Contacts of the helix formed by residues 383 - 388 (chain D) in PDB entry 3G1Q
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 383 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D MET* 3.4 34.1 - - - +
79D ILE* 4.7 2.8 - - - +
80D VAL 4.5 4.0 + - - -
81D GLY* 5.9 0.4 - - - -
357D LEU 2.8 18.2 + - - -
358D MET* 3.5 10.6 - - - +
381D ALA 4.2 0.2 - - - -
382D CYS* 1.3 73.3 - - - +
384D PRO* 1.4 61.5 - - - +
385D LEU* 3.4 4.3 + - - +
386D LEU* 3.0 19.5 + - - -
387D SER* 2.8 32.7 + - - -
413D ILE* 4.0 3.1 - - - -
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Residues in contact with PRO 384 (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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354D PRO* 3.7 16.8 - - + -
356D LEU 3.4 18.8 - - - +
357D LEU 3.2 16.6 - - - +
359D LEU* 3.9 16.4 - - + -
382D CYS 3.3 12.1 - - - +
383D SER* 1.4 81.6 - - - +
385D LEU* 1.3 56.2 + - - +
388D HIS* 2.8 46.8 + - + +
413D ILE* 3.7 35.2 - - + +
414D GLY* 4.6 2.7 - - - +
480D HEM 5.4 1.6 - - + -
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Residues in contact with LEU 385 (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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52D PRO* 3.7 31.6 - - + -
53D LEU* 3.7 24.9 - - + +
56D MET* 5.5 2.9 - - - -
352D ARG 5.0 1.6 - - - +
353D ASP* 5.6 1.1 - - - -
354D PRO* 3.6 24.0 - - + +
357D LEU* 3.4 31.8 + - + +
383D SER* 3.1 8.4 + - - +
384D PRO* 1.3 79.3 - - - +
386D LEU* 1.3 61.7 + - - +
389D HIS* 2.9 42.2 - - - +
457D TYR* 3.7 26.7 - - + +
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Residues in contact with LEU 386 (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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53D LEU* 4.4 7.0 - - + -
56D MET* 3.6 50.5 - - + +
57D GLN* 3.9 28.9 - - + +
60D LYS* 4.5 14.7 + - + +
68D PHE* 4.2 13.9 - - + -
79D ILE* 4.2 4.0 - - + -
81D GLY* 3.5 35.4 - - - +
383D SER* 3.0 11.4 + - - +
385D LEU* 1.3 75.0 - - - +
387D SER* 1.3 65.7 + - - +
389D HIS* 3.0 15.4 + - - +
390D ASP* 3.5 8.5 + - - +
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Residues in contact with SER 387 (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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80D VAL 4.1 9.9 + - - -
81D GLY* 4.6 7.5 - - - -
83D PRO* 4.4 9.7 - - - +
86D HIS* 2.7 41.0 + - - -
382D CYS* 4.6 0.5 - - - -
383D SER 2.8 21.1 + - - -
384D PRO 4.4 0.4 - - - -
386D LEU* 1.3 72.7 - - - +
388D HIS* 1.3 57.1 + - - +
390D ASP* 3.1 28.7 + - - +
394D PHE* 3.8 9.4 - - - -
411D ALA 4.1 5.3 - - - +
413D ILE* 4.3 5.6 - - - +
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Residues in contact with HIS 388 (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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350D ILE 3.7 6.5 - - - -
351D ARG* 3.0 69.6 + - + +
354D PRO* 3.9 7.4 - - + -
384D PRO* 2.8 24.5 + - - +
385D LEU* 5.0 0.2 - - - -
387D SER* 1.3 74.4 - - - +
389D HIS* 1.3 64.0 + - + +
390D ASP 3.5 0.7 - - - -
394D PHE* 3.5 16.5 - - - +
411D ALA 3.5 9.1 + - - -
412D PHE* 3.5 12.8 - - - -
413D ILE* 2.8 44.6 - - + +
414D GLY* 3.4 22.0 + - - -
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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