Contacts of the helix formed by residues 426 - 435 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262G ARG 5.3 4.2 + - - -
263G ILE* 3.5 10.1 - - - +
424G ASN 5.3 0.4 - - - -
425G LEU* 1.3 76.5 - - - +
427G ILE* 1.3 70.3 + - - +
428G TRP* 3.2 25.9 - - - +
429G HIS* 3.2 23.9 + - - +
430G TYR* 3.2 20.2 + - - -
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Residues in contact with ILE 427 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426G SER* 1.3 72.5 - - - +
428G TRP* 1.3 76.4 + - + +
430G TYR* 2.8 21.6 + - + +
431G THR* 2.8 37.4 + - - +
449G GLN* 4.2 31.6 - - + +
450G ILE* 4.2 14.8 - - + +
453G PHE* 3.6 42.0 - - + -
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Residues in contact with TRP 428 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244G LYS* 3.5 27.4 - - + -
261G ILE* 3.5 42.7 - - + +
262G ARG 6.0 0.4 - - - -
263G ILE* 4.5 13.7 - - + -
382G LEU* 4.7 14.8 - - + +
426G SER* 3.2 25.6 - - - +
427G ILE* 1.3 88.2 - - + +
429G HIS* 1.3 58.0 + - - +
431G THR* 3.8 6.6 - - - -
432G ALA* 2.9 33.3 + - - +
453G PHE* 3.9 21.1 - + - -
457G LYS* 3.8 28.9 - - + -
557G LEU* 5.8 0.7 - - + -
560G SER* 5.8 0.4 - - - -
561G LEU* 3.3 35.3 - - + +
564G ILE* 3.9 11.2 - - + -
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Residues in contact with HIS 429 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263G ILE* 2.8 40.0 - - + +
264G ASN 4.2 9.6 + - - -
266G SER* 3.4 15.6 + - - -
382G LEU* 3.5 23.4 - - + +
385G VAL* 3.3 42.8 - - + +
386G VAL* 3.0 22.7 - - + +
424G ASN 5.1 0.4 - - - -
425G LEU* 3.9 23.1 - - + +
426G SER* 3.2 26.6 + - - +
427G ILE 3.1 0.2 + - - -
428G TRP* 1.3 80.5 - - - +
430G TYR* 1.3 61.1 + - + +
432G ALA* 4.1 2.1 - - - +
433G PHE 3.4 11.3 + - - -
566G ALA 5.0 1.8 + - - -
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Residues in contact with TYR 430 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386G VAL* 4.3 18.6 - - + -
422G GLU* 4.1 27.3 + - + +
425G LEU* 4.2 22.7 - - + +
426G SER 3.2 23.3 - - - -
427G ILE* 2.8 17.2 + - + +
429G HIS* 1.3 75.6 - - + +
431G THR* 1.3 64.4 + - - +
432G ALA 3.3 0.2 - - - -
433G PHE 3.1 5.0 + - - -
434G PHE* 3.2 3.1 + - - +
442G MET* 2.9 49.8 - - + +
446G LYS* 3.9 35.3 + - + -
449G GLN* 5.8 1.6 - - - -
450G ILE* 3.8 4.6 - - + +
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Residues in contact with THR 431 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427G ILE* 2.8 25.8 + - - +
428G TRP 3.8 1.1 - - - -
430G TYR* 1.3 70.7 - - - +
432G ALA* 1.3 58.1 + - - +
434G PHE* 2.9 23.4 - - - +
435G PHE* 3.0 25.1 + - + -
450G ILE* 4.1 15.9 - - + +
453G PHE* 2.9 39.1 - - + -
454G CYS* 4.2 10.5 - - - -
557G LEU* 5.0 0.4 - - + -
561G LEU* 3.3 23.3 - - + -
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Residues in contact with ALA 432 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382G LEU* 4.2 7.6 - - + -
383G CYS* 3.0 40.0 - - + +
428G TRP 2.9 19.2 + - - +
429G HIS 4.3 1.8 - - - +
431G THR* 1.3 73.6 - - - +
433G PHE* 1.3 62.8 + - - +
434G PHE 3.0 1.8 - - - -
435G PHE* 3.5 12.9 + - - +
436G TYR 3.8 3.6 + - - -
561G LEU* 3.5 28.7 - - + +
562G LEU* 4.5 3.1 - - + +
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Residues in contact with PHE 433 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B PHE* 3.4 38.6 - + - -
383G CYS* 3.9 10.3 - - - +
384G PHE* 6.1 0.7 - + - -
386G VAL* 3.8 29.2 - - + -
387G PRO* 3.8 22.7 - - + -
390G LEU* 4.8 12.8 - - + -
429G HIS 3.4 5.5 + - - -
430G TYR 3.1 3.9 + - - +
432G ALA* 1.3 77.5 - - - +
434G PHE* 1.3 64.6 + - - +
436G TYR* 3.4 21.2 + + + +
438G PRO 5.1 5.3 - - - +
439G ALA* 5.4 0.5 - - - -
441G HIS* 3.5 39.7 - + + -
442G MET* 3.3 34.1 - - + -
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Residues in contact with PHE 434 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430G TYR 3.2 2.2 + - - +
431G THR 2.9 11.9 - - - +
433G PHE* 1.3 82.1 - - - +
435G PHE* 1.3 71.3 + + - -
436G TYR 2.6 20.3 + - - +
439G ALA* 3.6 39.8 - - + +
442G MET* 3.9 9.4 - - + -
447G VAL* 4.9 10.8 - - + -
450G ILE* 3.5 38.1 - - + -
524G PHE* 3.4 39.5 - + - -
527G TYR* 3.4 34.1 + + - -
528G ARG* 4.1 17.3 - - + -
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Residues in contact with PHE 435 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431G THR* 3.0 22.3 + - + +
432G ALA* 3.5 9.1 + - - +
433G PHE 3.4 0.8 - - - -
434G PHE* 1.3 99.9 - + - +
436G TYR* 1.3 56.0 + - - +
437G PRO* 3.0 13.8 - - - +
454G CYS* 3.9 16.4 - - - -
527G TYR* 4.0 6.1 - + - -
540G VAL* 3.5 6.4 - - - +
544G TRP* 3.0 21.7 + + - +
554G LEU* 4.5 24.5 - - + -
557G LEU* 3.0 38.1 - - + -
558G ALA* 3.3 35.2 - - + +
561G LEU* 4.2 12.1 - - + -
562G LEU* 4.2 8.0 - - + +
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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