Contacts of the helix formed by residues 426 - 435 (chain A) in PDB entry 4D1Q
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 426 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A ARG 5.7 3.4 - - - -
263A ILE* 3.9 6.8 - - - +
424A ASN 5.3 0.2 - - - -
425A LEU* 1.3 76.1 - - - +
427A ILE* 1.3 68.5 + - - +
428A TRP* 3.5 25.9 - - - +
429A HIS* 2.9 38.5 + - - +
430A TYR* 3.4 12.0 - - - -
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Residues in contact with ILE 427 (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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426A SER* 1.3 74.4 - - - +
428A TRP* 1.3 75.2 + - + +
430A TYR* 2.9 21.4 + - + -
431A THR* 2.7 33.7 + - - +
446A LYS* 5.3 1.1 - - - -
449A GLN* 4.7 20.2 - - + +
450A ILE* 4.3 22.4 - - + -
453A PHE* 3.7 43.3 - - + -
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Residues in contact with TRP 428 (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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244A LYS* 3.4 24.5 - - + -
261A ILE* 3.6 40.3 - - + +
262A ARG 6.1 0.7 - - - -
263A ILE* 3.6 28.5 - - + -
382A LEU* 3.7 9.0 - - + +
426A SER* 3.5 21.8 - - - +
427A ILE* 1.3 83.6 - - + +
429A HIS* 1.3 54.4 + - - +
431A THR* 3.3 6.4 + - - -
432A ALA* 2.8 37.8 + - - +
453A PHE* 3.6 28.9 - + - -
457A LYS* 3.8 23.8 - - + -
560A SER* 6.0 0.2 - - - -
561A LEU* 3.1 37.1 - - + +
564A ILE* 3.8 7.2 - - + -
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Residues in contact with HIS 429 (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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263A ILE* 3.1 34.4 - - + +
264A ASN 4.3 7.0 + - - -
266A SER* 3.8 13.9 + - - -
382A LEU* 4.0 27.8 - - + +
385A VAL* 3.4 31.2 - - + -
386A VAL* 4.4 5.5 - - + +
424A ASN 4.7 3.4 - - - -
425A LEU* 3.5 26.1 - - + -
426A SER* 2.9 35.8 + - - +
428A TRP* 1.3 79.5 - - - +
430A TYR* 1.3 66.3 + - + +
432A ALA* 3.5 3.3 + - - +
433A PHE* 3.2 20.6 + - - +
566A ALA 5.2 0.6 + - - -
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Residues in contact with TYR 430 (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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386A VAL* 3.5 25.1 - - + -
422A GLU* 4.2 19.1 + - - +
425A LEU* 3.5 31.6 - - + +
426A SER 3.4 26.0 + - - -
427A ILE* 2.9 14.5 + - + +
429A HIS* 1.3 74.9 - - + +
431A THR* 1.3 59.1 + - - +
433A PHE* 3.0 7.7 + - - +
434A PHE* 2.9 24.6 + - - +
442A MET* 3.3 39.6 - - + +
446A LYS* 3.5 41.1 + - + -
450A ILE* 4.1 4.0 - - + -
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Residues in contact with THR 431 (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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427A ILE* 2.7 27.8 + - - +
428A TRP 3.4 8.3 - - - -
430A TYR* 1.3 71.3 - - - +
432A ALA* 1.3 61.6 + - - +
434A PHE* 2.8 13.3 + - - +
435A PHE* 2.8 45.2 + - + -
450A ILE* 4.2 10.8 - - + +
453A PHE* 3.6 22.4 - - + -
454A CYS* 4.2 8.1 - - - -
557A LEU* 5.5 0.4 - - + -
561A LEU* 3.3 23.3 - - + -
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Residues in contact with ALA 432 (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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382A LEU* 3.6 37.0 - - + -
383A CYS* 3.0 21.8 - - + +
428A TRP 2.8 18.1 + - - +
429A HIS 3.6 4.5 - - - +
430A TYR 3.3 0.2 - - - -
431A THR* 1.3 78.6 - - - +
433A PHE* 1.3 61.7 + - - +
435A PHE* 3.5 16.0 + - - +
561A LEU* 3.9 17.2 - - + +
562A LEU* 4.3 4.1 - - + +
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Residues in contact with PHE 433 (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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383A CYS* 3.6 14.4 - - - +
384A PHE* 6.0 0.9 - + - -
386A VAL* 3.6 31.0 - - + -
387A PRO* 3.5 35.0 - - + -
390A LEU* 4.7 5.6 - - + -
429A HIS 3.2 10.8 + - - +
430A TYR 3.0 10.3 + - - +
432A ALA* 1.3 73.8 - - - +
434A PHE* 1.3 53.7 + - - +
436A TYR* 2.8 54.0 + + + +
438A PRO 4.9 7.8 - - - +
439A ALA* 5.9 0.2 - - - -
441A HIS* 3.1 45.8 - + + -
442A MET* 3.7 20.4 - - + -
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Residues in contact with PHE 434 (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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430A TYR 2.9 11.5 + - - +
431A THR* 2.9 14.8 - - - +
433A PHE* 1.3 76.2 - - - +
435A PHE* 1.3 68.4 + + - -
436A TYR 3.0 9.6 + - - +
439A ALA* 4.1 33.6 - - + +
442A MET* 4.4 12.0 - - + -
447A VAL* 4.0 15.7 - - + -
450A ILE* 3.7 27.8 - - + -
524A PHE* 3.5 27.8 - + - -
527A TYR* 3.3 42.1 + + - -
528A ARG* 3.9 27.6 - - + -
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Residues in contact with PHE 435 (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 THR* 2.8 17.9 + - + +
432A ALA* 3.8 9.9 - - - +
433A PHE 3.0 1.0 + - - -
434A PHE* 1.3 87.0 - + - +
436A TYR* 1.3 57.5 + - - +
437A PRO* 3.1 4.0 - - - +
454A CYS* 3.4 33.2 - - - -
524A PHE* 5.4 0.4 - + - -
527A TYR* 3.7 2.9 - + - -
540A VAL* 3.0 20.5 - - - +
544A TRP* 3.1 30.0 + + + -
554A LEU* 4.5 18.4 - - + -
557A LEU* 3.9 14.8 - - + -
558A ALA* 3.4 31.2 - - + -
561A LEU* 3.5 36.1 - - + -
562A LEU* 3.9 11.5 - - + +
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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