Contacts of the helix formed by residues 444 - 454 (chain A) in PDB entry 4X8G
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 HIS 444 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371A PRO* 6.3 3.4 - - + -
401A ILE* 6.2 4.5 - - + -
402A SER* 5.5 0.6 - - - -
405A ASP* 2.8 28.4 + - - +
442A GLN* 3.6 5.6 + - - +
443A MET* 1.3 72.5 - - - +
445A GLN* 1.3 74.5 + - + +
446A ALA* 3.6 25.0 + - + +
447A LEU* 2.9 29.6 + - + +
448A GLN* 3.1 9.9 + - - +
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Residues in contact with GLN 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A GLN* 3.9 14.0 + - - +
443A MET 3.3 3.3 + - - -
444A HIS* 1.3 82.1 + - + +
446A ALA* 1.3 57.2 + - - +
448A GLN* 3.4 28.3 + - - +
449A ASP* 3.0 63.3 + - - +
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Residues in contact with ALA 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ASP* 4.7 2.8 - - - +
394A ARG* 5.4 12.8 - - + +
444A HIS* 3.1 26.3 + - + +
445A GLN* 1.3 80.4 - - - +
447A LEU* 1.3 59.8 + - + +
449A ASP* 3.7 7.9 + - - +
450A PHE* 3.4 20.4 + - - +
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Residues in contact with LEU 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A PHE* 3.7 35.2 - - + -
371A PRO* 4.2 14.4 - - + -
394A ARG* 4.7 14.6 - - + +
405A ASP* 3.7 46.0 - - + +
407A PHE* 4.1 13.0 - - + -
410A LEU* 6.3 0.2 - - + -
443A MET* 3.9 17.7 - - + -
444A HIS* 2.9 15.2 + - + +
446A ALA* 1.3 78.0 - - + +
448A GLN* 1.3 64.9 + - - +
450A PHE* 3.3 13.2 + - + +
451A LEU* 3.3 22.0 + - + +
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Residues in contact with GLN 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A PHE* 3.6 37.0 - - + -
432A ASP* 3.8 16.5 + - - -
442A GLN* 4.0 5.5 - - - +
443A MET* 2.7 35.6 + - + +
444A HIS 3.1 9.7 + - - +
445A GLN* 3.4 30.6 + - - +
447A LEU* 1.3 75.8 - - - +
449A ASP* 1.3 62.4 + - - +
451A LEU* 3.5 7.1 + - - +
452A SER* 3.1 27.8 + - - +
459A PRO* 5.2 0.5 - - - +
461A LYS* 3.9 17.3 + - - +
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Residues in contact with ASP 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A ASP* 4.3 3.8 - - - +
259A THR* 4.3 31.7 + - + +
445A GLN* 3.0 46.7 + - - +
446A ALA* 3.8 8.5 - - - +
447A LEU 3.2 0.2 - - - -
448A GLN* 1.3 74.5 - - - +
450A PHE* 1.3 59.4 + - - +
452A SER* 3.3 7.2 + - - -
453A ALA* 2.9 30.7 + - - +
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Residues in contact with PHE 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A PHE* 3.8 22.7 - + + -
257A PRO 3.8 7.0 - - - -
258A ASP* 3.7 18.3 + - + +
296A TRP* 4.2 23.1 - + + -
368A PHE* 3.5 39.9 - + + -
392A VAL* 4.3 21.1 - - + -
394A ARG* 4.6 15.9 - - + -
446A ALA 3.4 11.1 + - - +
447A LEU* 3.3 10.4 + - - +
449A ASP* 1.3 78.5 - - - +
451A LEU* 1.3 67.5 + - + +
453A ALA* 3.2 6.3 + - - +
454A GLN* 2.9 55.1 + - + +
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Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A TRP* 4.1 22.7 - - + -
368A PHE* 4.6 7.2 - - + -
410A LEU* 3.7 29.4 - - + -
428A ILE* 3.8 30.0 - - + +
430A PHE* 4.6 14.1 - - + -
443A MET* 4.7 11.7 - - - -
447A LEU* 3.3 16.9 + - + +
448A GLN* 3.9 7.0 - - - +
449A ASP 3.3 0.2 - - - -
450A PHE* 1.3 87.9 - - + +
452A SER* 1.3 60.8 + - - +
454A GLN* 3.5 18.1 + - + +
455A GLN 4.0 3.1 + - - -
457A GLN 4.3 6.2 - - - +
459A PRO* 3.9 17.9 - - + +
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Residues in contact with SER 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A GLN 3.1 18.7 + - - -
449A ASP* 3.8 6.3 - - - -
451A LEU* 1.3 76.2 - - - +
453A ALA* 1.3 62.2 + - - +
454A GLN 3.2 0.2 - - - -
455A GLN* 3.3 17.1 + - - +
459A PRO* 3.6 24.1 - - - +
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Residues in contact with ALA 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A PRO* 3.7 31.0 - - + +
258A ASP* 3.7 24.0 - - - +
259A THR* 5.2 0.4 - - - -
262A PRO 5.0 2.9 - - - +
449A ASP 2.9 17.0 + - - +
450A PHE 3.2 6.7 + - - +
452A SER* 1.3 74.9 - - - +
454A GLN* 1.3 64.2 + - - +
455A GLN* 3.1 13.3 + - - +
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Residues in contact with GLN 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A TRP* 5.3 1.0 - - - -
256A PHE* 4.1 5.7 - - - -
257A PRO* 2.8 32.0 + - - +
295A PRO* 3.2 25.4 - - + +
296A TRP* 2.8 48.4 + - + +
428A ILE* 6.1 2.5 - - + -
450A PHE* 2.9 47.8 + - + +
451A LEU* 3.7 12.1 - - + +
452A SER 3.2 0.6 - - - -
453A ALA* 1.3 74.8 + - - +
455A GLN* 1.3 57.8 + - - +
456A VAL* 2.6 31.0 + - + +
457A GLN* 5.6 2.0 - - + +
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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