Contacts of the helix formed by residues 435 - 446 (chain A) in PDB entry 4X2Q
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 ASP 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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280A ASP* 3.9 7.2 + - - +
433A THR* 3.4 7.8 - - + +
434A ASN* 1.3 78.8 - - - +
436A ILE* 1.3 64.0 + - - +
437A ASN* 3.0 14.0 + - - +
438A LYS* 2.8 53.9 + - + +
439A ALA* 3.0 24.1 + - - +
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Residues in contact with ILE 436 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434A ASN 4.0 3.7 + - - +
435A ASP* 1.3 71.9 + - - +
437A ASN* 1.3 66.5 + - - +
439A ALA* 3.2 5.1 + - - +
440A LEU* 2.9 52.3 + - + +
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Residues in contact with ASN 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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413A MET* 5.7 0.4 - - - -
435A ASP* 3.0 7.2 + - - +
436A ILE* 1.3 85.8 - - - +
438A LYS* 1.3 58.4 + - + +
440A LEU* 4.2 6.8 - - - +
441A THR* 3.1 30.5 + - - +
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Residues in contact with LYS 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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278A PHE* 3.7 38.2 - - + -
280A ASP* 4.3 8.4 + - - +
311A GLU* 4.5 11.1 + - - -
413A MET* 3.7 28.3 - - + -
433A THR* 3.9 12.1 - - + -
435A ASP* 2.8 40.8 + - + +
437A ASN* 1.3 72.8 - - + +
439A ALA* 1.3 64.5 + - - +
441A THR* 3.4 6.1 - - - +
442A VAL* 3.2 30.6 + - - +
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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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431A VAL* 5.0 4.2 - - + +
433A THR* 4.6 16.5 - - - +
435A ASP 3.0 17.9 + - - +
436A ILE* 3.8 4.0 - - - +
438A LYS* 1.3 75.2 - - - +
440A LEU* 1.3 58.7 + - + +
442A VAL* 3.3 4.3 + - - +
443A SER* 2.9 34.6 + - - -
453A ILE* 4.3 28.2 - - + +
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Residues in contact with LEU 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 ILE* 2.9 39.3 + - + +
437A ASN* 4.6 6.7 - - - +
439A ALA* 1.3 78.6 - - + +
441A THR* 1.3 51.2 + - - +
443A SER* 3.6 8.2 + - - +
444A SER* 2.6 34.3 + - - -
153B PHE* 5.4 8.1 - - + -
155B ARG* 4.9 9.6 + - - +
151C PHE* 4.6 25.8 - - + -
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Residues in contact with THR 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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413A MET* 3.5 27.6 - - - -
417A ILE* 4.4 6.6 - - + +
437A ASN 3.1 23.1 + - - +
438A LYS 3.4 7.4 - - - +
440A LEU* 1.3 77.4 - - - +
442A VAL* 1.3 66.5 + - + +
444A SER* 3.4 7.1 + - - -
445A ALA* 3.3 22.9 - - - +
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Residues in contact with VAL 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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276A ILE* 3.9 9.6 - - + -
278A PHE* 4.1 24.5 - - + -
413A MET* 4.4 4.5 - - + +
416A VAL* 5.6 1.3 - - + -
417A ILE* 4.3 20.4 - - + -
431A VAL* 3.8 31.0 - - + -
438A LYS 3.2 19.0 + - - +
439A ALA 3.9 1.8 - - - +
441A THR* 1.3 82.0 - - + +
443A SER* 1.3 65.7 + - - +
445A ALA 3.5 0.9 + - - -
446A MET* 3.2 45.6 + - + +
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Residues in contact with SER 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 ALA 2.9 20.2 + - - -
440A LEU* 3.6 13.9 + - - +
442A VAL* 1.3 79.4 - - - +
444A SER* 1.3 54.2 + - - +
446A MET* 3.9 2.8 + - - -
451A VAL* 3.8 34.1 - - - +
453A ILE* 3.8 14.3 - - - +
153B PHE* 5.8 1.7 - - - -
489B LYS* 2.8 32.9 + - - -
491B VAL* 4.6 13.7 - - - +
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Residues in contact with SER 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 LEU 2.6 23.0 + - - -
441A THR* 3.4 10.2 + - - -
443A SER* 1.3 83.2 + - - +
445A ALA* 1.3 60.1 + - - +
446A MET 3.2 0.4 - - - -
72B LEU* 5.8 0.5 - - - +
155B ARG* 3.2 36.8 + - - +
157B GLU* 4.2 6.2 - - - +
489B LYS* 2.7 20.8 + - - +
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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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417A ILE* 3.8 22.9 - - + -
421A ASN* 3.1 21.6 + - - -
441A THR* 3.3 18.1 + - - +
442A VAL 3.5 1.6 + - - +
444A SER* 1.3 78.7 + - - +
446A MET* 1.3 61.3 + - - +
447A GLN* 3.4 4.0 + - - +
72B LEU* 4.6 27.6 - - + +
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Residues in contact with MET 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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274A PRO* 5.5 0.7 - - + -
276A ILE* 3.8 14.6 - - + -
417A ILE* 4.0 24.9 - - + +
420A ALA* 3.9 22.4 - - + -
421A ASN* 3.3 17.0 - - - +
427A LEU* 4.6 4.9 - - + -
429A ALA* 3.7 29.8 - - + -
442A VAL* 3.2 42.7 + - + +
443A SER* 4.0 9.0 - - - +
444A SER 3.2 1.2 - - - -
445A ALA* 1.3 74.9 - - - +
447A GLN* 1.3 60.8 - - - +
448A ALA* 2.8 13.7 + - + -
451A VAL* 4.6 2.9 - - + -
489B LYS* 3.0 21.7 + - - +
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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