Contacts of the helix formed by residues 440 - 452 (chain D) in PDB entry 1A4Y
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 GLU 440 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439D SER* 1.3 72.4 - - - +
441D GLU* 1.3 72.0 + - - +
443D GLU* 3.1 5.9 + - + +
444D ASP* 2.9 40.0 + - - +
5E ARG* 3.2 23.5 - - + +
108E GLU* 3.3 20.9 + - - +
109E ASN* 3.4 27.2 + - - +
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Residues in contact with GLU 441 (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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411D ASP* 5.2 1.1 - - - +
439D SER* 3.2 21.8 - - - +
440D GLU* 1.3 86.1 + - - +
442D MET* 1.3 57.4 + - + +
444D ASP* 3.6 7.8 + - - +
445D ARG* 3.1 35.2 + - - +
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Residues in contact with MET 442 (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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411D ASP* 3.4 48.5 - - + +
414D ILE* 3.2 28.3 - - + -
415D LEU* 4.0 7.2 - - - -
418D VAL* 4.1 8.7 - - + -
438D TRP* 3.8 17.5 - - + -
439D SER* 3.2 8.5 + - - +
440D GLU 3.2 0.2 - - - -
441D GLU* 1.3 76.7 - - + +
443D GLU* 1.3 56.1 - - - +
444D ASP 3.2 0.4 - - - -
445D ARG* 3.2 39.3 + - + +
446D LEU* 2.8 36.3 + - + +
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Residues in contact with GLU 443 (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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438D TRP* 3.1 28.5 + - - +
439D SER 2.9 13.0 + - - +
440D GLU* 3.3 16.8 - - + +
442D MET* 1.3 77.3 - - - +
444D ASP* 1.3 62.0 + - - +
446D LEU* 3.2 7.6 + - - +
447D GLN* 2.8 37.4 + - + +
450D GLU* 5.6 1.2 - - - +
460D SER 5.4 1.0 - - - +
5E ARG* 3.6 32.8 + - + +
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Residues in contact with ASP 444 (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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440D GLU* 2.9 29.5 + - - +
441D GLU* 3.6 8.4 - - - +
443D GLU* 1.3 79.2 - - - +
445D ARG* 1.3 57.3 + - - +
447D GLN* 2.9 9.5 + - - +
448D ALA* 2.7 37.2 + - - +
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Residues in contact with ARG 445 (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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415D LEU* 2.9 36.1 - - - +
418D VAL* 4.0 21.0 - - + +
441D GLU* 3.1 21.6 + - - +
442D MET* 3.3 35.2 - - + +
444D ASP* 1.3 79.8 - - - +
446D LEU* 1.3 61.4 + - - +
448D ALA* 3.3 8.5 + - - +
449D LEU* 3.0 21.7 + - - +
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Residues in contact with LEU 446 (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 ILE* 4.3 11.2 - - + -
418D VAL* 3.6 24.7 - - + -
431D LEU* 5.6 2.9 - - + -
433D LEU* 4.7 7.2 - - + -
438D TRP* 3.7 45.1 - - + +
442D MET* 2.8 26.0 + - + +
443D GLU* 3.5 7.9 - - - +
445D ARG* 1.3 70.4 - - - +
447D GLN* 1.3 60.5 + - - +
449D LEU* 3.2 20.9 + - + +
450D GLU* 2.8 39.5 + - - +
458D VAL* 4.6 17.5 - - + -
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Residues in contact with GLN 447 (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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443D GLU* 2.8 22.2 + - + +
444D ASP* 2.9 12.1 + - - +
446D LEU* 1.3 77.1 - - - +
448D ALA* 1.3 63.3 + - - +
450D GLU* 3.1 22.8 + - - +
451D LYS* 3.0 23.0 + - - +
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Residues in contact with ALA 448 (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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444D ASP 2.7 15.6 + - - +
445D ARG* 3.4 13.9 - - - +
447D GLN* 1.3 73.8 - - - +
449D LEU* 1.3 63.2 + - - +
451D LYS* 3.1 7.9 + - - +
452D ASP* 2.9 23.9 + - - +
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Residues in contact with LEU 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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418D VAL* 4.2 15.9 - - + +
421D VAL* 3.8 27.4 - - + +
422D ARG* 3.7 36.1 - - + +
431D LEU* 6.1 1.1 - - + -
445D ARG 3.0 10.9 + - - +
446D LEU* 3.4 29.8 - - + +
448D ALA* 1.3 78.1 - - - +
450D GLU* 1.3 57.8 + - - +
452D ASP* 4.4 6.5 - - + -
453D LYS* 2.8 41.0 + - + +
456D LEU* 4.0 13.2 - - + -
458D VAL* 4.5 6.7 - - + -
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Residues in contact with GLU 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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443D GLU* 5.6 1.0 - - - +
446D LEU* 2.8 26.1 + - - +
447D GLN* 3.2 29.2 - - - +
449D LEU* 1.3 80.5 - - - +
451D LYS* 1.3 62.4 + - - +
452D ASP 3.5 0.2 + - - -
453D LYS 3.7 3.7 - - - +
454D PRO* 3.6 21.3 - - - +
456D LEU* 5.0 8.2 - - - +
458D VAL* 3.6 39.6 - - + +
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Residues in contact with LYS 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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112A PRO* 5.2 5.0 - - - +
447D GLN* 3.0 19.2 + - - +
448D ALA* 3.1 8.0 + - - +
450D GLU* 1.3 77.1 - - - +
452D ASP* 1.3 62.7 + - - +
454D PRO* 3.8 11.8 - - - +
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Residues in contact with ASP 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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112A PRO* 4.9 2.8 - - - +
140A GLN* 5.0 4.2 + - - +
142A ARG* 3.2 25.6 + - - +
448D ALA 2.9 15.0 + - - +
449D LEU* 3.8 9.0 - - + +
451D LYS* 1.3 79.3 - - - +
453D LYS* 1.3 58.9 + - + +
454D PRO* 3.0 10.3 - - - +
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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