Contacts of the strand formed by residues 321 - 331 (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 321 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313K GLU* 6.1 2.2 - - + -
314K MET 3.0 13.0 - - - +
315K GLU* 3.4 31.0 - - + +
319K GLY 3.1 22.9 - - - +
320K ASP* 1.3 78.8 - - - +
322K VAL* 1.3 75.3 + - - +
323K LYS* 5.0 9.8 - - - +
348K THR* 4.6 1.2 + - - -
440K TRP* 4.6 0.6 - - - -
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Residues in contact with VAL 322 (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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312K ILE 3.4 5.4 - - - +
313K GLU* 3.5 3.6 - - - +
314K MET* 3.1 60.8 + - + +
321K LYS* 1.3 86.8 - - - +
323K LYS* 1.3 67.1 + - - +
348K THR* 3.6 28.5 - - - +
349K ALA* 3.6 14.1 - - + -
440K TRP* 3.8 37.0 - - + +
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Residues in contact with LYS 323 (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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245K GLU* 4.9 13.6 + - - +
311K LEU* 4.0 19.3 - - + -
312K ILE 3.5 3.8 - - - -
313K GLU* 4.9 8.3 - - + +
321K LYS* 5.0 6.9 - - - +
322K VAL* 1.3 81.9 - - - +
324K ALA* 1.3 60.5 + - - +
325K HIS* 4.0 3.6 - - + +
345K TYR* 4.3 0.5 + - - -
346K ARG 5.4 0.7 - - - +
347K GLY* 3.6 10.1 - - - -
348K THR* 3.4 30.9 + - + +
349K ALA* 3.1 22.4 + - - +
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Residues in contact with ALA 324 (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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310K LEU 3.2 7.8 - - - +
311K LEU* 4.0 1.3 - - - +
312K ILE* 2.8 57.6 + - + +
314K MET* 5.4 0.7 - - + -
323K LYS* 1.3 73.4 - - - +
325K HIS* 1.3 57.9 + - - +
326K TYR* 3.6 12.1 - - + -
345K TYR* 4.3 6.7 - - + -
349K ALA* 4.2 4.5 - - + -
437K TRP* 3.9 25.1 - - + -
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Residues in contact with HIS 325 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245K GLU* 5.8 6.7 - - + +
249K TRP* 4.4 15.3 - + - -
309K GLU* 3.2 32.0 + - + -
310K LEU 3.5 7.3 + - - -
311K LEU* 3.8 22.5 - - + +
323K LYS* 5.3 2.7 - - + -
324K ALA* 1.3 70.1 - - - +
326K TYR* 1.3 72.8 + - - +
327K GLY 4.1 1.9 + - - -
344K LYS 4.3 1.1 - - - -
345K TYR* 3.0 12.2 - - - -
346K ARG* 2.8 94.4 + - + +
347K GLY* 5.1 0.2 - - - -
455K ARG* 5.4 1.6 + - - -
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Residues in contact with TYR 326 (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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309K GLU* 3.2 1.8 - - - -
310K LEU* 3.0 43.7 + - + +
312K ILE* 5.2 0.4 - - + -
324K ALA* 3.6 24.0 - - + -
325K HIS* 1.3 78.3 + - - +
327K GLY* 1.3 60.1 + - - +
328K GLY 2.9 21.5 + - - +
329K PHE* 4.3 0.8 - - + +
342K VAL* 3.2 32.8 - - + -
343K ASN 3.4 13.5 - - - +
345K TYR* 3.4 25.7 - + + -
350K GLY 4.6 0.7 + - - -
351K ASN* 2.6 32.8 + - - -
352K ALA 3.9 0.7 + - - -
353K LEU* 3.1 35.9 + - + +
354K MET* 3.5 13.0 - - + -
437K TRP* 4.8 0.6 - + - -
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Residues in contact with GLY 327 (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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307K PRO* 5.4 1.0 - - - +
308K THR 3.5 11.4 + - - +
309K GLU* 3.7 15.0 - - - -
325K HIS* 4.1 2.7 + - - -
326K TYR* 1.3 70.4 - - - +
328K GLY* 1.3 55.7 + - - +
343K ASN 3.1 1.1 + - - -
344K LYS* 3.1 30.9 + - - -
457K PHE* 3.5 34.0 - - - -
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Residues in contact with GLY 328 (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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307K PRO* 6.3 0.2 - - - -
308K THR 3.4 4.3 - - - -
326K TYR* 3.4 2.9 - - - +
327K GLY* 1.3 76.9 - - - +
329K PHE* 1.3 63.9 + - - +
330K THR* 5.1 0.7 - - - -
341K SER* 5.7 0.7 - - - -
342K VAL* 3.2 4.8 - - - +
343K ASN* 3.0 44.9 + - - +
344K LYS* 4.5 4.5 - - - -
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Residues in contact with PHE 329 (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* 4.9 4.0 - - + -
299K ILE* 4.7 7.9 - - + -
303K THR* 3.5 17.3 - - + -
308K THR* 3.0 32.5 + - + +
310K LEU* 3.2 48.9 - - + -
326K TYR* 4.3 1.6 - - + +
328K GLY* 1.3 75.9 - - - +
330K THR* 1.3 76.3 + - - +
331K VAL* 3.4 32.5 - - + -
340K ILE* 4.2 14.4 - - + -
341K SER 3.3 13.9 - - - -
342K VAL* 4.3 9.2 - - + -
403K TRP* 5.0 3.6 - + - -
452K MET* 4.9 8.7 - - + -
454K ILE* 3.8 21.5 - - + -
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Residues in contact with THR 330 (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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303K THR* 3.6 21.5 - - - +
304K ARG* 5.2 4.0 - - - +
306K GLY 5.5 2.7 - - - +
308K THR* 5.8 1.3 - - - +
328K GLY* 5.7 0.2 - - - -
329K PHE* 1.3 87.7 - - - +
331K VAL* 1.3 65.5 + - - +
332K GLN* 4.1 18.5 + - - +
339K GLN 3.6 1.0 - - - +
340K ILE* 3.5 2.6 - - - -
341K SER* 3.0 41.4 + - - +
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Residues in contact with VAL 331 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296K ASN* 5.0 3.8 - - + +
299K ILE* 5.0 6.7 - - + -
300K SER* 3.1 36.7 - - - +
303K THR* 3.0 10.3 + - + +
304K ARG* 3.7 9.5 + - - +
329K PHE* 3.4 30.7 - - + -
330K THR* 1.3 75.5 + - - +
332K GLN* 1.3 72.2 + - - +
338K TYR* 3.3 33.7 - - + +
339K GLN 3.2 4.5 - - - +
340K ILE* 4.5 1.8 - - + -
403K TRP* 3.5 24.2 - - + -
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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