Contacts of the helix formed by residues 389 - 405 (chain E) in PDB entry 4K4I
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 ARG 389 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387E MET 3.6 0.8 + - - -
388E PRO* 1.3 71.3 - - - +
390E GLU* 1.3 69.3 + - + +
392E ALA* 3.3 7.8 + - - +
393E THR* 3.1 27.5 + - - +
418E TYR* 2.8 74.9 + - + +
421E GLY* 3.5 16.8 - - - -
422E LYS 2.8 37.0 + - - +
423E ALA* 3.0 22.7 + - - +
425E CYS* 4.8 4.7 - - - -
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Residues in contact with GLU 390 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388E PRO* 3.1 16.9 + - - +
389E ARG* 1.3 88.0 + - + +
391E GLU* 1.3 66.4 + - - +
393E THR* 3.1 18.4 + - - -
394E GLU* 3.1 17.7 + - - +
423E ALA 5.2 0.5 - - - +
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Residues in contact with GLU 391 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387E MET* 4.2 8.7 - - + -
388E PRO* 2.9 27.8 + - + +
390E GLU* 1.3 74.6 - - - +
392E ALA* 1.3 66.1 + - - +
394E GLU* 3.1 11.7 + - - +
395E ILE* 3.0 24.4 + - + +
479E LEU* 3.7 20.2 + - + +
484E ARG* 4.1 18.7 + - - +
485E ARG 4.2 10.7 + - - +
487E ARG* 2.6 51.1 + - - +
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Residues in contact with ALA 392 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387E MET* 3.8 14.1 - - - -
388E PRO 3.3 3.0 + - - +
389E ARG 3.3 12.2 + - - +
391E GLU* 1.3 78.9 - - - +
393E THR* 1.3 63.3 + - - +
395E ILE* 3.2 3.0 + - - +
396E GLU* 3.0 23.9 + - - +
418E TYR* 3.7 21.3 - - + -
425E CYS* 4.2 13.5 - - - -
428E VAL* 3.9 26.8 - - + +
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Residues in contact with THR 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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389E ARG* 3.1 9.4 + - - +
390E GLU* 3.1 13.9 + - - -
392E ALA* 1.3 75.2 - - - +
394E GLU* 1.3 60.1 + - - +
395E ILE 3.2 0.2 + - - -
396E GLU* 3.2 8.2 + - - +
397E GLN* 2.8 41.0 + - + +
418E TYR* 2.5 34.7 + - - +
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Residues in contact with GLU 394 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390E GLU 3.1 11.3 + - - +
391E GLU* 3.1 10.6 + - - +
393E THR* 1.3 80.8 - - - +
395E ILE* 1.3 52.4 + - - +
397E GLN* 3.7 7.3 - - + +
398E THR* 2.6 37.6 + - - +
479E LEU* 3.9 17.9 - - + +
484E ARG* 3.2 30.7 + - - -
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Residues in contact with ILE 395 (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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387E MET* 4.0 22.9 - - - -
391E GLU* 3.0 22.5 + - + +
392E ALA 3.6 6.3 - - - +
394E GLU* 1.3 75.2 - - - +
396E GLU* 1.3 66.0 + - - +
398E THR* 3.3 7.7 + - - -
399E VAL* 3.0 22.0 + - - +
428E VAL* 3.9 26.5 - - + -
456E PHE* 4.0 11.2 - - + -
477E CYS* 4.0 24.0 - - - -
479E LEU* 4.0 19.5 - - + +
487E ARG* 4.1 13.7 - - + -
489E LEU* 4.1 15.9 - - + -
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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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392E ALA 3.0 12.5 + - - +
393E THR* 3.6 11.1 - - - +
395E ILE* 1.3 78.8 - - - +
397E GLN* 1.3 85.9 + - - +
399E VAL* 3.1 3.9 + - - +
400E GLN* 2.8 33.3 + - - +
412E CYS* 3.2 7.8 - - - +
413E VAL 4.5 2.2 - - - -
414E ALA* 3.9 34.8 - - + +
418E TYR* 5.9 1.8 - - + -
428E VAL* 4.8 0.9 - - + +
430E VAL* 4.3 20.2 - - + -
606E CA 2.3 30.6 - - - -
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Residues in contact with GLN 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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393E THR* 2.8 32.3 + - + +
394E GLU* 3.7 8.5 - - + +
396E GLU* 1.3 87.1 + - - +
