Contacts of the helix formed by residues 430 - 437 (chain M) in PDB entry 6M6A
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 430 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428M LEU 2.8 1.0 + - - -
429M PRO* 1.3 84.3 - - + +
431M TRP* 1.3 66.9 + - + +
433M PRO* 3.5 8.3 - - - +
434M LEU* 2.7 45.7 + - + +
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Residues in contact with TRP 431 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428M LEU* 3.0 45.2 + - + +
430M GLU* 1.3 85.1 + - + +
432M ASP* 1.3 64.9 + - - +
434M LEU* 3.3 19.2 + - + -
435M VAL 3.4 0.2 + - - -
485M HIS* 2.5 80.0 + + - +
488M VAL* 4.3 12.1 - - + -
489M GLY* 3.3 26.2 + - - -
519M PRO* 5.9 8.7 - - + -
520M VAL* 6.0 0.4 - - + -
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Residues in contact with ASP 432 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427M PRO 3.0 8.9 - - - +
428M LEU 3.5 1.7 + - - +
431M TRP* 1.3 76.0 - - - +
433M PRO* 1.3 57.5 - - + +
435M VAL* 3.3 8.8 - - + +
436M GLU* 2.7 42.0 + - + +
455M LEU* 4.0 7.7 - - + +
482M ARG* 2.9 32.2 - - + +
485M HIS 3.6 0.2 - - - -
486M ARG* 2.8 56.7 + - - +
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Residues in contact with PRO 433 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428M LEU 3.8 1.3 - - - +
429M PRO* 3.2 30.3 - - + +
430M GLU* 3.5 15.5 - - - +
432M ASP* 1.3 89.7 - - + +
434M LEU* 1.3 58.9 + - - +
436M GLU* 3.7 14.4 - - + +
437M LYS* 2.9 35.1 + - - +
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Residues in contact with LEU 434 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430M GLU* 2.7 31.3 + - + +
431M TRP* 3.3 20.6 + - + -
433M PRO* 1.3 72.0 - - - +
435M VAL* 1.3 60.5 + - - +
437M LYS* 2.4 51.8 + - - +
438M GLY 4.2 1.0 + - - -
485M HIS* 3.5 22.7 - - + -
518M LEU* 3.7 18.2 - - + +
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Residues in contact with VAL 435 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431M TRP 3.4 2.7 + - - +
432M ASP* 3.3 13.0 - - - +
434M LEU* 1.3 78.9 - - - +
436M GLU* 1.3 59.7 + - - +
438M GLY 2.8 9.7 + - - -
481M LEU* 4.4 8.1 - - + +
482M ARG* 3.7 20.0 - - + -
485M HIS* 3.3 32.9 + - + +
514M ARG* 2.4 55.6 + - + +
515M PHE* 3.6 27.8 - - + -
518M LEU* 3.8 7.2 - - + -
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Residues in contact with GLU 436 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432M ASP* 2.7 24.5 + - - +
433M PRO* 3.1 17.9 + - + +
435M VAL* 1.3 78.6 - - - +
437M LYS* 1.3 61.9 + - - +
438M GLY 3.4 0.2 + - - -
439M PHE* 3.7 7.3 + - - +
452M GLU* 4.1 14.1 - - - +
482M ARG* 3.5 50.8 + - - +
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Residues in contact with LYS 437 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433M PRO 2.9 13.9 + - - +
434M LEU* 2.4 58.4 + - - +
436M GLU* 1.3 76.9 - - - +
438M GLY* 1.3 65.4 + - - +
439M PHE 3.3 6.1 + - - +
440M PRO* 5.3 0.9 - - - +
518M LEU* 4.2 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