Contacts of the strand formed by residues 249 - 255 (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 TRP 249 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211K CYS* 3.6 1.6 - - - +
240K CYS* 3.1 8.0 - - - -
241K ASP* 2.8 42.1 + - + +
244K THR* 2.9 37.4 + - - -
245K GLU* 3.1 17.1 + - + +
247K GLY* 3.5 10.7 + - - -
248K GLY* 1.3 78.4 - - - +
250K THR* 1.3 59.2 + - - +
251K VAL 3.9 0.2 - - - -
309K GLU* 3.9 18.6 - - + -
311K LEU* 3.9 28.5 - - + +
325K HIS* 4.4 7.6 - + - -
453K LYS* 3.5 31.6 - - + -
454K ILE* 3.1 47.8 - - - -
455K ARG* 3.4 40.8 - - + -
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Residues in contact with THR 250 (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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210K GLU* 4.1 4.9 + - - +
211K CYS* 3.0 40.7 + - - +
227K ILE* 4.6 4.7 - - + -
238K VAL* 4.1 21.3 - - + -
248K GLY 3.7 2.9 + - - -
249K TRP* 1.3 70.6 - - - +
251K VAL* 1.3 66.6 + - - +
252K ILE* 3.3 5.4 + - + +
294K LEU* 6.0 0.2 - - + -
302K LEU* 4.2 24.4 - - + +
453K LYS* 3.1 3.3 - - - -
454K ILE* 2.8 42.2 + - + +
455K ARG* 5.6 0.7 - - - -
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Residues in contact with VAL 251 (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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238K VAL* 4.1 11.8 - - - +
239K TYR* 3.1 32.2 + - + +
241K ASP* 4.4 10.3 - - + +
250K THR* 1.3 72.7 - - - +
252K ILE* 1.3 60.4 + - - +
253K GLN 3.5 22.7 - - - +
254K ASN* 4.1 10.1 - - + -
289K PRO* 6.2 2.9 - - + -
292K TYR* 2.6 45.1 + - + +
294K LEU* 4.9 0.7 - - - +
451K SER* 5.3 2.5 - - - -
452K MET 3.4 5.4 - - - +
453K LYS* 3.7 24.2 - - + +
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Residues in contact with ILE 252 (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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250K THR* 3.7 5.8 - - + +
251K VAL* 1.3 73.5 - - - +
253K GLN* 1.3 57.2 + - + +
292K TYR* 3.6 5.7 - - - -
293K TRP* 3.8 5.3 - - + -
294K LEU* 3.1 39.4 + - + -
299K ILE* 3.2 51.1 - - + -
302K LEU* 5.3 2.2 - - + -
310K LEU* 4.2 1.8 - - + -
329K PHE* 4.9 1.3 - - + -
452K MET* 2.7 65.2 + - + -
453K LYS* 3.0 9.4 - - - +
454K ILE* 3.4 32.3 - - + -
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Residues in contact with GLN 253 (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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251K VAL* 3.5 5.7 - - - +
252K ILE* 1.3 79.8 - - - +
254K ASN* 1.3 70.9 + - - +
255K ARG* 3.7 10.4 - - - +
262K PHE* 4.6 5.8 - - + -
292K TYR 3.5 7.2 - - - +
293K TRP* 3.5 35.0 - - + -
412K PRO* 3.4 31.4 - - - +
413K ASN* 4.4 4.5 - - - +
450K MET* 3.4 6.5 + - - +
451K SER* 3.3 14.2 - - - +
452K MET* 2.8 56.7 + - - +
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Residues in contact with ASN 254 (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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251K VAL* 4.1 12.3 - - + -
253K GLN* 1.3 78.9 - - - +
255K ARG* 1.3 74.1 + - - +
256K GLN* 3.2 27.7 + - - +
262K PHE* 4.0 0.3 - - - -
289K PRO* 3.9 11.4 - - + +
290K GLY 2.7 26.7 + - - +
291K GLU* 3.2 5.4 - - - +
292K TYR* 3.1 35.9 + - + +
449K LYS* 5.8 0.5 - - - +
450K MET 3.1 16.1 + - - +
451K SER* 3.5 15.2 - - - -
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Residues in contact with ARG 255 (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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253K GLN* 3.7 19.7 - - - +
254K ASN* 1.3 86.7 - - - +
256K GLN* 1.3 66.1 + - - +
260K VAL 4.0 7.9 + - - -
262K PHE* 3.0 54.0 - - - +
291K GLU* 3.1 16.7 + - - +
412K PRO 2.4 32.8 + - - +
413K ASN 3.6 2.4 - - - -
414K GLY 2.8 28.7 + - - -
415K ARG* 4.9 3.4 - - - +
416K TYR* 4.6 20.6 - - + +
435K VAL* 3.8 12.7 - - + +
448K ARG 4.3 1.1 - - - -
449K LYS* 3.5 2.6 - - - +
450K MET* 2.7 45.6 + - + +
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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