Contacts of the helix formed by residues 426 - 435 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262H ARG 5.6 2.5 - - - -
263H ILE* 4.1 8.7 - - - +
425H LEU* 1.3 75.2 - - - +
427H ILE* 1.3 68.1 + - - +
428H TRP* 3.2 30.9 + - - +
429H HIS* 2.9 24.9 + - - +
430H TYR* 3.4 18.7 - - - -
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Residues in contact with ILE 427 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426H SER* 1.3 74.9 - - - +
428H TRP* 1.3 76.3 + - + +
430H TYR* 2.8 21.8 + - + -
431H THR* 2.6 31.5 + - - +
446H LYS* 5.2 2.9 - - + +
449H GLN* 4.4 22.0 - - - +
450H ILE* 4.1 29.2 - - + -
453H PHE* 3.6 43.5 - - + -
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Residues in contact with TRP 428 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H ASP* 6.1 0.2 - - - -
244H LYS* 3.6 25.4 - - + -
261H ILE* 3.5 40.3 - - + +
263H ILE* 3.5 22.4 - - + -
382H LEU* 4.4 11.2 - - + -
426H SER* 3.2 24.5 - - - +
427H ILE* 1.3 85.5 - - + +
429H HIS* 1.3 53.8 + - - +
431H THR* 3.2 7.9 + - - -
432H ALA* 2.7 38.5 + - - +
453H PHE* 3.8 26.0 - + - -
457H LYS* 4.1 19.1 - - + -
561H LEU* 3.2 38.8 - - + +
564H ILE* 3.7 11.0 - - + -
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Residues in contact with HIS 429 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263H ILE* 3.2 32.9 - - + +
264H ASN* 4.1 8.1 + - + -
266H SER* 3.7 13.9 + - - -
382H LEU* 3.1 33.5 - - + +
385H VAL* 3.7 20.4 - - + -
386H VAL* 4.0 15.7 - - + +
424H ASN 4.7 0.7 - - - -
425H LEU* 3.5 24.9 - - + +
426H SER* 2.9 39.0 + - - +
427H ILE 3.0 0.6 + - - -
428H TRP* 1.3 81.1 - - - +
430H TYR* 1.3 57.9 + - + +
432H ALA* 3.4 7.0 - - - +
433H PHE* 3.0 27.4 + - - +
566H ALA 5.4 0.2 + - - -
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Residues in contact with TYR 430 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386H VAL* 3.9 22.0 - - + -
422H GLU* 4.3 23.1 + - - +
425H LEU* 4.0 28.1 - - + +
426H SER 3.4 26.7 - - - -
427H ILE* 2.8 13.1 + - + +
429H HIS* 1.3 71.3 - - + +
431H THR* 1.3 59.6 + - - +
433H PHE* 3.4 2.0 + - - +
434H PHE* 2.9 23.9 + - - +
442H MET* 3.1 47.3 - - + +
446H LYS* 3.5 42.6 + - + -
450H ILE* 3.5 5.3 - - + +
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Residues in contact with THR 431 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427H ILE* 2.6 35.0 + - - +
428H TRP* 3.3 5.5 + - - -
430H TYR* 1.3 73.4 - - - +
432H ALA* 1.3 66.8 + - - +
434H PHE* 2.8 19.6 + - - +
435H PHE* 2.9 23.1 + - + -
450H ILE* 3.8 28.0 - - + +
453H PHE* 3.7 24.3 - - + -
454H CYS* 3.9 4.0 - - - -
561H LEU* 3.7 15.7 - - + -
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Residues in contact with ALA 432 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382H LEU* 3.9 26.2 - - + -
383H CYS* 3.5 23.0 - - + +
428H TRP 2.7 21.1 + - - +
429H HIS 3.4 6.1 - - - +
431H THR* 1.3 72.1 - - - +
433H PHE* 1.3 56.6 + - - +
435H PHE* 2.8 31.6 + - - +
561H LEU* 3.6 19.0 - - + +
562H LEU* 4.5 2.9 - - + +
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Residues in contact with PHE 433 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383H CYS* 3.8 22.8 - - - +
386H VAL* 3.5 36.8 - - + -
387H PRO* 3.6 22.0 - - + -
390H LEU* 5.1 4.9 - - + -
429H HIS 3.0 14.4 + - - +
430H TYR 3.5 9.0 - - - +
431H THR 3.2 0.2 - - - -
432H ALA* 1.3 73.3 - - - +
434H PHE* 1.3 65.0 + - - +
436H TYR* 2.8 32.1 + + + +
438H PRO 4.7 10.1 - - - -
439H ALA* 5.9 0.3 - - - -
441H HIS* 3.3 44.6 - + + -
442H MET* 3.8 17.9 - - + -
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Residues in contact with PHE 434 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430H TYR 2.9 14.5 + - - +
431H THR 2.8 14.3 + - - +
433H PHE* 1.3 75.4 - - - +
435H PHE* 1.3 68.8 + + - +
436H TYR 2.9 7.4 + - - +
439H ALA* 4.0 34.9 - - + +
442H MET* 4.4 12.3 - - + -
447H VAL* 4.6 12.3 - - + -
450H ILE* 3.3 29.6 - - + -
524H PHE* 3.2 43.3 - + - -
527H TYR* 2.9 33.5 + + - -
528H ARG* 3.9 19.1 - - + -
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Residues in contact with PHE 435 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431H THR* 2.9 27.3 + - + -
432H ALA* 2.8 17.7 + - - +
434H PHE* 1.3 76.7 - + - +
436H TYR* 1.3 57.3 + - - -
437H PRO* 3.1 5.5 - - - +
454H CYS* 3.9 14.4 - - - -
527H TYR* 3.5 12.6 - + - -
540H VAL* 4.2 1.0 - - - +
544H TRP* 3.0 53.1 + + - +
554H LEU* 4.1 14.6 - - + -
557H LEU* 3.8 26.2 - - + -
558H ALA* 3.9 21.3 - - + -
561H LEU* 3.6 30.7 - - + -
562H LEU* 4.2 16.9 - - + +
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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