Contacts of the helix formed by residues 441 - 451 (chain A) in PDB entry 1MD9
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 ALA 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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426A GLU* 3.8 40.8 - - + +
432A GLN* 5.1 1.1 - - - +
439A LYS* 4.1 7.7 + - - +
440A VAL* 1.3 70.8 - - - +
442A ALA* 1.3 67.3 + - - +
443A GLU 3.4 1.3 - - - +
444A GLU* 3.3 36.9 + - + +
445A VAL* 3.8 6.4 + - - +
501A LYS* 6.0 0.4 - - - +
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Residues in contact with ALA 442 (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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426A GLU 5.5 0.6 + - - -
431A ASP* 4.3 15.8 + - + +
432A GLN* 5.6 0.6 - - - +
433A ILE* 4.5 5.4 - - + -
440A VAL* 3.0 9.4 + - - -
441A ALA* 1.3 68.9 - - - +
443A GLU* 1.3 68.3 + - - +
445A VAL* 2.8 18.4 + - - +
446A GLU* 3.0 12.8 + - - +
460A MSE 3.5 42.8 - - + +
522A LYS* 3.7 12.8 - - - +
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Residues in contact with GLU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LYS* 3.1 56.4 + - + +
311A SER* 3.5 30.3 + - - +
312A ALA 4.5 1.4 + - - -
426A GLU* 3.4 21.3 + - - +
441A ALA* 3.4 1.4 - - + +
442A ALA* 1.3 78.5 - - - +
444A GLU* 1.3 78.0 + - - +
446A GLU* 2.9 16.8 + - - +
447A ASN* 2.8 28.0 + - - +
522A LYS* 4.7 1.7 - - - +
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Residues in contact with GLU 444 (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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441A ALA* 3.3 29.2 + - + +
442A ALA 2.9 2.6 + - - -
443A GLU* 1.3 85.9 + - - +
445A VAL* 1.3 62.7 + - + +
447A ASN* 3.4 10.6 + - - +
448A HIS* 3.0 32.9 + - + +
497A LEU* 4.5 7.0 - - + +
501A LYS* 2.4 46.7 + - - +
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Residues in contact with VAL 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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440A VAL* 4.5 3.4 - - + -
441A ALA 4.2 7.9 - - - +
442A ALA 2.8 11.9 + - - +
444A GLU* 1.3 71.3 - - + +
446A GLU* 1.3 65.4 + - - +
448A HIS* 3.5 10.5 + - - +
449A LEU* 3.3 23.6 + - + +
460A MSE 3.7 23.1 - - + -
492A LEU* 4.2 25.1 - - + -
497A LEU* 4.0 6.3 - - + -
501A LYS* 3.1 48.9 - - + +
503A PRO* 4.3 5.2 - - + -
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Residues in contact with GLU 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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311A SER* 4.7 9.1 + - - +
442A ALA* 3.0 11.0 + - - +
443A GLU* 2.9 19.3 + - - +
445A VAL* 1.3 76.0 - - - +
447A ASN* 1.3 58.0 + - - +
449A LEU* 2.8 32.6 + - - +
450A LEU* 2.9 17.3 + - + +
458A ALA* 3.1 30.7 - - + +
459A ALA* 3.9 0.6 - - - -
460A MSE 2.9 25.4 + - + +
474A VAL* 5.7 0.7 - - + -
522A LYS* 2.4 36.1 + - - -
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Residues in contact with ASN 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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311A SER* 3.4 16.8 + - - -
312A ALA* 3.2 18.5 + - - +
313A GLU* 2.5 60.0 + - - +
443A GLU* 2.8 21.3 + - - +
444A GLU* 3.4 11.1 + - - +
446A GLU* 1.3 72.9 - - - +
448A HIS* 1.3 69.6 + - - +
450A LEU* 3.5 6.5 + - - +
495A ARG* 6.1 0.4 - - - +
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Residues in contact with HIS 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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444A GLU* 3.0 34.9 + - + +
445A VAL* 3.5 9.0 - - - +
446A GLU 3.0 0.4 - - - -
447A ASN* 1.3 84.1 - - - +
449A LEU* 1.3 54.9 + - - +
451A ALA* 2.6 38.2 + - - +
491A PHE* 4.0 6.7 - - - -
492A LEU* 3.7 14.8 - - + -
495A ARG* 2.6 51.0 + - + +
497A LEU* 3.1 35.4 - - + +
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Residues in contact with LEU 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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445A VAL* 3.3 20.9 - - + +
446A GLU* 2.8 16.6 + - - +
448A HIS* 1.3 76.5 - - - +
450A LEU* 1.3 59.6 + - - +
452A HIS* 2.9 16.5 + - - +
455A VAL* 3.2 21.4 - - + +
458A ALA* 4.6 8.7 - - + -
474A VAL* 3.9 20.9 - - + -
476A ILE* 3.9 23.6 - - + -
488A LEU* 4.4 22.0 - - + +
491A PHE* 4.6 7.0 - - + -
492A LEU* 3.2 41.1 - - + -
503A PRO* 4.6 0.9 - - + -
506A VAL* 6.4 0.2 - - + -
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Residues in contact with LEU 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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284A MSE 4.6 12.1 - - + -
311A SER* 3.7 30.7 - - - +
313A GLU* 3.8 12.9 - - + +
314A ALA* 4.3 20.0 - - + -
317A ARG* 5.8 2.3 + - - -
446A GLU* 2.9 18.6 + - + +
447A ASN* 3.7 7.6 - - - +
448A HIS 3.0 0.6 + - - -
449A LEU* 1.3 75.6 - - - +
451A ALA* 1.3 57.1 + - - +
452A HIS 3.1 10.8 + - - +
455A VAL* 4.0 11.4 - - + +
456A HIS 4.1 7.4 - - - +
457A ASP* 3.6 39.3 - - - +
458A ALA* 4.0 7.9 - - + +
479A ARG* 5.2 3.1 + - - -
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Residues in contact with ALA 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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313A GLU* 3.4 33.1 - - - +
447A ASN 4.4 0.7 - - - +
448A HIS 2.6 16.3 + - - +
450A LEU* 1.3 77.6 - - - +
452A HIS* 1.3 57.6 + - - -
453A PRO* 3.6 8.1 - - - +
491A PHE* 4.0 9.1 - - + -
495A ARG* 3.9 22.0 - - - +
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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