Contacts of the helix formed by residues 426 - 435 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262B ARG 5.6 4.0 + - - -
263B ILE* 4.8 6.2 - - - +
424B ASN 5.4 0.4 - - - -
425B LEU* 1.3 76.5 - - - +
427B ILE* 1.3 71.9 + - - +
428B TRP* 3.0 29.6 + - - +
429B HIS* 2.7 29.6 + - - +
430B TYR* 3.7 9.7 + - - -
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Residues in contact with ILE 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B SER* 1.3 75.4 - - - +
428B TRP* 1.3 76.1 + - + +
429B HIS 2.8 1.7 + - - -
430B TYR* 2.8 33.3 + - + -
431B THR* 2.9 36.5 + - - +
449B GLN* 4.9 13.9 - - + +
450B ILE* 4.3 22.7 - - + +
453B PHE* 3.6 33.9 - - + -
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Residues in contact with TRP 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B LYS* 3.5 21.8 - - + -
261B ILE* 4.0 32.4 - - + +
263B ILE* 3.7 31.6 - - + -
382B LEU* 3.7 6.6 - - + +
426B SER* 3.0 23.8 - - - +
427B ILE* 1.3 85.8 - - + +
429B HIS* 1.3 57.6 + - - +
431B THR* 3.6 6.3 + - - -
432B ALA* 3.0 31.4 + - - +
453B PHE* 3.9 22.3 - + - -
457B LYS* 3.5 35.7 - - + -
560B SER* 5.5 0.2 - - - -
561B LEU* 3.3 39.0 - - + +
564B ILE* 3.6 9.6 - - + -
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Residues in contact with HIS 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B ILE* 3.4 28.8 - - + +
264B ASN 4.4 8.9 + - - -
266B SER* 3.7 14.5 + - - -
382B LEU* 3.3 39.2 - - + +
385B VAL* 3.7 24.5 - - + -
386B VAL* 4.2 11.3 - - + +
424B ASN 4.7 0.7 - - - -
425B LEU* 3.5 29.3 - - + +
426B SER* 2.7 38.9 + - - +
428B TRP* 1.3 72.5 - - - +
430B TYR* 1.3 64.4 + - + +
432B ALA* 3.3 4.5 + - - +
433B PHE* 3.1 20.8 + - - +
566B ALA 5.1 0.2 + - - -
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Residues in contact with TYR 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B VAL* 3.9 18.8 - - + -
422B GLU* 3.9 21.3 + - - +
425B LEU* 4.1 18.5 - - + +
426B SER* 3.8 21.1 - - - -
427B ILE* 2.8 25.5 + - + +
429B HIS* 1.3 68.3 - - - +
431B THR* 1.3 66.8 + - - +
433B PHE* 2.9 16.5 + - - +
434B PHE* 3.0 10.7 + - - +
442B MET* 3.2 36.4 - - + +
446B LYS* 3.2 42.7 + - + -
449B GLN* 5.9 2.5 - - - -
450B ILE* 4.1 7.0 - - + -
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Residues in contact with THR 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B ILE* 2.9 35.1 + - - +
428B TRP 3.8 0.2 - - - -
430B TYR* 1.3 74.8 - - - +
432B ALA* 1.3 63.6 + - - +
434B PHE* 2.9 21.4 + - - +
435B PHE* 2.9 40.0 + - + -
450B ILE* 3.8 12.0 - - + +
453B PHE* 3.6 11.7 - - + -
454B CYS* 3.6 21.5 - - - -
561B LEU* 3.7 14.8 - - + -
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Residues in contact with ALA 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B LEU* 3.9 24.2 - - + -
383B CYS* 2.9 30.2 - - + +
428B TRP 3.0 19.7 + - - +
429B HIS 3.6 5.2 - - - +
430B TYR 3.3 0.2 - - - -
431B THR* 1.3 77.3 - - - +
433B PHE* 1.3 61.0 + - - +
435B PHE* 3.6 11.8 + - - +
436B TYR 4.1 0.3 + - - -
561B LEU* 3.9 17.2 - - + +
562B LEU* 4.0 10.2 - - + +
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Residues in contact with PHE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383B CYS* 3.8 14.3 - - - +
386B VAL* 3.6 24.2 - - + -
387B PRO* 3.5 32.8 - - + -
390B LEU* 5.2 5.4 - - + -
429B HIS 3.1 11.3 + - - +
430B TYR 2.9 10.8 + - - +
432B ALA* 1.3 73.4 - - - +
434B PHE* 1.3 53.9 + - - +
436B TYR* 2.7 47.5 + + + +
438B PRO 5.1 5.8 - - - +
439B ALA* 5.8 0.2 - - - -
441B HIS* 3.2 42.6 - + + -
442B MET* 3.4 23.8 - - + -
505G PHE* 3.7 24.7 - + - -
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Residues in contact with PHE 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B TYR 3.0 1.4 + - - +
431B THR 3.0 9.9 - - - +
433B PHE* 1.3 81.5 - - - +
435B PHE* 1.3 72.4 + + - -
436B TYR 3.0 7.9 + - - +
439B ALA* 4.0 29.7 - - + +
442B MET* 4.3 7.3 - - + -
443B GLN* 5.6 0.2 - - - -
447B VAL* 4.2 14.8 - - + -
450B ILE* 3.4 39.3 - - + -
524B PHE* 3.3 42.4 - + - -
527B TYR* 3.2 47.3 + + + -
528B ARG* 4.6 11.4 - - + -
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Residues in contact with PHE 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B THR* 2.9 35.7 + - + +
432B ALA* 4.0 9.9 - - - +
433B PHE 3.0 1.4 + - - -
434B PHE* 1.3 94.7 - + - +
436B TYR* 1.3 59.7 + - - +
437B PRO* 3.2 2.1 - - - +
454B CYS* 3.4 25.6 - - - -
527B TYR* 3.6 8.3 - + - -
540B VAL* 3.3 6.8 - - - +
544B TRP* 2.9 42.0 + + + +
554B LEU* 4.4 22.0 - - + -
557B LEU* 3.7 17.9 - - + -
558B ALA* 3.9 25.6 - - + -
561B LEU* 4.1 15.3 - - + -
562B LEU* 4.3 8.6 - - + +
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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