Contacts of the strand formed by residues 324 - 330 (chain D) in PDB entry 6S6A
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 THR 324 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257D GLU* 6.1 0.9 - - - +
319D LYS* 3.4 6.4 - - - +
320D LEU* 3.0 40.4 + - + +
322D ASN* 3.3 17.0 + - - -
323D THR* 1.3 76.9 - - - +
325D VAL* 1.3 62.9 + - - +
326D LEU* 4.3 5.6 - - + -
340D ILE* 3.7 26.5 - - + -
341D LEU 3.4 16.2 - - - +
342D ARG* 3.2 22.5 + - - +
343D GLU* 4.4 0.9 - - - +
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Residues in contact with VAL 325 (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 ILE* 3.8 18.8 - - + -
318D ILE 3.3 3.1 - - - +
319D LYS* 3.6 30.5 - - + +
324D THR* 1.3 73.9 - - - +
326D LEU* 1.3 75.3 + - - +
327D TYR* 4.1 5.8 - - + -
339D CYS 3.6 1.4 - - - +
340D ILE* 3.4 3.6 - - - +
341D LEU* 2.6 45.8 + - + +
343D GLU* 4.0 21.1 - - - +
346D PHE* 4.0 32.1 - - + -
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Residues in contact with LEU 326 (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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238B PHE* 4.1 17.0 - - + -
284D LEU* 3.6 39.3 - - + +
285D CYS* 6.0 4.3 - - - -
288D MET* 3.8 20.2 - - + -
317D ILE* 3.7 0.9 - - - -
318D ILE* 2.9 40.8 + - + +
320D LEU* 3.9 26.5 - - + -
324D THR* 4.4 7.9 - - + -
325D VAL* 1.3 74.3 - - - +
327D TYR* 1.3 61.3 + - - +
338D VAL* 5.2 3.4 - - + -
339D CYS 3.2 6.7 - - - +
340D ILE* 3.4 32.1 - - + -
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Residues in contact with TYR 327 (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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250D PHE* 6.4 0.2 - + - -
256D ILE* 5.9 1.3 - - + -
288D MET* 3.9 3.3 - - - +
315D MET* 4.9 4.4 - - + +
316D ALA 3.5 9.6 - - - -
317D ILE* 3.8 20.4 - - + -
325D VAL* 4.1 9.6 - - + -
326D LEU* 1.3 76.7 - - - +
328D LEU* 1.3 80.8 + - - +
329D LYS* 3.7 17.4 - - + +
337D LEU 3.6 1.2 - - - +
338D VAL* 3.2 4.2 - - - +
339D CYS* 2.6 50.3 + - + +
341D LEU* 4.4 14.4 - - + -
346D PHE* 3.8 24.5 - + - -
349D LYS* 2.8 31.5 + - - -
352D ILE* 3.9 23.7 - - + +
353D ASP* 3.6 14.0 + - - -
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Residues in contact with LEU 328 (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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288D MET* 3.8 15.9 - - + +
289D ILE* 3.9 29.8 - - + -
292D VAL* 4.1 32.1 - - + -
310D TYR* 5.3 3.1 - - + -
314D SER* 4.2 14.4 - - - +
315D MET* 3.4 3.9 - - - +
316D ALA* 2.9 38.9 + - + +
327D TYR* 1.3 74.8 - - - +
329D LYS* 1.3 81.1 + - - +
330D GLU 4.6 0.2 - - - +
336D ALA* 4.5 13.0 - - + -
337D LEU 3.2 8.5 - - - +
338D VAL* 4.0 12.3 - - + +
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Residues in contact with LYS 329 (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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314D SER 3.8 6.1 - - - -
315D MET* 4.1 17.9 - - + +
327D TYR* 3.7 22.3 + - + +
328D LEU* 1.3 86.4 - - - +
330D GLU* 1.3 64.4 + - - +
331D VAL* 4.0 0.2 - - - +
336D ALA* 3.6 0.7 - - - -
337D LEU* 2.9 37.5 + - + +
349D LYS* 5.1 1.6 - - - +
353D ASP* 2.6 33.9 + - - +
356D PHE* 3.5 43.0 - - + -
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Residues in contact with GLU 330 (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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310D TYR* 2.8 40.8 - - + +
311D ASP 3.6 10.8 - - - +
312D LYS* 3.6 40.1 + - - +
314D SER 3.0 20.2 + - - +
328D LEU* 4.6 0.2 - - - +
329D LYS* 1.3 74.0 - - - +
331D VAL* 1.3 72.2 + - - +
332D THR* 3.2 21.3 - - - +
333D LYS* 3.6 4.3 + - - -
356D PHE* 3.4 16.8 - - - -
360D ARG* 3.8 15.5 + - - -
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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