Contacts of the helix formed by residues 441 - 456 (chain I) in PDB entry 5G04
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 441 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D ASP* 4.0 20.2 - - + -
24D CYS* 3.7 31.9 - - + +
419I ARG* 4.6 9.9 + - - -
439I LYS 4.0 3.1 + - - -
440I MET* 1.3 72.7 - - - +
442I GLN* 1.3 68.5 + - + +
443I LYS* 3.3 14.1 - - + +
444I ASP* 3.3 20.8 + - - +
445I ILE* 3.2 25.1 + - - +
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Residues in contact with GLN 442 (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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24D CYS* 4.8 2.6 + - - +
26D GLU* 4.2 22.0 - - - +
440I MET 4.0 5.0 + - - +
441I THR* 1.3 75.9 - - - +
443I LYS* 1.3 63.7 + - - +
445I ILE* 3.4 19.5 + - - +
446I THR* 3.3 25.8 + - - -
69O GLN* 4.1 28.1 + - + +
131O VAL* 4.8 13.5 - - - +
134O LEU* 5.9 2.1 - - - +
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Residues in contact with LYS 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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441I THR* 3.3 11.7 - - + +
442I GLN* 1.3 73.1 - - - +
444I ASP* 1.3 65.7 + - - +
446I THR* 3.5 7.3 + - - -
447I PHE* 3.1 32.5 + - + +
452O GLU* 5.3 11.3 - - - +
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Residues in contact with ASP 444 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416I ALA* 3.5 29.9 - - - +
419I ARG* 3.8 28.9 + - - +
440I MET* 3.5 27.9 - - + +
441I THR* 3.3 28.0 + - - +
443I LYS* 1.3 78.3 - - - +
445I ILE* 1.3 56.0 + - - +
447I PHE* 3.4 4.9 - - - +
448I VAL* 3.1 30.0 + - - +
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Residues in contact with ILE 445 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308I LEU* 4.1 19.5 - - + +
420I TRP* 5.1 4.0 - - + -
440I MET* 3.7 39.3 - - + -
441I THR 3.2 15.1 + - - +
442I GLN* 3.7 22.2 - - - +
443I LYS 3.3 0.8 - - - -
444I ASP* 1.3 71.5 - - - +
446I THR* 1.3 66.2 + - - +
447I PHE 3.1 1.3 - - - -
448I VAL* 3.2 5.2 + - + +
449I ALA* 3.0 23.4 + - - +
65O LEU* 4.4 4.9 - - + -
69O GLN* 4.2 11.0 - - - +
131O VAL* 3.8 29.6 - - + -
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Residues in contact with THR 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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442I GLN 3.3 9.7 + - - -
443I LYS* 3.5 10.0 + - - -
445I ILE* 1.3 76.7 - - - +
447I PHE* 1.3 61.9 + - - +
449I ALA* 3.3 7.6 - - - +
450I GLU* 3.2 23.5 + - + +
65O LEU* 5.3 1.1 - - - -
69O GLN* 2.6 32.4 + - - +
214O PHE* 6.4 2.0 - - + -
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Residues in contact with PHE 447 (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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412I LYS* 4.1 13.5 - - + -
413I ASN* 3.3 41.5 - - - -
416I ALA* 3.9 20.6 - - + -
443I LYS* 3.1 26.0 + - + +
444I ASP* 3.4 8.7 - - - +
445I ILE 3.1 0.2 - - - -
446I THR* 1.3 76.4 - - - +
448I VAL* 1.3 58.0 + - + +
450I GLU* 3.5 17.2 + - - +
451I PHE* 3.0 28.2 + - + +
452O GLU* 4.6 25.8 - - + -
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Residues in contact with VAL 448 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308I LEU* 3.9 18.2 - - + -
416I ALA* 3.8 32.3 - - + +
417I PHE* 4.0 28.0 - - + +
420I TRP* 4.4 21.3 - - + -
440I MET* 5.4 1.3 - - + -
444I ASP* 3.1 24.5 + - - +
445I ILE* 3.2 4.9 + - + +
447I PHE* 1.3 74.0 - - + +
449I ALA* 1.3 66.5 + - - +
451I PHE* 3.4 6.0 - - + +
