Contacts of the helix formed by residues 389 - 407 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387I MET 3.6 1.7 + - - -
388I PRO* 1.3 72.1 - - - +
390I GLU* 1.3 61.4 + - + +
392I ALA* 3.3 8.9 + - - +
393I THR* 2.9 31.7 + - - +
418I TYR* 2.8 68.2 + - + +
421I GLY* 3.4 17.4 - - - -
422I LYS 2.6 44.3 + - - +
423I ALA* 3.0 22.8 + - - +
425I CYS* 4.5 5.2 - - - -
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Residues in contact with GLU 390 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388I PRO* 3.1 6.8 - - + +
389I ARG* 1.3 83.0 - - + +
391I GLU* 1.3 57.3 + - - +
393I THR* 3.2 11.9 + - - +
394I GLU* 2.8 38.5 + - + +
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Residues in contact with GLU 391 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387I MET* 3.6 7.0 - - - +
388I PRO* 3.0 23.0 + - + +
390I GLU* 1.3 77.3 - - - +
392I ALA* 1.3 54.8 + - - +
394I GLU* 3.2 12.8 + - - +
395I ILE* 2.8 38.4 + - + +
479I LEU* 3.6 21.2 + - + +
484I ARG* 3.8 21.3 + - - +
485I ARG 4.2 11.3 + - - +
487I ARG* 2.8 52.7 + - - +
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Residues in contact with ALA 392 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387I MET* 3.9 21.2 - - - -
388I PRO 3.4 2.0 + - - -
389I ARG* 3.3 12.3 + - - +
391I GLU* 1.3 75.5 - - - +
393I THR* 1.3 61.9 + - - +
395I ILE* 3.2 3.7 + - - +
396I GLU* 2.9 28.6 + - - +
418I TYR* 3.7 21.0 - - + -
425I CYS* 4.2 11.9 - - - -
428I VAL* 3.9 19.4 - - + +
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Residues in contact with THR 393 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389I ARG* 2.9 20.1 + - - +
390I GLU* 3.2 14.6 - - - -
392I ALA* 1.3 76.6 - - - +
394I GLU* 1.3 57.4 + - + +
396I GLU* 3.3 9.3 + - - +
397I GLN* 2.9 49.8 + - + +
418I TYR* 2.4 32.9 + - - +
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Residues in contact with GLU 394 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390I GLU* 2.8 28.2 + - - +
391I GLU* 3.2 15.1 + - - +
393I THR* 1.3 72.9 - - - +
395I ILE* 1.3 60.6 + - - +
397I GLN* 3.3 15.7 + - - +
398I THR* 2.9 28.6 + - - -
479I LEU* 3.5 17.7 - - + +
484I ARG* 2.7 33.8 + - - -
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Residues in contact with ILE 395 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387I MET* 4.0 23.1 - - - -
391I GLU* 2.8 28.9 + - + +
392I ALA* 3.2 6.2 + - - +
394I GLU* 1.3 73.9 - - - +
396I GLU* 1.3 62.7 + - - +
398I THR* 3.4 7.1 + - - -
399I VAL* 3.2 22.3 + - + +
428I VAL* 4.0 15.3 - - + -
456I PHE* 4.0 14.1 - - + -
477I CYS* 3.9 22.9 - - - -
479I LEU* 4.0 18.4 - - + +
487I ARG* 4.0 13.0 - - + -
489I LEU* 4.0 25.6 - - + -
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Residues in contact with GLU 396 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392I ALA 2.9 16.0 + - - +
393I THR* 3.3 11.0 + - - +
395I ILE* 1.3 75.6 - - - +
397I GLN* 1.3 59.7 + - - +
399I VAL* 3.2 3.6 + - - +
400I GLN* 2.8 49.6 + - - +
412I CYS* 3.9 9.1 - - + +
413I VAL* 3.7 6.1 - - - +
414I ALA* 2.8 44.9 + - + +
418I TYR* 4.0 18.8 + - - -
428I VAL* 5.0 0.4 - - + +
430I VAL* 4.5 15.7 - - + -
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Residues in contact with GLN 397 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393I THR* 2.9 38.6 + - + +
394I GLU* 3.7 15.1 - - - +
396I GLU* 1.3 78.0 - - - +
398I THR* 1.3 54.4 + - - +
400I GLN* 2.9 19.1 + - - +
401I LYS* 2.7 37.0 + - - +
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Residues in contact with THR 398 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394I GLU 2.9 15.0 + - - -
395I ILE 3.5 8.1 - - - -
396I GLU 3.2 0.2 - - - -
397I GLN* 1.3 75.0 - - - +
