Contacts of the helix formed by residues 330 - 337 (chain D) in PDB entry 4QG0
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 ASP 330 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324B GLY 4.5 9.7 - - - +
325B ILE* 6.0 0.9 - - - +
119C ASN* 4.8 0.5 + - - -
125C HIS* 3.3 23.7 + - - -
328D ASN 3.9 3.0 + - - +
329D PHE* 1.3 82.1 - - - +
331D TYR* 1.3 60.2 + - - +
332D LYS* 3.4 11.8 + - - +
333D ARG* 3.2 30.0 + - + +
334D PHE* 3.3 17.5 + - - +
358D ASN* 6.4 0.2 - - - +
701D DUT 5.4 0.3 + - - +
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Residues in contact with TYR 331 (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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122D ILE* 4.8 6.6 + - - +
123D HIS* 3.1 28.8 + + - -
173D TYR* 5.4 0.4 - + - -
174D LEU* 3.4 26.9 - - + -
313D TRP* 3.6 37.5 - + + -
317D ALA* 4.5 19.7 - - + -
327D ASN* 5.3 2.0 - - - -
329D PHE* 3.5 34.5 - + + -
330D ASP* 1.3 71.6 + - - +
332D LYS* 1.3 96.2 + - + +
334D PHE* 3.2 3.8 + - - +
335D ILE* 2.9 37.2 + - + +
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Residues in contact with LYS 332 (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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123C HIS 5.9 2.4 + - - +
125C HIS* 5.2 11.2 - - + +
332C LYS* 5.5 7.3 - - - +
122D ILE 5.7 3.0 + - - -
123D HIS* 6.6 0.4 - - - +
330D ASP* 3.3 8.4 + - - +
331D TYR* 1.3 109.2 + - + +
333D ARG* 1.3 67.0 + - - +
335D ILE* 3.1 9.9 + - + +
336D LYS* 2.9 33.7 + - - +
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Residues in contact with ARG 333 (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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125C HIS* 3.2 36.6 + - + +
330D ASP* 3.2 29.8 + - - +
331D TYR 3.2 0.2 - - - -
332D LYS* 1.3 79.1 - - - +
334D PHE* 1.3 63.3 + - - +
336D LYS* 3.1 11.4 + - - +
337D PHE* 3.2 39.4 + - + -
354D LYS* 3.9 5.9 - - - +
355D GLU* 2.6 41.1 + - - +
358D ASN* 3.9 6.1 - - - +
701D DUT 3.0 84.1 + - - -
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Residues in contact with PHE 334 (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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178D LEU* 5.5 3.8 - - + -
308D ILE* 4.0 23.1 - - + -
313D TRP* 3.4 32.8 - + + -
329D PHE* 4.3 13.2 - + + -
330D ASP 3.3 9.9 + - - +
331D TYR* 3.2 12.5 + - - +
332D LYS 3.2 0.4 - - - -
333D ARG* 1.3 79.8 - - - +
335D ILE* 1.3 64.1 + - - +
337D PHE* 3.1 7.1 + - - +
338D ALA* 3.1 31.2 + - + -
349D ILE* 5.0 12.1 - - + -
350D CYS 6.0 0.2 - - - -
351D ALA* 4.3 20.4 - - + -
355D GLU* 5.7 7.2 - - + -
359D LEU* 3.4 35.4 - - + -
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Residues in contact with ILE 335 (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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174D LEU* 4.9 4.5 - - + +
177D CYS* 4.4 23.1 - - + +
178D LEU* 4.1 21.2 - - + +
181D ALA* 3.9 30.0 - - + +
182D LEU* 5.9 0.3 - - - +
185D LYS* 4.7 2.9 + - - +
313D TRP* 3.8 24.7 - - + -
331D TYR* 2.9 30.8 + - + +
332D LYS* 3.1 11.6 + - + +
334D PHE* 1.3 76.7 - - - +
336D LYS* 1.3 66.4 + - + +
338D ALA* 3.2 20.4 + - - +
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Residues in contact with LYS 336 (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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117C VAL* 4.7 11.5 - - + +
125C HIS* 3.1 38.5 + - + +
127C GLU* 3.3 46.6 - - + +
185D LYS* 2.9 24.3 + - - +
332D LYS* 2.9 20.3 + - - +
333D ARG* 3.1 10.3 + - - +
335D ILE* 1.3 80.6 - - + +
337D PHE* 1.3 67.0 + - + +
338D ALA 3.3 0.7 - - - -
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Residues in contact with PHE 337 (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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117C VAL* 4.6 22.4 - - + -
125C HIS* 4.7 5.4 - + - -
333D ARG* 3.2 56.6 + - + +
334D PHE* 3.1 8.4 + - - +
336D LYS* 1.3 85.3 - - + +
338D ALA* 1.3 59.9 + - - +
351D ALA* 3.9 3.1 - - + -
352D ARG* 3.3 57.3 + - + +
354D LYS* 4.7 3.1 - - + -
355D GLU* 4.4 12.3 - - + -
521D TYR* 3.0 22.8 + - - -
701D DUT 3.6 25.8 - - - -
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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