452I LEU* 2.9 27.5 + - + +
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Residues in contact with ALA 449 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305I MET* 4.8 6.5 - - - +
308I LEU* 3.8 14.3 - - + +
445I ILE 3.0 10.6 + - - +
446I THR* 3.3 12.3 - - + +
448I VAL* 1.3 78.6 - - - +
450I GLU* 1.3 61.9 + - - +
452I LEU* 3.3 4.2 + - - +
453I THR* 3.1 25.1 + - - -
65O LEU* 3.0 37.0 - - + -
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Residues in contact with GLU 450 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413I ASN* 5.3 3.1 - - - +
446I THR* 3.2 13.6 + - + +
447I PHE* 3.7 18.7 - - + +
449I ALA* 1.3 75.4 - - - +
451I PHE* 1.3 71.5 + - - +
453I THR* 2.9 9.7 + - - -
454I GLU* 2.8 48.5 + - + +
455I HIS* 5.7 0.6 - - - -
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Residues in contact with PHE 451 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413I ASN* 3.4 41.7 - - + +
414I PHE* 4.0 29.8 - + - -
417I PHE* 3.4 41.7 - + + -
447I PHE* 3.0 17.6 + - + +
448I VAL* 3.3 13.2 + - + +
450I GLU* 1.3 80.4 + - - +
452I LEU* 1.3 68.0 + - + +
455I HIS* 3.1 60.8 + + - +
456I PHE* 3.7 26.5 - + - -
472I VAL* 5.4 0.7 - - + -
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Residues in contact with LEU 452 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301I GLN* 3.6 11.3 - - - +
304I PHE* 3.7 26.9 - - + +
305I MET* 3.8 24.2 - - + +
308I LEU* 3.8 22.0 - - + -
417I PHE* 3.6 29.6 - - + -
420I TRP* 5.1 4.5 - - + -
448I VAL* 2.9 16.9 + - + +
449I ALA 3.5 8.5 - - - +
451I PHE* 1.3 82.8 - - + +
453I THR* 1.3 64.0 + - - +
456I PHE* 3.3 46.2 + - + +
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Residues in contact with THR 453 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301I GLN* 3.8 19.6 + - - +
305I MET* 5.4 3.1 - - - +
449I ALA 3.1 14.9 + - - -
450I GLU* 2.9 14.1 + - - -
452I LEU* 1.3 78.6 - - - +
454I GLU* 1.3 62.7 + - - +
457I ASN* 3.4 26.7 + - - +
62O GLN* 4.4 16.1 - - + +
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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
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450I GLU* 2.8 34.2 + - + +
453I THR* 1.3 76.2 - - - +
455I HIS* 1.3 90.8 + - + +
457I ASN* 3.7 11.5 - - - +
474I ARG* 5.5 3.5 + - - -
490I PRO 5.5 2.6 - - - +
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Residues in contact with HIS 455 (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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413I ASN* 3.2 19.5 + - - -
414I PHE* 6.1 2.3 - + - -
450I GLU* 5.7 1.0 + - - -
451I PHE* 3.1 47.1 + + - +
454I GLU* 1.3 99.3 + - + +
456I PHE* 1.3 76.8 + - + +
457I ASN 3.0 15.3 + - - +
471I ASN* 3.8 34.1 + - - +
472I VAL* 4.6 4.7 - - + +
473I GLU 5.9 0.2 + - - -
474I ARG* 3.4 48.6 - - - -
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Residues in contact with PHE 456 (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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283I MET* 5.4 5.6 - - + -
287I LEU* 4.2 17.0 - - + -
299I SER* 5.8 1.9 - - - -
300I VAL* 3.9 39.5 - - + +
301I GLN* 3.6 27.1 + - - +
304I PHE* 3.9 22.7 - + - -
414I PHE* 6.2 0.2 - + - -
417I PHE* 3.9 25.4 - + - -
451I PHE* 3.7 20.9 - + - -
452I LEU* 3.3 32.8 + - + +
455I HIS* 1.3 82.6 - - + +
457I ASN* 1.3 62.0 + - - +
470I PHE* 4.9 7.5 - - - +
472I VAL* 3.7 22.7 - - + -
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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