Contacts of the helix formed by residues 390 - 402 (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 THR 390 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350E ALA* 4.1 11.2 - - + -
352E ASP* 3.9 14.1 - - - +
353E VAL* 3.7 3.1 - - - -
386E ARG* 3.3 26.1 + - - +
388E LYS* 4.1 9.0 - - + +
389E ILE* 1.3 76.1 - - - +
391E MET* 1.3 60.5 + - - +
392E LYS* 3.5 11.1 + - - +
393E ASP* 2.8 50.0 + - - +
394E PHE* 3.3 7.3 + - - -
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Residues in contact with MET 391 (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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352E ASP* 3.3 34.2 + - - +
353E VAL* 3.5 7.4 - - - +
354E ASN* 3.4 39.3 - - + +
357E ILE* 3.7 36.3 - - + -
358E ILE* 4.1 19.3 - - + -
390E THR* 1.3 72.1 - - - +
392E LYS* 1.3 59.2 + - + +
394E PHE* 3.0 4.9 + - - +
395E GLU* 2.8 52.5 + - + +
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Residues in contact with LYS 392 (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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352E ASP* 5.1 0.6 + - - +
390E THR* 3.1 10.6 + - - +
391E MET* 1.3 79.8 - - + +
393E ASP* 1.3 54.6 + - - +
395E GLU* 3.4 15.8 - - - +
396E GLU* 2.7 45.1 + - + +
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Residues in contact with ASP 393 (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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377E ALA* 3.8 21.3 - - - +
380E LEU* 3.5 19.6 - - + +
381E ALA* 3.6 6.8 - - - +
386E ARG* 3.1 34.9 + - - -
389E ILE* 3.6 10.8 - - + -
390E THR* 2.8 36.4 + - - +
392E LYS* 1.3 80.3 - - - +
394E PHE* 1.3 51.7 + - - +
396E GLU* 3.2 3.0 + - - +
397E ALA* 2.7 35.9 + - - +
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Residues in contact with PHE 394 (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* 4.5 4.9 - - + -
344E THR* 4.3 10.8 - - + -
349E LEU* 3.9 16.8 - - + -
353E VAL* 3.9 26.0 - - + -
355E LEU* 5.2 0.9 - - + -
358E ILE* 3.2 36.6 - - + -
373E LEU* 4.0 15.1 - - + +
374E VAL* 4.0 26.5 - - + -
377E ALA* 3.8 14.6 - - + -
389E ILE* 3.2 26.5 - - + -
390E THR 3.3 13.4 + - - -
391E MET* 3.0 6.8 + - - +
393E ASP* 1.3 74.0 - - - +
395E GLU* 1.3 71.6 + - - +
397E ALA* 2.9 13.0 + - - +
398E ILE* 3.0 18.8 + - - +
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Residues in contact with GLU 395 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357E ILE* 5.6 0.9 - - - +
358E ILE* 5.9 2.2 - - + -
361E ARG* 3.8 31.1 + - - +
391E MET* 2.8 48.8 + - + +
392E LYS* 3.4 21.7 + - - +
394E PHE* 1.3 79.4 - - + +
396E GLU* 1.3 64.4 + - + +
397E ALA 3.0 0.5 + - - -
398E ILE* 3.1 19.1 + - - +
399E ASP* 3.4 10.0 - - - +
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Residues in contact with GLU 396 (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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380E LEU* 3.7 22.3 - - + +
392E LYS* 2.7 27.7 + - + +
393E ASP* 3.6 7.2 - - - +
395E GLU* 1.3 74.1 - - + +
397E ALA* 1.3 62.2 + - - +
399E ASP* 3.7 11.5 + - - +
400E ARG* 3.7 15.1 + - - +
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Residues in contact with ALA 397 (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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373E LEU* 3.5 29.8 - - + +
376E GLU* 4.1 9.4 - - + +
377E ALA 4.0 11.2 - - - +
380E LEU* 4.3 4.0 - - + -
393E ASP 2.7 17.2 + - - +
394E PHE* 2.9 8.4 + - - +
396E GLU* 1.3 76.5 - - - +
398E ILE* 1.3 56.4 + - - +
400E ARG* 2.7 30.1 + - - +
401E VAL* 2.8 14.0 + - - +
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Residues in contact with ILE 398 (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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358E ILE* 4.5 10.8 - - + +
361E ARG* 3.8 42.2 - - + +
362E THR* 3.6 26.7 - - + -
365E PHE* 4.6 5.5 - - + -
373E LEU* 3.4 19.0 - - + +
394E PHE 3.0 19.7 + - - +
395E GLU* 3.3 11.2 - - - +
397E ALA* 1.3 75.8 - - - +
399E ASP* 1.3 67.8 + - - +
400E ARG 3.0 0.2 - - - -
401E VAL* 4.1 1.6 - - - +
402E ILE* 3.0 43.6 + - + +
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Residues in contact with ASP 399 (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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361E ARG* 4.9 7.0 + - - -
395E GLU 3.4 11.0 - - - +
396E GLU* 3.7 9.9 + - - +
397E ALA 3.2 0.8 - - - -
398E ILE* 1.3 90.8 - - - +
400E ARG* 1.3 56.5 + - - +
402E ILE* 4.6 2.0 - - - -
403E ALA* 3.2 37.8 + - - +
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Residues in contact with ARG 400 (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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376E GLU* 2.7 52.0 + - + +
379E LEU* 5.1 2.2 - - - +
380E LEU* 4.7 10.7 - - - +
383E ARG* 4.1 26.8 - - - +
396E GLU 3.7 8.4 + - - +
397E ALA* 2.7 18.1 + - - +
399E ASP* 1.3 79.7 - - - +
401E VAL* 1.3 62.0 + - - +
402E ILE 3.3 4.9 - - - +
403E ALA* 4.3 1.6 + - - -
192F ARG* 5.8 1.6 + - - -
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Residues in contact with VAL 401 (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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365E PHE* 3.6 26.9 - - + -
369E ASP* 4.3 16.2 - - + +
372E ASN* 4.2 11.2 - - + -
373E LEU* 3.6 36.6 - - + +
376E GLU* 4.2 13.9 - - + -
397E ALA 2.8 16.9 + - - +
398E ILE 4.2 2.9 - - - +
400E ARG* 1.3 72.5 - - - +
402E ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 402 (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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361E ARG 5.5 3.4 - - - +
363E PRO 5.8 1.3 - - - +
365E PHE* 3.6 34.1 - - + -
398E ILE* 3.0 24.8 + - + +
399E ASP* 4.6 2.5 - - - +
400E ARG 4.2 2.2 - - - +
401E VAL* 1.3 82.1 - - + +
403E ALA* 1.3 100.7 + - + +
410E LEU* 6.1 1.8 - - + +
411E LEU* 6.4 3.1 - - + -
192F ARG* 4.3 9.4 + - - -
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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