Contacts of the helix formed by residues 438 - 448 (chain A) in PDB entry 3W6R
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 LEU 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A THR* 3.1 18.1 + - + +
437A ARG* 1.3 102.0 - - + +
439A ASN* 1.3 65.5 + - - +
440A ARG 3.4 2.7 - - - -
441A ALA* 3.2 17.1 + - + -
442A PHE* 2.9 40.4 + - + -
461A ALA* 3.6 22.7 - - - +
464A GLU* 3.7 43.7 - - + +
465A LEU* 3.8 18.6 - - + -
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Residues in contact with ASN 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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434A LEU* 5.3 2.5 - - - -
435A THR 3.1 10.7 + - - +
436A PHE 3.2 15.7 + - - +
437A ARG 3.5 0.2 - - - -
438A LEU* 1.3 79.4 - - - +
440A ARG* 1.3 94.6 + - - +
442A PHE* 3.4 5.8 + - - +
443A MET* 3.2 26.4 + - - +
505A VAL* 3.1 38.6 + - - +
506A ALA 3.2 14.5 + - - -
507A HIS 3.5 4.1 - - - +
508A ALA* 3.5 21.6 + - + -
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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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436A PHE 4.9 0.8 + - - -
437A ARG 5.2 1.0 + - - +
438A LEU 3.4 0.2 - - - -
439A ASN* 1.3 101.3 + - - +
441A ALA* 1.3 61.0 + - - +
443A MET* 3.3 13.6 + - - +
444A GLU* 2.9 48.0 + - - +
508A ALA* 4.2 21.6 - - + +
516A THR* 3.5 21.8 - - - +
520A ASP* 3.0 31.9 + - - -
523A ARG* 4.1 20.0 - - - +
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Residues in contact with ALA 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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437A ARG 5.2 1.9 + - - +
438A LEU* 3.2 32.3 + - + +
440A ARG* 1.3 79.2 - - - +
442A PHE* 1.3 56.0 + - - +
444A GLU* 3.5 7.6 + - - +
445A ALA* 3.0 29.2 + - - +
461A ALA* 4.8 11.1 - - + +
464A GLU* 5.4 2.0 - - - +
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Residues in contact with PHE 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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434A LEU* 3.9 35.7 - - + -
438A LEU* 2.9 44.2 + - + +
439A ASN* 3.8 4.7 - - - +
441A ALA* 1.3 74.2 - - - +
443A MET* 1.3 64.4 + - - +
445A ALA* 3.4 4.7 + - - +
446A ALA* 3.1 25.3 + - - +
458A MET* 3.6 31.6 - - + +
461A ALA* 3.6 39.7 - - + -
462A VAL* 3.8 14.4 - - + -
465A LEU* 4.0 17.3 - - + -
505A VAL* 5.5 2.2 - - + -
527A VAL* 3.6 19.8 - - + +
531A LEU* 4.2 5.6 - - + -
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Residues in contact with MET 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 ASN* 3.2 37.0 + - - +
440A ARG* 3.3 30.9 + - - +
442A PHE* 1.3 76.1 - - - +
444A GLU* 1.3 62.9 + - - +
446A ALA* 3.4 2.9 + - - +
447A GLU* 3.1 33.9 + - - +
505A VAL* 4.2 3.1 - - + -
506A ALA 4.0 10.5 - - - +
520A ASP* 3.9 26.0 - - - +
523A ARG* 3.8 42.6 - - + +
524A GLN* 4.1 8.3 - - + -
527A VAL* 3.7 17.3 - - + -
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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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440A ARG* 2.9 34.3 + - - +
441A ALA* 3.9 6.1 - - - +
443A MET* 1.3 72.9 - - - +
445A ALA* 1.3 65.9 + - - +
447A GLU* 3.2 18.1 + - - +
448A ILE* 3.3 19.2 + - - +
523A ARG* 4.1 15.4 + - - +
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Residues in contact with ALA 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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441A ALA 3.0 19.0 + - - +
442A PHE* 3.6 7.0 - - - +
444A GLU* 1.3 77.5 - - - +
446A ALA* 1.3 59.3 + - - +
447A GLU 3.4 0.3 + - - -
448A ILE* 3.5 9.7 + - - +
454A SER* 2.8 25.4 + - - -
457A ALA* 3.6 36.8 - - + +
458A MET* 3.6 18.4 - - - +
461A ALA* 5.2 1.6 - - + -
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Residues in contact with ALA 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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442A PHE 3.1 17.1 + - - +
443A MET 3.8 4.0 - - - +
444A GLU 3.3 0.2 - - - -
445A ALA* 1.3 76.5 - - - +
447A GLU* 1.3 60.7 + - + +
448A ILE 3.4 0.6 + - - -
454A SER* 4.0 4.7 - - - -
458A MET* 3.9 4.0 - - - -
523A ARG 5.6 0.2 - - - +
526A LYS* 3.4 40.2 - - + +
527A VAL* 3.7 17.9 - - + +
530A ARG* 3.4 29.3 + - + -
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Residues in contact with GLU 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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443A MET* 3.1 21.3 + - - +
444A GLU* 3.2 10.0 + - - +
446A ALA* 1.3 77.5 - - + +
448A ILE* 1.3 64.9 + - - +
449A THR* 3.4 12.6 + - - +
523A ARG* 2.8 61.5 + - - +
526A LYS* 5.3 6.3 - - + -
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Residues in contact with ILE 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 3.3 15.1 + - - +
445A ALA* 3.6 8.3 - - - +
446A ALA 3.4 0.2 - - - -
447A GLU* 1.3 76.5 - - - +
449A THR* 1.3 61.0 + - - +
450A ASP* 3.6 23.6 - - + +
453A ASN* 3.9 18.2 - - + +
454A SER* 3.4 13.2 - - - +
457A ALA* 4.0 27.6 - - + -
530A ARG* 3.0 23.7 + - - -
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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