Contacts of the helix formed by residues 265 - 271 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264K ARG* 1.3 76.9 - - - +
266K TRP* 1.3 70.1 + - - +
267K ASP 3.5 1.1 - - - +
268K PRO* 3.5 19.8 - - + +
269K TYR* 3.3 16.8 + - - -
377K THR* 3.1 7.9 - - - -
378K TYR* 3.9 32.5 + - + +
379K ASP* 3.1 29.7 - - - +
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Residues in contact with TRP 266 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265K LYS* 1.3 71.1 - - - +
267K ASP* 1.3 74.2 + - + +
269K TYR* 2.8 16.8 + - - +
270K LYS* 2.9 13.9 + - + +
334K GLU* 3.2 35.3 + - + -
337K LYS* 4.1 19.3 - - + -
338K TYR* 3.6 36.0 - + - -
375K PHE* 3.5 35.7 - + + -
377K THR* 2.8 35.6 + - + +
379K ASP* 2.8 18.3 + - - +
380K ARG* 3.4 53.0 - - + +
382K ASN* 4.1 2.9 - - - -
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Residues in contact with ASP 267 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265K LYS* 4.5 0.8 - - - +
266K TRP* 1.3 82.2 - - + +
268K PRO* 1.3 75.5 - - + +
270K LYS* 2.8 45.9 + - - +
271K GLN* 2.9 32.0 + - - +
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Residues in contact with PRO 268 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264K ARG* 3.9 27.6 - - + +
265K LYS* 3.5 32.5 - - + +
267K ASP* 1.3 94.1 - - + +
269K TYR* 1.3 50.5 + - - +
271K GLN* 3.2 5.8 + - + -
272K GLY* 2.7 41.7 + - - +
273K PHE* 3.9 5.2 - - + -
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Residues in contact with TYR 269 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262K PHE* 2.5 33.0 + - - -
264K ARG 3.4 28.0 - - - -
265K LYS 3.3 6.4 + - - +
266K TRP 2.8 12.9 + - - +
268K PRO* 1.3 76.1 - - - +
270K LYS* 1.3 60.8 + - - +
273K PHE* 3.5 26.2 - + - -
293K TRP* 3.1 46.7 + + - -
295K GLY* 3.4 0.7 - - - -
296K ASN* 3.1 12.4 + - - +
375K PHE* 3.8 21.8 - + + -
377K THR* 4.1 8.7 - - + -
401K GLY 3.3 25.1 + - - -
413K ASN* 3.0 38.3 + - - +
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Residues in contact with LYS 270 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266K TRP* 2.9 14.6 + - - +
267K ASP* 2.8 37.8 + - - +
269K TYR* 1.3 76.4 - - - +
271K GLN* 1.3 67.1 + - - +
295K GLY* 2.8 7.6 - - - -
296K ASN* 2.7 31.2 + - - +
297K ASP* 3.0 36.2 + - - +
298K LYS* 5.0 0.3 - - - +
334K GLU* 3.1 26.7 + - - +
338K TYR* 3.0 26.0 - - + +
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Residues in contact with GLN 271 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267K ASP* 2.9 38.2 + - - +
268K PRO* 3.8 4.3 - - + +
270K LYS* 1.3 94.9 + - - +
272K GLY* 1.3 68.3 + - - +
295K GLY* 3.1 12.1 + - - -
297K ASP* 5.1 0.4 - - - -
298K LYS* 4.2 16.3 + - - +
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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