Contacts of the helix formed by residues 448 - 459 (chain D) in PDB entry 3HU1
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 448 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391D ALA* 4.2 10.1 - - + -
393D ASP* 4.1 13.0 - - - +
394D VAL* 3.7 5.6 - - - -
425D LYS* 4.6 8.5 + - + -
446D ALA* 3.9 13.0 - - + +
447D VAL* 1.3 75.2 - - - +
449D MET* 1.3 62.1 + - - +
450D ASP* 3.5 13.0 - - - +
451D ASP* 2.7 49.7 + - - +
452D PHE* 3.4 9.7 + - - -
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Residues in contact with MET 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D ASP* 3.4 35.7 + - + +
394D VAL* 3.5 12.0 - - - +
395D ASP* 3.5 28.0 - - + +
398D GLN* 3.8 26.9 - - + -
399D VAL* 4.0 21.3 - - + -
402D GLU* 5.0 3.4 - - - +
448D THR* 1.3 70.1 - - - +
450D ASP* 1.3 59.7 + - - +
452D PHE* 3.0 11.1 + - + +
453D ARG* 2.9 66.8 + - + +
456D LEU* 5.2 0.7 - - + -
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Residues in contact with ASP 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D ASP* 5.0 2.1 + - - +
425D LYS* 3.1 26.8 + - - +
448D THR* 3.5 11.6 + - - +
449D MET* 1.3 77.4 - - - +
451D ASP* 1.3 55.4 - - - +
453D ARG* 3.3 19.5 + - - +
454D TRP* 3.0 26.7 + - - +
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Residues in contact with ASP 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418D ALA* 3.3 23.5 - - - +
421D GLN* 3.5 16.0 - - + +
422D ALA* 3.5 22.2 + - - +
425D LYS* 2.8 34.2 + - - +
447D VAL* 3.9 5.8 - - + -
448D THR* 2.7 43.1 + - - +
450D ASP* 1.3 74.1 - - - +
452D PHE* 1.3 56.3 + - - +
454D TRP* 3.0 6.2 + - - +
455D ALA* 2.8 26.5 + - - +
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Residues in contact with PHE 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D LEU* 5.0 1.8 - - + -
385D THR* 4.5 14.4 - - + -
388D MET* 4.6 3.4 - - + -
390D LEU* 3.8 22.9 - - + -
394D VAL* 3.9 18.2 - - + -
396D LEU* 4.7 6.1 - - + -
399D VAL* 4.0 39.9 - - + -
414D LEU* 4.9 7.9 - - + -
415D CYS* 4.2 22.2 - - - -
418D ALA* 4.0 19.5 - - + -
447D VAL* 3.7 21.8 - - + -
448D THR 3.4 13.4 + - - -
449D MET* 3.0 12.2 + - - +
451D ASP* 1.3 76.7 - - - +
453D ARG* 1.3 52.6 + - - +
455D ALA* 3.1 3.0 + - - +
456D LEU* 2.7 41.0 + - + +
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Residues in contact with ARG 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398D GLN* 5.2 4.9 - - - +
402D GLU* 4.8 10.9 + - - +
449D MET* 2.9 52.7 + - + +
450D ASP* 3.7 20.8 + - - +
452D PHE* 1.3 74.5 - - - +
454D TRP* 1.3 60.7 + - - +
456D LEU* 3.7 13.6 - - + +
457D SER* 3.1 23.6 + - - -
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Residues in contact with TRP 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417D GLU* 3.0 32.8 - - + -
421D GLN* 3.3 47.2 - - + +
424D ARG* 3.4 26.5 - - - -
425D LYS* 5.9 0.2 - - - +
450D ASP 3.0 12.5 + - - +
451D ASP 3.0 6.7 + - - +
453D ARG* 1.3 75.6 - - - +
455D ALA* 1.3 68.9 + - - +
457D SER* 2.6 28.0 + - - -
458D GLN* 3.4 44.8 + - + +
13E SER* 5.1 7.6 - - - -
211E LYS* 6.2 1.1 - - - -
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Residues in contact with ALA 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414D LEU* 3.6 39.7 - - + +
417D GLU* 4.2 8.5 - - + +
418D ALA* 3.7 17.0 - - + +
451D ASP 2.8 12.9 + - - +
452D PHE* 3.1 8.7 + - - +
454D TRP* 1.3 82.8 - - - +
456D LEU* 1.3 61.1 + - - +
458D GLN* 3.2 7.4 + - - +
459D SER* 3.2 18.2 + - - -
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Residues in contact with LEU 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399D VAL* 4.3 25.8 - - + +
402D GLU* 3.8 41.3 - - + +
403D THR* 3.8 29.4 - - + -
406D HIS* 5.7 0.9 - - + -
414D LEU* 4.0 11.9 - - + -
449D MET* 5.2 1.1 - - + -
452D PHE* 2.7 30.0 + - + +
453D ARG* 3.7 14.1 - - + +
455D ALA* 1.3 72.2 - - - +
457D SER* 1.3 62.2 + - - +
458D GLN 3.3 0.7 + - - -
459D SER* 3.3 17.6 + - - +
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Residues in contact with SER 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D ARG 3.1 13.5 + - - -
454D TRP* 2.6 31.1 + - - -
456D LEU* 1.3 75.8 - - - +
458D GLN* 1.3 69.5 + - - +
459D SER 3.6 0.7 - - - +
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Residues in contact with GLN 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417D GLU* 6.0 6.1 - - + -
454D TRP* 3.4 56.8 + - + +
455D ALA* 3.2 8.4 + - - +
456D LEU 3.2 0.6 - - - -
457D SER* 1.3 86.9 + - - +
459D SER* 1.3 65.4 + - - +
460D ASN* 4.7 4.3 + - - +
211E LYS* 5.6 5.3 - - - +
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Residues in contact with SER 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D HIS* 2.7 37.0 + - - -
410D ASP* 4.8 2.3 + - - +
414D LEU* 3.6 17.4 - - - +
455D ALA 3.2 11.3 + - - -
456D LEU* 3.3 18.6 + - - +
457D SER 3.6 1.1 - - - +
458D GLN* 1.3 82.4 - - - +
460D ASN* 1.4 64.0 + - - +
461D PRO* 4.7 0.9 - - - +
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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