Contacts of the helix formed by residues 407 - 413 (chain D) in PDB entry 1H26
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 GLN 407 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216D ASP* 3.5 2.6 + - - -
401D ALA 3.4 12.9 + - - -
402D PRO* 3.2 24.7 + - - +
404D HIS 3.1 22.5 + - - +
405D ALA 4.1 3.3 + - - +
406D GLN* 1.3 75.1 + - - +
408D SER* 1.3 66.3 + - - +
409D ILE 3.1 3.4 + - - -
410D ARG* 3.0 44.9 + - - +
411D GLU* 3.1 33.3 + - + +
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Residues in contact with SER 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D ASP* 1.9 62.1 + - - -
219D VAL* 4.3 9.6 - - - +
220D GLU* 3.5 23.4 + - - +
223D GLU* 5.9 0.2 - - - +
407D GLN* 1.3 72.7 - - - +
409D ILE* 1.3 56.5 + - - +
411D GLU* 3.6 8.6 + - - +
412D LYS* 2.9 25.8 + - - +
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Residues in contact with ILE 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D ASP* 3.8 2.0 + - - +
219D VAL* 3.8 24.9 - - + -
335D PHE* 3.8 26.0 - - + +
338D GLU* 3.1 52.0 - - + +
339D LEU* 4.0 14.4 - - + -
341D LEU* 5.5 0.4 - - + -
342D ILE* 3.7 28.0 - - + -
407D GLN 3.1 1.0 - - - -
408D SER* 1.3 75.5 - - - +
410D ARG* 1.3 65.5 + - - +
412D LYS* 3.0 7.7 + - - +
413D TYR* 2.9 29.4 + - + +
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Residues in contact with ARG 410 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335D PHE* 4.1 23.7 - - + -
339D LEU* 5.3 3.6 - - + -
401D ALA* 3.9 11.3 - - + +
402D PRO* 3.5 49.2 - - - +
406D GLN 5.9 0.7 - - - +
407D GLN* 3.0 40.0 + - - +
409D ILE* 1.3 73.1 - - - +
411D GLU* 1.3 76.9 + - - +
413D TYR 2.9 9.0 + - - -
414D LYS* 3.3 21.2 + - - +
422D SER* 3.2 33.1 + - - -
423D LEU* 5.1 11.5 - - - +
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Residues in contact with GLU 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407D GLN* 3.1 29.0 + - + +
408D SER* 3.7 9.4 - - - +
410D ARG* 1.3 85.3 + - - +
412D LYS* 1.3 65.6 + - - +
414D LYS* 2.8 56.0 + - - +
415D ASN* 4.1 1.4 + - - +
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Residues in contact with LYS 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D VAL* 4.0 13.2 + - + +
222D GLY* 6.2 0.6 - - - -
223D GLU* 3.3 40.5 + - + +
229D ASN* 2.5 30.5 + - - +
232D LEU* 4.4 5.9 - - - +
338D GLU* 2.5 33.6 + - - +
408D SER 2.9 16.1 + - - +
409D ILE 3.0 9.2 + - - +
411D GLU* 1.3 77.9 - - - +
413D TYR* 1.3 75.2 + - + +
414D LYS 3.1 4.0 + - - -
415D ASN* 3.4 14.0 + - - +
418D TYR* 3.5 29.6 - - + -
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Residues in contact with TYR 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D ASN* 3.7 12.3 + - - -
331D SER 3.7 22.2 - - - -
334D MET* 3.5 18.4 - - + +
335D PHE* 3.8 24.9 - + + -
338D GLU* 2.8 28.4 + - - -
409D ILE* 2.9 23.2 + - + +
410D ARG 2.9 0.4 + - - -
411D GLU 2.9 0.4 + - - -
412D LYS* 1.3 103.8 - - + +
414D LYS* 1.3 53.3 - - - +
415D ASN 3.5 1.8 - - - +
418D TYR* 3.3 39.9 - + + -
420D GLY* 3.1 10.5 - - - -
421D VAL* 3.4 6.0 + - + -
422D SER* 2.0 49.0 + - - +
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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