Contacts of the helix formed by residues 354 - 361 (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 ASN 354 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352E ASP 3.1 8.5 + - - +
353E VAL* 1.3 71.3 - - - +
355E LEU* 1.3 63.8 + - - +
356E GLU* 3.1 14.8 - - - +
357E ILE* 3.0 44.7 + - + +
358E ILE* 3.2 21.5 + - - +
391E MET* 3.4 19.1 - - + +
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Residues in contact with LEU 355 (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* 4.5 16.6 - - + +
340E LEU* 3.5 38.5 - - + +
341E GLU* 4.0 33.4 - - + +
344E THR* 4.1 14.1 - - + +
349E LEU* 5.2 4.9 - - + -
353E VAL* 3.5 17.9 + - + +
354E ASN* 1.3 69.9 - - - +
356E GLU* 1.3 61.3 + - - +
358E ILE* 3.0 16.3 + - + +
359E ALA* 2.8 29.1 + - - +
394E PHE* 5.2 1.6 - - + -
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Residues in contact with GLU 356 (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* 4.1 22.4 - - - +
334E LEU* 4.6 3.5 - - - +
337E LYS* 3.7 34.2 + - + +
354E ASN* 3.1 9.7 - - - +
355E LEU* 1.3 77.4 - - - +
357E ILE* 1.3 65.2 + - + +
359E ALA* 2.9 10.9 + - - +
360E LYS* 2.8 47.2 + - - +
588E GLU* 4.7 4.9 - - - +
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Residues in contact with ILE 357 (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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354E ASN* 3.0 41.2 - - + +
356E GLU* 1.3 75.7 - - + +
358E ILE* 1.3 59.0 + - - +
360E LYS* 2.8 33.3 + - + +
361E ARG* 2.9 34.1 + - + +
391E MET* 3.7 19.5 - - + -
395E GLU* 5.6 0.9 - - - +
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Residues in contact with ILE 358 (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* 3.7 16.2 - - + -
353E VAL* 4.6 1.6 - - + -
354E ASN 3.2 13.2 + - - +
355E LEU* 3.0 22.0 + - + +
357E ILE* 1.3 77.5 - - - +
359E ALA* 1.3 63.9 + - - +
361E ARG* 3.0 13.4 + - - +
362E THR* 2.8 19.4 + - + +
373E LEU* 3.9 23.1 - - + -
391E MET* 4.1 15.5 - - + -
394E PHE* 3.2 49.1 - - + -
395E GLU* 5.5 2.0 - - + +
398E ILE* 4.5 7.9 - - + -
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Residues in contact with ALA 359 (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* 3.5 32.5 - - - +
336E ARG* 2.9 26.2 + - + -
337E LYS* 3.9 18.2 - - + +
340E LEU* 4.0 6.0 - - + +
355E LEU 2.8 12.7 + - - +
356E GLU 3.2 8.7 - - - +
358E ILE* 1.3 75.9 - - - +
360E LYS* 1.3 60.2 + - - +
362E THR* 2.8 19.3 + - - -
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Residues in contact with LYS 360 (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* 4.0 21.1 - - + -
336E ARG* 4.2 4.3 + - - +
356E GLU* 2.8 38.3 + - - +
357E ILE* 2.8 21.3 + - + +
359E ALA* 1.3 79.9 - - - +
361E ARG* 1.3 58.8 + - + +
362E THR 3.1 3.5 + - - -
363E PRO* 3.4 11.8 - - - +
417E LYS* 5.7 2.9 + - - -
588E GLU* 3.0 50.8 + - + +
590E GLU* 5.3 0.2 - - - +
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Residues in contact with ARG 361 (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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357E ILE* 2.9 35.3 + - + +
358E ILE* 3.0 3.0 + - - +
360E LYS* 1.3 79.1 - - + +
362E THR* 1.3 62.4 + - - +
363E PRO* 3.2 11.4 - - - +
365E PHE* 5.0 1.4 - - - -
395E GLU* 3.8 42.8 + - - +
398E ILE* 3.8 31.2 - - + +
399E ASP* 4.9 7.1 + - - -
402E ILE* 5.5 2.8 - - - +
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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