398E THR* 1.3 60.2 + - - +
400E GLN* 2.6 34.4 + - - +
401E LYS* 2.8 63.6 + - - +
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Residues in contact with THR 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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394E GLU* 2.6 23.1 + - - +
395E ILE 3.3 8.3 + - - -
397E GLN* 1.3 75.9 - - - +
399E VAL* 1.3 64.1 + - - +
401E LYS* 3.6 6.7 + - - +
402E ALA* 3.3 19.8 + - - +
451E LEU* 4.3 2.4 - - + +
454E GLU* 3.7 23.1 - - - +
456E PHE* 3.8 33.7 - - + -
479E LEU* 3.7 12.8 - - - +
480E PRO* 5.7 2.7 - - + +
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Residues in contact with VAL 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395E ILE 3.0 14.4 + - - +
396E GLU 3.1 6.5 + - - +
398E THR* 1.3 76.7 - - - +
400E GLN* 1.3 63.8 + - - +
402E ALA 3.5 0.7 + - - -
403E ALA* 3.0 21.1 + - - +
412E CYS* 5.3 0.2 - - - -
430E VAL* 4.1 29.6 - - + -
432E ILE* 4.2 17.3 - - + -
447E LEU* 4.0 12.7 - - + +
451E LEU* 4.0 18.6 - - + -
456E PHE* 4.0 4.9 - - + -
489E LEU* 3.9 27.6 - - + -
491E ILE* 4.4 9.2 - - + -
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Residues in contact with GLN 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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396E GLU* 2.8 17.8 + - - +
397E GLN* 2.6 38.1 + - - +
399E VAL* 1.3 74.6 - - - +
401E LYS* 1.3 59.7 + - + +
403E ALA* 3.1 3.6 + - - +
404E GLN* 2.8 55.6 + - - +
410E LEU 5.7 0.7 - - - +
412E CYS* 3.3 27.1 + - + +
606E CA 2.3 29.6 - - - -
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Residues in contact with LYS 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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397E GLN* 2.8 57.5 + - - +
398E THR* 3.9 5.7 - - - +
400E GLN* 1.3 76.8 - - + +
402E ALA* 1.3 66.4 + - - +
404E GLN* 2.9 20.0 + - + +
405E ALA* 3.1 14.1 + - - +
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Residues in contact with ALA 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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398E THR 3.3 8.4 + - - +
399E VAL 4.1 0.2 - - - +
401E LYS* 1.3 79.7 - - - +
403E ALA* 1.3 59.2 + - - +
404E GLN 3.6 0.2 + - - -
405E ALA* 3.9 12.4 - - - +
406E PHE* 3.5 21.1 - - - -
447E LEU* 3.8 13.5 - - + -
450E SER* 4.0 16.1 + - - +
451E LEU* 3.5 31.4 - - + -
454E GLU* 4.3 5.4 - - - +
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Residues in contact with ALA 403 (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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399E VAL 3.0 19.3 + - - +
400E GLN 3.6 3.4 - - - +
402E ALA* 1.3 74.8 - - - +
404E GLN* 1.3 66.2 + - - +
406E PHE* 3.3 14.9 + - - +
407E ASN 3.4 1.9 + - - -
410E LEU* 3.3 31.7 - - + +
412E CYS* 4.1 18.6 - - - -
432E ILE* 4.7 3.4 - - + -
443E ILE* 5.2 1.1 - - + -
447E LEU* 3.7 21.5 - - + +
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Residues in contact with GLN 404 (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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400E GLN* 2.8 37.6 + - - +
401E LYS* 2.9 14.9 + - + +
403E ALA* 1.3 73.9 - - - +
405E ALA* 1.3 56.9 + - - +
407E ASN 2.5 43.9 + - - -
408E SER* 3.5 23.7 + - - +
410E LEU* 3.4 27.7 + - - +
412E CYS* 5.1 1.4 - - - -
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Residues in contact with ALA 405 (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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401E LYS 3.1 6.7 + - - +
402E ALA* 3.9 13.7 - - - +
404E GLN* 1.3 76.2 - - - +
406E PHE* 1.3 65.2 + - + +
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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