Contacts of the helix formed by residues 432 - 439 (chain A) in PDB entry 3MOS
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 432 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A ALA* 4.7 3.8 - - - +
394A THR* 4.0 26.7 - - + +
429A MET 3.9 4.6 - - - +
430A ALA* 3.6 9.4 - - - +
431A LEU* 1.3 104.0 + - - +
433A ASP* 1.3 60.2 + - - +
434A LEU 3.3 2.9 - - - -
435A ALA* 3.4 8.1 + - + +
436A MET* 2.9 29.0 + - + +
562A HIS* 3.3 8.5 - - - -
563A TYR* 3.9 21.3 - - + -
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Residues in contact with ASP 433 (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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390A ALA* 3.7 14.5 - - + +
394A THR* 5.7 0.9 - - + -
430A ALA* 3.5 22.7 - - + +
432A GLU* 1.3 73.9 + - - +
434A LEU* 1.3 61.5 + - - +
436A MET* 4.1 10.5 - - + -
437A PHE* 2.8 38.3 + - + +
469A PHE* 3.5 21.4 - - + -
471A ARG* 2.7 56.7 + - - +
562A HIS* 3.6 1.0 - - - -
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Residues in contact with LEU 434 (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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433A ASP* 1.3 74.9 - - - +
435A ALA* 1.3 60.5 + - - +
437A PHE* 4.5 2.0 - - - +
438A ARG* 2.9 42.0 + - + +
445A VAL* 3.8 25.6 - - + -
447A TYR* 4.3 6.1 - - + -
469A PHE* 4.7 3.6 - - + -
471A ARG* 3.8 33.7 - - + +
537A ILE* 4.3 11.9 - - + -
560A GLU* 4.0 3.6 - - + +
562A HIS* 3.1 30.6 + - + +
566A GLY 3.6 3.8 - - - +
567A GLY* 4.1 9.0 - - - -
568A ILE* 3.8 30.3 - - + +
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Residues in contact with ALA 435 (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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432A GLU* 3.5 13.2 - - + +
434A LEU* 1.3 78.5 - - - +
436A MET* 1.3 62.2 + - - +
438A ARG* 4.0 1.6 - - - +
439A SER* 3.2 24.6 + - - -
562A HIS* 3.3 8.6 + - + -
565A GLU* 3.6 24.0 - - + +
566A GLY* 3.3 17.8 + - - -
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Residues in contact with MET 436 (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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390A ALA 4.8 1.6 - - - +
393A PHE* 3.7 25.8 - - + +
394A THR* 3.8 24.2 - - + +
397A PHE* 3.4 53.8 - - + -
400A ILE* 4.6 2.9 - - + -
432A GLU* 2.9 17.3 + - + +
433A ASP* 3.6 7.9 - - - +
435A ALA* 1.3 76.5 - - - +
437A PHE* 1.3 95.8 + - + +
439A SER* 2.9 23.3 + - - -
440A VAL* 3.6 7.7 + - + +
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Residues in contact with PHE 437 (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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393A PHE* 4.1 13.9 - + + -
400A ILE* 3.7 45.3 - - + -
412A LEU* 4.2 12.3 - - + -
433A ASP* 2.8 33.6 + - + +
434A LEU 4.6 0.2 - - - +
436A MET* 1.3 94.0 - - + +
438A ARG* 1.4 53.3 + - - +
440A VAL* 3.0 17.0 + - + +
443A SER* 2.7 29.3 + - - -
445A VAL* 3.9 17.3 - - + -
467A ILE* 4.3 11.9 - - + -
469A PHE* 3.4 57.9 - + + -
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Residues in contact with ARG 438 (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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434A LEU* 2.9 24.6 + - - +
435A ALA 4.1 2.5 - - - +
437A PHE* 1.4 76.2 - - - +
439A SER* 1.3 56.3 + - - +
445A VAL* 4.1 14.1 - - + +
537A ILE* 4.0 25.2 + - + +
538A LYS* 2.8 45.0 + - + +
566A GLY* 2.8 49.0 + - - +
567A GLY* 3.7 7.4 + - - -
570A GLU* 4.8 2.8 + - - +
571A ALA* 3.6 33.0 - - - +
574A SER* 5.6 4.2 + - - -
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Residues in contact with SER 439 (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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397A PHE* 3.5 20.4 - - - -
435A ALA 3.2 13.9 + - - -
436A MET* 2.9 15.2 + - - -
437A PHE 3.2 0.4 - - - -
438A ARG* 1.3 75.0 - - - +
440A VAL* 1.3 61.8 + - - +
441A PRO* 3.4 8.9 - - - +
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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