Contacts of the helix formed by residues 437 - 446 (chain A) in PDB entry 4X2N
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 SER 437 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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376A LYS* 4.2 7.6 - - - +
435A ASP 3.8 1.2 + - - -
436A PRO* 1.3 76.1 - - - +
438A VAL* 1.3 63.5 + - - +
439A GLU* 3.5 8.9 + - - +
440A GLU* 3.0 38.4 + - - +
441A MET* 3.0 23.6 + - - +
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Residues in contact with VAL 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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372A ARG* 3.8 44.9 - - - +
376A LYS* 3.8 33.1 - - + +
379A MET* 4.3 8.3 - - + -
384A LEU* 3.9 25.2 - - + +
437A SER* 1.3 72.1 - - - +
439A GLU* 1.3 62.2 + - + +
441A MET* 3.3 2.5 + - - +
442A ARG* 2.7 34.5 + - - +
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Residues in contact with GLU 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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384A LEU 5.4 0.2 - - - +
437A SER* 3.2 7.7 + - - +
438A VAL* 1.3 85.2 - - + +
440A GLU* 1.3 57.3 + - + +
442A ARG* 2.7 44.4 + - - +
443A LYS* 3.0 45.6 + - - +
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Residues in contact with GLU 440 (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 VAL* 4.2 4.8 - - + +
433A PRO* 3.6 30.5 - - + +
435A ASP 4.5 1.2 - - - +
436A PRO* 3.4 14.2 - - + +
437A SER* 3.0 41.4 + - - +
439A GLU* 1.3 75.0 - - + +
441A MET* 1.3 63.2 + - - +
443A LYS* 3.5 9.4 + - + +
444A VAL* 3.5 23.6 + - - +
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Residues in contact with MET 441 (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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376A LYS* 3.4 21.8 - - + +
377A ARG* 3.5 25.4 - - - +
379A MET 5.8 0.7 - - - +
384A LEU* 3.5 24.5 - - + -
428A TYR* 3.7 25.8 - - + -
432A VAL* 3.7 17.3 - - + -
436A PRO* 3.6 30.5 - - + -
437A SER 3.0 15.7 + - - +
438A VAL 3.6 2.5 - - - +
440A GLU* 1.3 74.7 - - - +
442A ARG* 1.3 60.3 + - - +
444A VAL* 3.2 3.2 + - + +
445A VAL* 2.9 49.1 + - + +
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Residues in contact with ARG 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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384A LEU* 3.7 33.6 - - + +
385A ASP* 4.1 10.8 - - - +
438A VAL 2.7 21.7 + - - +
439A GLU* 2.7 39.5 + - - +
441A MET* 1.3 72.2 - - - +
443A LYS* 1.4 70.7 + - - +
446A CYS* 2.9 49.0 + - + +
447A GLU* 2.9 46.9 + - - +
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Residues in contact with LYS 443 (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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439A GLU* 3.0 32.9 + - - +
440A GLU* 3.9 9.2 - - + +
441A MET 3.3 0.2 - - - -
442A ARG* 1.4 86.1 - - - +
444A VAL* 1.3 59.6 + - + +
447A GLU* 3.4 27.0 - - + +
448A GLN* 2.9 30.3 + - - +
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Residues in contact with VAL 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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428A TYR* 3.9 21.8 - - + -
431A LEU* 3.8 54.3 - - + +
432A VAL* 3.8 8.3 - - + -
440A GLU 3.5 12.5 + - - +
441A MET 3.2 7.4 + - - +
443A LYS* 1.3 79.8 - - + +
445A VAL* 1.3 61.8 + - + +
448A GLN* 3.6 14.6 - - - +
449A LYS 3.1 9.5 + - - -
450A LEU* 3.0 28.6 + - + -
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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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379A MET 5.4 0.2 - - - +
381A PRO* 3.8 27.2 - - + +
384A LEU* 3.7 15.9 - - + -
402A TYR* 3.8 14.6 - - - +
428A TYR* 3.6 33.7 - - + +
441A MET* 2.9 36.5 + - + +
444A VAL* 1.3 73.0 - - + +
446A CYS* 1.4 57.6 + - - +
449A LYS* 3.4 12.2 - - - +
450A LEU 3.9 0.9 - - - -
451A ARG* 3.0 38.2 + - - +
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Residues in contact with CYS 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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381A PRO* 3.3 44.9 - - - -
384A LEU* 3.9 8.5 - - - -
385A ASP* 4.0 15.0 - - + +
442A ARG* 2.9 35.5 + - + +
445A VAL* 1.4 76.9 - - - +
447A GLU* 1.3 63.5 + - + +
449A LYS* 2.9 31.9 + - - +
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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