Contacts of the strand formed by residues 347 - 355 (chain D) in PDB entry 5HP1
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 347 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269D GLN 5.9 1.6 - - - -
270D ILE 4.9 5.9 + - - -
314D VAL* 4.4 7.0 - - + +
315D HIS* 3.2 21.6 + - - +
316D GLY* 3.7 10.9 + - - +
317D VAL* 3.5 31.0 - - + +
318D TYR* 5.8 5.6 - - + -
342D TYR* 3.7 10.8 - - - +
343D GLN 4.3 3.3 + - - -
344D GLU* 3.0 26.1 + - + +
345D PRO 3.9 7.9 - - - +
346D PHE* 1.3 85.8 - - - +
348D ASN* 1.3 63.3 + - - +
349D LEU* 3.4 8.3 + - - +
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Residues in contact with ASN 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D ILE* 4.3 13.3 - - - +
314D VAL* 5.6 8.7 - - + +
317D VAL* 4.5 14.0 - - - +
340D GLN* 3.8 12.2 - - - +
341D ILE 3.6 7.4 - - - +
342D TYR* 3.6 24.3 - - - +
346D PHE* 3.6 8.9 + - - +
347D LYS* 1.3 74.8 + - - +
349D LEU* 1.3 64.7 + - - +
350D LYS 4.2 0.9 - - - +
351D THR* 4.0 19.8 - - + +
426D TRP* 3.5 33.7 - - - -
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Residues in contact with LEU 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D VAL* 4.7 7.6 - - + -
318D TYR 4.0 32.8 - - - +
319D TYR* 3.7 24.7 - - + +
325D LEU* 3.7 29.6 - - + -
341D ILE 2.7 12.5 + - - +
342D TYR* 4.6 2.9 - - - -
343D GLN* 3.8 15.7 - - + +
347D LYS 3.4 8.1 + - - +
348D ASN* 1.3 75.2 - - - +
350D LYS* 1.3 59.1 + - - +
383D TRP* 3.7 23.4 - - + +
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Residues in contact with LYS 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D TRP* 4.2 16.9 + - - +
240D THR 3.1 27.1 + - - -
241D VAL* 4.6 12.6 - - + +
339D TYR* 3.6 12.0 + - + -
340D GLN* 3.4 3.3 - - - +
341D ILE* 2.8 44.3 + - + +
348D ASN* 3.3 1.5 - - - +
349D LEU* 1.3 80.5 - - - +
351D THR* 1.3 74.6 + - - +
352D GLY* 5.3 0.4 - - - -
378D GLU* 3.1 30.5 - - - +
382D ILE* 3.9 26.2 - - + -
383D TRP* 4.0 15.7 - - + -
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Residues in contact with THR 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D VAL* 3.7 14.5 - - - +
242D GLN* 2.9 39.8 + - - -
243D PRO* 4.9 0.3 - - - +
339D TYR* 3.5 9.9 - - - -
340D GLN* 4.1 4.9 - - + -
348D ASN* 4.0 21.8 - - + +
350D LYS* 1.3 95.0 + - - +
352D GLY* 1.3 60.4 + - - +
426D TRP* 4.0 24.7 - - + -
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Residues in contact with GLY 352 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240D THR 5.2 2.7 - - - -
242D GLN* 4.1 13.6 - - - +
338D THR* 3.5 6.1 - - - +
339D TYR* 2.9 52.2 + - - +
340D GLN* 5.1 0.2 + - - -
350D LYS* 5.3 0.7 - - - -
351D THR* 1.3 77.0 - - - +
353D LYS* 1.3 61.9 + - - +
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Residues in contact with LYS 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D GLN* 4.0 32.4 - - + +
332D GLN* 5.6 0.2 - - + -
336D GLN* 3.0 32.8 + - + +
337D TRP 3.2 17.5 - - - +
338D THR* 3.8 18.8 - - + -
339D TYR* 3.6 6.9 - - - -
352D GLY* 1.3 75.0 - - - +
354D TYR* 1.3 65.8 + - - +
355D ALA* 4.5 4.5 + - - +
356D ARG* 5.9 0.8 - - - +
426D TRP 5.2 1.6 - - - +
427D TYR 5.3 7.0 - - - +
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Residues in contact with TYR 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335D GLY 3.7 0.3 - - - +
336D GLN* 3.4 6.1 - - - +
337D TRP* 2.7 54.5 + + + +
339D TYR* 4.6 10.0 - - + -
353D LYS* 1.3 74.0 - - - +
355D ALA* 1.3 72.3 + - - +
357D MET* 2.9 36.6 - - + +
367D GLN 4.2 3.4 - - - -
370D GLU* 3.6 12.9 + - + +
371D ALA* 3.8 40.4 - - + -
374D LYS* 3.2 51.0 + - + +
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Residues in contact with ALA 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335D GLY 3.2 7.0 - - - -
336D GLN* 3.1 37.7 - - - +
353D LYS* 4.7 3.8 - - - +
354D TYR* 1.3 83.8 - - - +
356D ARG* 1.3 86.2 + - - +
357D MET* 3.3 4.1 + - - -
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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