Contacts of the helix formed by residues 296 - 304 (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 ASN 296 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269K TYR* 3.1 16.1 + - - +
270K LYS* 2.7 10.6 + - - -
293K TRP* 3.0 41.0 - - - +
295K GLY* 1.3 67.9 - - - -
297K ASP* 1.3 54.2 + - - +
298K LYS 3.0 1.1 - - - -
299K ILE* 2.4 32.6 + - - +
300K SER* 2.7 16.8 + - - -
331K VAL* 5.0 3.0 - - + +
338K TYR* 3.6 42.9 - - + -
375K PHE* 3.5 24.3 - - - -
403K TRP* 5.4 3.4 - - - -
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Residues in contact with ASP 297 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270K LYS* 3.0 50.7 + - - +
271K GLN* 5.1 0.3 - - - -
296K ASN* 1.3 71.7 - - - +
298K LYS* 1.3 66.0 + - - +
299K ILE 2.8 7.1 + - - -
300K SER* 3.3 11.9 - - - +
301K GLN* 3.0 29.9 + - + +
304K ARG* 5.5 1.6 - - - +
333K ASN* 5.7 1.8 - - - -
334K GLU* 4.9 2.8 - - - +
338K TYR* 3.1 18.5 + - + -
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Residues in contact with LYS 298 (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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236K TYR* 3.3 56.2 + - + +
237K ARG 4.7 1.8 + - - -
270K LYS 5.3 0.4 - - - +
271K GLN 4.2 11.4 + - - +
294K LEU* 3.7 31.8 - - + +
295K GLY* 3.1 24.2 - - - +
297K ASP* 1.3 83.6 + - - +
299K ILE* 1.3 55.7 + - - -
301K GLN* 4.6 4.2 + - - +
302K LEU* 3.6 24.7 + - - +
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Residues in contact with ILE 299 (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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252K ILE* 3.2 38.1 - - + -
293K TRP* 3.7 13.7 - - + -
294K LEU* 3.3 14.6 - - + +
295K GLY 2.6 27.8 - - - +
296K ASN* 2.4 43.9 + - - +
297K ASP 2.8 0.6 + - - -
298K LYS* 1.3 69.2 - - - +
300K SER* 1.3 55.1 + - - +
301K GLN 3.2 0.7 - - - -
302K LEU* 2.9 9.3 + - + +
303K THR* 2.7 51.2 + - + +
329K PHE* 4.7 11.2 - - + -
331K VAL* 5.0 6.7 - - + -
403K TRP* 5.8 4.0 - - + -
452K MET* 6.6 0.2 - - + -
454K ILE* 5.1 1.1 - - + -
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Residues in contact with SER 300 (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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296K ASN 2.7 13.0 + - - -
297K ASP* 3.0 17.7 + - - +
299K ILE* 1.3 70.5 - - - +
301K GLN* 1.3 74.4 + - - +
303K THR* 2.6 22.7 + - - -
304K ARG* 2.6 32.9 + - - +
331K VAL* 3.1 31.7 - - - +
332K GLN 3.5 20.6 + - - -
333K ASN* 4.2 1.0 + - - -
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Residues in contact with GLN 301 (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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229K PRO* 3.3 41.1 - - - +
230K ASP* 4.8 12.4 - - + +
233K VAL* 5.6 3.6 - - + +
236K TYR* 4.4 6.3 + - - -
297K ASP* 3.0 17.5 + - + +
298K LYS* 4.6 4.4 + - - +
300K SER* 1.3 80.8 + - - +
302K LEU* 1.3 72.1 + - - +
304K ARG* 2.9 37.5 + - - +
305K MET* 3.4 17.2 + - - +
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Residues in contact with LEU 302 (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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209K LYS 6.0 0.2 - - - +
210K GLU* 4.6 21.1 - - + -
227K ILE* 5.0 2.5 - - + -
229K PRO* 5.3 3.1 - - + -
236K TYR* 3.6 17.9 - - + +
250K THR* 4.2 17.9 - - + -
252K ILE* 5.3 2.2 - - + -
294K LEU* 4.2 13.5 - - + -
298K LYS 3.6 19.9 + - - +
299K ILE* 2.9 16.2 + - + +
301K GLN* 1.3 87.2 - - - +
303K THR* 1.3 58.6 + - - +
304K ARG 3.5 0.2 + - - -
305K MET* 3.5 26.9 + - + +
308K THR* 4.1 4.5 + - - -
454K ILE* 3.2 36.1 - - + +
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Residues in contact with THR 303 (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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299K ILE* 2.7 25.4 + - + +
300K SER* 2.6 19.0 + - - -
302K LEU* 1.3 73.6 - - - +
304K ARG* 1.3 57.1 + - - +
305K MET 3.3 2.0 - - - -
306K GLY 3.1 19.4 - - - +
308K THR* 3.2 19.0 + - + -
329K PHE* 3.5 48.0 - - + +
330K THR* 3.6 13.2 - - - +
331K VAL* 3.0 22.6 + - + +
454K ILE* 4.3 4.9 - - + -
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Residues in contact with ARG 304 (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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297K ASP* 5.3 2.0 - - - +
300K SER* 2.6 34.4 + - - +
301K GLN* 2.9 32.2 + - - +
303K THR* 1.3 79.3 - - - +
305K MET* 1.3 55.2 + - - +
306K GLY 3.2 5.4 - - - +
330K THR* 5.2 5.2 - - - -
331K VAL 3.7 18.6 + - - +
332K GLN* 4.4 19.5 + - - +
333K ASN* 4.3 20.6 - - - +
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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