Contacts of the helix formed by residues 437 - 447 (chain A) in PDB entry 6P0D
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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290A LEU* 4.2 4.5 - - - +
293A ALA* 3.6 16.5 - - - +
297A GLU* 2.7 32.6 + - - +
384A GLU* 3.3 9.4 - - - -
435A ARG 3.1 0.2 + - - -
436A HIS* 1.3 75.2 - - - +
438A GLU* 1.3 64.2 + - - +
439A ALA 3.3 2.5 - - - -
440A ARG* 3.1 42.4 + - - +
441A PHE* 3.3 11.1 - - - -
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Residues in contact with GLU 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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289A TYR* 3.5 32.7 - - + +
290A LEU* 3.0 44.8 + - + +
293A ALA* 4.3 3.8 - - + -
398A PRO* 5.9 1.0 - - - +
399A LEU* 3.9 15.6 + - - +
433A ALA 3.9 3.5 - - - +
434A CYS* 3.4 19.4 - - - -
435A ARG* 2.8 45.6 + - - +
436A HIS 3.3 0.6 - - - -
437A SER* 1.3 78.3 - - - +
439A ALA* 1.3 58.7 + - - +
441A PHE* 3.1 3.3 + - - -
442A ILE* 2.9 30.3 + - - +
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Residues in contact with ALA 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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380A GLY 4.5 1.8 - - - -
383A ALA* 3.8 23.7 - - - +
384A GLU* 3.9 8.7 - - + -
431A PHE* 3.7 15.7 - - + +
434A CYS* 3.4 27.7 - - + +
436A HIS 4.6 2.3 + - - +
437A SER 3.3 0.6 - - - -
438A GLU* 1.3 78.2 - - - +
440A ARG* 1.3 64.3 + - - +
442A ILE* 4.3 0.9 - - - -
443A ALA* 3.0 27.2 + - - +
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Residues in contact with ARG 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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297A GLU* 3.9 27.7 + - - +
300A GLU* 4.5 6.3 + - - -
380A GLY* 3.4 23.3 - - - +
381A LEU* 4.4 8.6 - - + +
384A GLU* 2.8 42.9 + - - +
437A SER* 3.1 24.5 + - - +
439A ALA* 1.3 79.4 - - - +
441A PHE* 1.3 67.7 + - + +
444A ARG* 3.0 69.3 + - - +
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Residues in contact with PHE 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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289A TYR* 3.5 18.2 - - + +
293A ALA* 3.5 28.5 - - + -
296A PHE* 3.5 39.5 - + + -
297A GLU* 3.7 22.7 - - + -
300A GLU* 4.0 8.7 - - - -
437A SER* 3.3 27.8 - - - -
438A GLU 3.1 4.6 + - - +
440A ARG* 1.3 90.1 - - + +
442A ILE* 1.3 61.3 + - - +
444A ARG* 3.7 27.0 - - - +
445A SER* 2.8 35.0 + - - -
450A LEU* 4.0 12.7 - - + +
452A LEU* 4.5 6.3 - - + -
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Residues in contact with ILE 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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289A TYR* 3.7 20.4 - - + +
399A LEU* 4.7 2.0 - - + -
404A VAL* 3.5 37.9 - - + -
408A PHE* 4.1 5.6 - - + -
430A LEU* 4.1 26.0 - - + -
431A PHE* 4.0 15.9 - - + -
434A CYS* 3.9 13.9 - - - -
438A GLU 2.9 21.0 + - - +
439A ALA 3.9 3.8 - - - +
441A PHE* 1.3 76.1 - - - +
443A ALA* 1.3 62.9 + - - +
445A SER* 3.6 4.0 - - - -
446A LEU* 3.0 46.4 + - + +
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Residues in contact with ALA 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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354A LEU* 3.4 15.7 - - + +
379A VAL* 4.0 13.0 - - + +
380A GLY* 3.8 20.9 - - - +
383A ALA* 3.9 15.9 - - + -
431A PHE* 4.0 12.3 - - + -
439A ALA 3.0 17.9 + - - +
442A ILE* 1.3 76.8 - - - +
444A ARG* 1.3 62.8 + - - +
446A LEU 3.2 1.4 + - - -
447A SER* 2.9 20.0 + - - -
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Residues in contact with ARG 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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300A GLU* 3.0 39.3 + - - -
378A ASP* 2.6 43.1 + - - +
379A VAL* 6.0 0.2 - - - -
380A GLY* 4.2 2.0 - - - +
381A LEU* 4.2 8.1 - - - +
440A ARG* 3.0 44.1 + - - +
441A PHE* 3.7 22.8 - - - +
443A ALA* 1.3 75.4 - - - +
445A SER* 1.3 63.7 + - - +
447A SER* 3.0 12.3 + - - -
449A ARG 3.0 47.5 + - - +
450A LEU* 3.9 20.2 + - + -
451A ARG* 4.2 14.9 - - - +
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Residues in contact with SER 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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289A TYR* 4.6 3.8 + - - -
296A PHE* 5.3 1.2 - - - -
333A LEU* 5.1 2.9 + - - +
336A ASN* 3.2 36.2 + - - +
347A LEU* 4.0 9.4 - - - +
408A PHE* 3.9 24.1 - - - -
441A PHE 2.8 24.9 + - - -
442A ILE 3.6 3.8 - - - -
444A ARG* 1.3 76.6 - - - +
446A LEU* 1.3 61.6 + - - +
448A GLY* 3.1 10.9 + - - -
450A LEU* 3.5 17.3 - - - +
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Residues in contact with LEU 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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347A LEU* 3.9 26.7 - - + +
349A VAL* 3.6 31.1 - - + +
350A GLY* 5.0 0.2 - - - -
354A LEU* 3.8 20.0 - - + -
408A PHE* 3.8 27.4 - - + -
411A ILE* 4.1 16.2 - - + -
427A ILE* 3.8 36.3 - - + -
430A LEU* 5.0 1.6 - - + -
431A PHE* 4.7 0.4 - - + -
442A ILE* 3.0 36.4 + - + +
443A ALA* 3.7 3.8 - - - +
445A SER* 1.3 76.4 - - - +
447A SER* 1.3 60.5 + - - +
448A GLY 3.2 0.9 + - - -
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Residues in contact with SER 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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349A VAL 5.4 1.3 - - - -
350A GLY* 5.4 5.9 - - - -
351A ASP* 3.7 20.3 - - - +
354A LEU* 3.6 15.9 - - - +
379A VAL* 4.7 9.1 + - - +
443A ALA 2.9 14.6 + - - -
444A ARG* 3.0 18.7 + - - +
445A SER 3.2 0.2 - - - -
446A LEU* 1.3 75.4 - - - +
448A GLY* 1.3 59.6 + - - +
449A ARG* 3.4 22.7 + - - +
768A ARG* 4.8 3.4 + - - -
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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