
344E THR* 3.2 14.7 + - - +
345E ARG* 3.2 33.0 + - + +
355E LEU* 4.0 10.7 - - + +
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Residues in contact with ILE 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E LYS 4.0 3.4 - - - +
162E ASP* 3.8 30.5 - - + +
163E VAL 3.7 8.3 - - - +
164E GLY* 3.5 33.7 - - - +
338E LYS* 2.9 21.8 + - + +
339E ILE* 3.0 8.9 + - - +
341E GLU* 1.3 76.6 - - + +
343E HIS* 1.3 74.9 + - + +
344E THR 3.1 0.2 - - - -
345E ARG* 3.2 56.0 + - - +
346E ASN 5.0 0.2 + - - -
1604E ADP 4.2 1.3 - - + -
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Residues in contact with HIS 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E ASP 5.8 0.4 - - - -
339E ILE* 3.0 38.8 + - + +
340E LEU* 5.0 0.4 - - - -
342E ILE* 1.3 85.2 - - + +
344E THR* 1.3 60.1 + - - +
345E ARG 3.5 0.4 - - - -
346E ASN 5.1 1.0 + - - -
347E LYS* 3.5 19.2 - - - +
370E LEU 5.2 0.2 - - - -
371E GLU* 3.8 30.5 + - + +
374E VAL* 3.6 27.5 - - + +
1604E ADP 3.0 53.8 + + - -
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Residues in contact with THR 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340E LEU* 2.6 28.1 + - - +
341E GLU* 3.2 11.8 + - - +
342E ILE 3.1 0.2 - - - -
343E HIS* 1.3 82.7 - - - +
345E ARG* 1.3 64.0 + - - +
346E ASN 3.2 3.1 - - - -
347E LYS* 3.0 24.5 + - + +
349E LEU* 3.7 38.4 - - + +
355E LEU* 4.1 9.7 - - + +
374E VAL* 4.1 20.0 - - + -
394E PHE* 4.3 10.1 - - + -
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Residues in contact with ARG 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E LYS* 2.9 43.1 + - - +
162E ASP* 4.5 9.1 + - - -
341E GLU* 3.2 30.6 + - + +
342E ILE* 3.2 39.7 + - - +
343E HIS 3.5 0.4 - - - -
344E THR* 1.3 77.8 - - - +
346E ASN* 1.3 69.5 + - - +
347E LYS 4.5 2.1 - - - +
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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