Contacts of the helix formed by residues 442 - 454 (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 GLY 442 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440I HIS 3.6 0.4 + - - -
441I ARG* 1.3 72.6 - - - +
443I ILE* 1.3 64.1 + - - +
444I PHE* 3.4 2.8 + - - +
445I SER* 4.2 4.8 + - - -
446I ARG* 3.4 31.3 + - - +
471I GLN* 5.2 4.9 - - - +
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Residues in contact with ILE 443 (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* 5.2 2.5 - - + -
406I PHE* 4.2 21.8 - - + +
407I ASN* 5.1 4.0 - - + -
410I LEU* 4.3 25.8 - - + -
432I ILE* 5.5 3.4 - - + -
439I SER 3.5 19.3 - - - +
440I HIS* 3.3 22.7 + - - +
441I ARG 3.2 3.8 - - - +
442I GLY* 1.3 78.1 - - - +
444I PHE* 1.3 68.8 + - - +
446I ARG* 3.1 26.9 + - - +
447I LEU* 2.8 45.2 + - + +
493I VAL* 4.9 7.9 - - + -
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Residues in contact with PHE 444 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442I GLY 3.4 1.9 - - - -
443I ILE* 1.3 79.2 - - - +
445I SER* 1.3 68.6 + - - +
447I LEU* 3.4 4.4 + - + +
448I LEU* 3.1 44.4 + - + +
463I SER 3.8 2.0 - - - -
464I GLN* 3.5 42.4 - - + -
471I GLN* 3.5 47.4 - - + +
472I LYS 3.5 24.2 - - - -
473I TYR* 3.6 28.7 - - + -
491I ILE* 4.0 7.6 - - + -
493I VAL* 3.8 22.4 - - + +
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Residues in contact with SER 445 (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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442I GLY 4.2 4.1 + - - -
443I ILE 3.4 0.2 - - - -
444I PHE* 1.3 88.4 - - - +
446I ARG* 1.3 62.0 + - - +
448I LEU* 3.3 8.4 + - - +
449I ASP* 2.9 41.3 + - - +
452I ARG* 5.1 0.4 + - - +
464I GLN* 4.9 7.8 + - - -
471I GLN* 5.3 0.9 + - - -
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Residues in contact with ARG 446 (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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406I PHE* 3.0 56.4 + - + +
441I ARG 5.3 1.0 + - - -
442I GLY* 3.4 20.5 + - - +
443I ILE* 3.1 30.6 + - - +
445I SER* 1.3 79.3 - - - +
447I LEU* 1.3 54.5 + - - +
449I ASP* 3.1 10.2 + - - +
450I SER* 2.8 35.5 + - - -
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Residues in contact with LEU 447 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399I VAL* 4.0 8.7 - - + +
402I ALA* 3.6 29.4 - - + -
403I ALA* 3.8 14.4 - - + +
406I PHE* 3.7 10.8 - - + -
432I ILE* 3.6 31.6 - - + -
443I ILE* 2.8 32.6 + - + +
444I PHE* 3.6 4.9 - - + +
446I ARG* 1.3 76.7 - - - +
448I LEU* 1.3 59.2 + - + +
450I SER* 3.3 2.6 - - - -
451I LEU* 2.8 49.4 + - + +
491I ILE* 4.3 14.4 - - + -
493I VAL* 5.2 3.8 - - + -
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Residues in contact with LEU 448 (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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444I PHE* 3.1 52.1 + - + +
445I SER* 3.6 9.0 - - - +
447I LEU* 1.3 82.5 - - + +
449I ASP* 1.3 52.6 + - - +
451I LEU* 3.2 2.6 + - + +
452I ARG* 2.7 59.9 + - - +
457I LEU* 3.9 10.7 - - + +
463I SER 3.8 13.0 - - - +
473I TYR* 3.7 35.9 - - + -
491I ILE* 4.3 18.4 - - + -
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Residues in contact with ASP 449 (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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445I SER* 2.9 26.0 + - - +
446I ARG* 3.1 11.2 + - - +
448I LEU* 1.3 73.7 - - - +
450I SER* 1.3 59.2 + - - +
452I ARG* 3.1 27.5 + - - +
453I GLN* 2.8 41.7 + - - +
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Residues in contact with SER 450 (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* 4.1 16.5 + - - +
406I PHE* 4.1 19.2 - - - -
446I ARG 2.8 16.6 + - - -
447I LEU* 3.3 11.0 - - - -
449I ASP* 1.3 74.9 - - - +
451I LEU* 1.3 63.6 + - - -
453I GLN* 3.2 20.4 + - - +
454I GLU* 3.3 27.4 + - - +
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Residues in contact with LEU 451 (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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398I THR* 4.0 17.3 - - + +
399I VAL* 4.5 6.7 - - + -
402I ALA* 3.7 21.5 - - + -
447I LEU* 2.8 41.6 + - + +
448I LEU* 4.7 0.9 - - - -
450I SER* 1.3 70.1 - - - +
452I ARG* 1.3 66.1 + - - +
454I GLU* 3.8 6.2 + - + -
455I GLY 3.7 1.6 + - - -
456I PHE* 3.0 52.3 + - + +
457I LEU* 3.5 25.1 + - + -
491I ILE* 3.8 28.0 - - + -
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Residues in contact with ARG 452 (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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445I SER* 5.1 0.6 + - - +
448I LEU* 2.7 40.7 + - - +
449I ASP* 3.3 30.2 + - - +
451I LEU* 1.3 72.6 - - - +
453I GLN* 1.3 55.1 + - - +
455I GLY* 2.5 31.2 + - - -
457I LEU* 4.2 23.8 - - + +
460I ASP* 2.6 37.7 + - - -
463I SER* 4.1 10.9 + - - -
473I TYR* 4.1 9.4 - - - -
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Residues in contact with GLN 453 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449I ASP* 2.8 27.5 + - - +
450I SER* 3.2 19.6 + - - +
452I ARG* 1.3 73.2 - - + +
454I GLU* 1.3 67.8 + - + +
455I GLY 3.1 1.1 + - - -
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Residues in contact with GLU 454 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402I ALA* 6.6 0.4 - - + -
450I SER* 3.3 24.7 + - - +
451I LEU* 4.2 9.0 - - + +
452I ARG 3.1 1.0 - - - -
453I GLN* 1.3 83.6 + - - +
455I GLY* 1.3 58.2 + - - +
456I PHE* 3.6 6.2 + - + +
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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