Contacts of the helix formed by residues 265 - 272 (chain H) in PDB entry 3GHG
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 LYS 265 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264H ARG* 1.3 80.2 - - - +
266H TRP* 1.3 66.9 + - - +
267H ASP* 3.4 1.6 - - + +
268H PRO* 3.5 15.3 - - + +
269H TYR* 3.1 17.7 + - - -
377H THR* 3.4 10.6 - - - +
378H TYR* 3.3 43.7 + - + +
379H ASP* 3.3 34.9 - - - +
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Residues in contact with TRP 266 (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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265H LYS* 1.3 76.7 - - - +
267H ASP* 1.3 57.6 + - + +
269H TYR* 3.0 4.3 + - - +
270H LYS* 2.7 43.7 + - + +
296H ASN* 5.7 0.7 - - - -
334H GLU* 3.3 30.9 + - + -
337H LYS* 4.5 11.2 - - + -
338H TYR* 3.3 37.7 - + - -
375H PHE* 3.4 49.4 - + + -
376H SER 4.4 0.4 - - - -
377H THR* 3.0 27.6 + - + +
379H ASP* 3.2 9.3 + - - +
380H ARG* 2.9 52.0 - - + +
382H ASN* 4.1 11.4 - - - -
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Residues in contact with ASP 267 (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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265H LYS* 4.4 1.4 - - + +
266H TRP* 1.3 84.4 - - + +
268H PRO* 1.3 68.5 - - + +
270H LYS* 3.6 16.0 - - - +
271H GLN* 3.0 43.3 + - - +
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Residues in contact with PRO 268 (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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264H ARG* 4.0 28.7 - - + +
265H LYS* 3.5 26.7 - - + +
267H ASP* 1.3 94.7 - - + +
269H TYR* 1.3 58.2 + - - +
270H LYS 3.1 1.3 - - - -
271H GLN* 4.3 4.3 - - + +
272H GLY* 2.9 32.6 + - - +
273H PHE* 3.5 8.1 - - + -
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Residues in contact with TYR 269 (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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262H PHE 2.8 16.6 + - - -
264H ARG 3.1 40.2 - - - -
265H LYS 3.1 14.2 + - - +
266H TRP* 3.0 4.8 + - - +
268H PRO* 1.3 77.2 - - - +
270H LYS* 1.3 55.7 + - - +
272H GLY 3.9 0.7 + - - -
273H PHE* 3.8 21.4 - + - -
293H TRP* 3.2 45.9 + + - -
296H ASN* 3.0 30.7 + - - +
375H PHE* 3.6 12.1 - + + -
377H THR* 3.4 14.4 - - + -
401H GLY 2.8 42.5 + - - -
413H ASN* 3.2 18.5 - - - +
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Residues in contact with LYS 270 (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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266H TRP* 2.7 25.9 + - + +
267H ASP* 3.6 15.5 - - - +
269H TYR* 1.3 76.2 - - - +
271H GLN* 1.3 73.0 + - - +
272H GLY 3.2 1.6 - - - -
295H GLY* 3.2 3.3 - - - -
296H ASN* 3.1 24.3 + - - +
297H ASP* 3.1 47.4 + - - +
334H GLU* 2.5 37.3 + - - +
338H TYR* 3.2 16.4 - - + +
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Residues in contact with GLN 271 (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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267H ASP* 3.0 36.1 + - - +
268H PRO* 4.4 3.6 - - + +
270H LYS* 1.3 95.0 - - - +
272H GLY* 1.3 67.1 + - - +
295H GLY* 3.6 6.9 + - - -
297H ASP* 4.8 2.9 - - - +
298H LYS* 4.2 15.6 + - - +
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Residues in contact with GLY 272 (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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268H PRO* 2.9 13.6 + - - +
269H TYR 3.9 2.0 + - - -
270H LYS 3.2 3.0 - - - -
271H GLN* 1.3 88.2 - - - +
273H PHE* 1.3 63.1 + - - +
293H TRP* 3.1 14.4 - - - -
294H LEU* 3.5 1.6 - - - -
295H GLY* 3.2 15.3 - - - -
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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