399I VAL* 1.3 63.7 + - - +
401I LYS* 3.7 8.3 + - - +
402I ALA* 3.2 22.7 + - - +
451I LEU* 4.0 5.8 - - + +
456I PHE* 3.8 40.8 - - + -
479I LEU* 3.5 15.1 - - + +
480I PRO* 5.8 0.3 - - - +
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Residues in contact with VAL 399 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395I ILE 3.2 14.4 + - - +
396I GLU 3.7 5.6 - - - +
398I THR* 1.3 78.7 - - - +
400I GLN* 1.3 60.0 + - - +
402I ALA* 3.4 2.4 + - - +
403I ALA* 2.9 26.9 + - - +
412I CYS* 5.0 0.7 - - - -
430I VAL* 3.8 38.4 - - + -
432I ILE* 4.1 17.0 - - + -
447I LEU* 4.0 6.4 - - + +
451I LEU* 4.5 7.9 - - + -
456I PHE* 4.2 17.5 - - + -
489I LEU* 4.2 5.2 - - + -
491I ILE* 4.2 24.9 - - + -
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Residues in contact with GLN 400 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396I GLU* 2.8 27.7 + - - +
397I GLN* 2.9 26.3 + - - +
399I VAL* 1.3 74.9 - - - +
401I LYS* 1.3 55.2 + - - +
403I ALA* 3.2 2.8 + - - +
404I GLN* 2.8 65.1 + - - +
412I CYS* 3.1 44.8 + - + +
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Residues in contact with LYS 401 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397I GLN 2.7 19.3 + - - +
398I THR* 3.9 7.0 - - - +
400I GLN* 1.3 71.6 - - - +
402I ALA* 1.3 63.9 + - - +
404I GLN* 3.2 9.3 + - - +
405I ALA* 3.1 22.9 + - + +
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Residues in contact with ALA 402 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398I THR 3.2 15.7 + - - +
401I LYS* 1.3 82.9 - - - +
403I ALA* 1.3 62.4 + - - +
405I ALA* 3.4 11.9 - - - +
406I PHE* 3.4 18.2 - - - -
447I LEU* 3.6 22.0 - - + -
450I SER* 4.1 16.4 + - - +
451I LEU* 3.7 15.7 - - + -
454I GLU* 6.6 0.4 - - + -
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Residues in contact with ALA 403 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399I VAL 2.9 18.6 + - - +
400I GLN 3.6 3.4 - - - +
402I ALA* 1.3 76.5 - - - +
404I GLN* 1.3 58.7 + - + +
406I PHE* 3.0 23.0 + - - +
407I ASN 3.5 0.2 + - - -
410I LEU* 3.2 31.1 - - + +
412I CYS* 3.8 21.5 - - - -
432I ILE* 4.6 3.1 - - + -
443I ILE* 5.2 2.0 - - + -
447I LEU* 3.8 20.3 - - + +
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Residues in contact with GLN 404 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400I GLN* 2.8 48.7 + - - +
401I LYS* 3.2 7.4 + - - +
403I ALA* 1.3 69.7 - - + +
405I ALA* 1.3 61.0 + - - +
406I PHE 3.1 2.0 - - - -
407I ASN 3.0 29.1 + - - +
408I SER* 3.3 33.4 + - - +
410I LEU* 4.0 18.5 + - + +
412I CYS* 5.8 0.6 - - - +
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Residues in contact with ALA 405 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401I LYS 3.1 11.0 + - - +
402I ALA* 3.4 14.6 - - - +
403I ALA 3.2 0.2 - - - -
404I GLN* 1.3 77.6 - - - +
406I PHE* 1.3 65.2 + - + +
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Residues in contact with PHE 406 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402I ALA 3.4 23.6 - - - -
403I ALA* 3.0 14.6 + - - +
405I ALA* 1.3 81.9 - - + +
407I ASN* 1.3 63.6 - - - +
443I ILE* 4.2 24.9 - - + +
446I ARG* 3.0 63.8 + - + +
447I LEU* 3.7 27.4 - - - -
450I SER* 4.1 13.7 - - - -
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Residues in contact with ASN 407 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403I ALA 3.5 1.0 + - - -
404I GLN* 3.0 11.7 + - - +
406I PHE* 1.3 84.2 - - + +
408I SER* 1.3 63.7 + - - +
409I GLY 2.8 17.3 + - - -
410I LEU* 3.3 29.6 + - + +
434I HIS* 3.0 18.8 + - - -
436I ASP* 5.1 0.2 + - - -
439I SER* 2.5 30.9 + - - +
443I ILE* 5.1 4.5 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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