Contacts of the strand formed by residues 335 - 345 (chain H) in PDB entry 3QS7
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 HIS 335 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249H LEU* 4.0 21.1 + - + -
250H ASN* 4.7 6.0 - - - -
274H ALA* 4.0 7.0 - - + -
275H VAL 3.1 32.6 + - - -
276H HIS* 3.6 20.3 - + - +
281H PHE* 3.9 13.9 - + - -
331H SER* 5.0 0.7 - - - -
332H SER* 2.9 42.3 + - - +
334H LYS* 1.4 94.5 + - + +
336H PRO* 1.4 75.9 - - + +
337H SER 3.7 1.4 + - - -
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Residues in contact with PRO 336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249H LEU* 3.4 33.2 - - - +
331H SER* 5.0 0.9 - - - -
335H HIS* 1.4 89.8 - - + +
337H SER* 1.3 64.3 + - - +
338H GLN* 3.1 5.7 + - - +
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Residues in contact with SER 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329H THR* 4.1 11.7 - - - -
330H CYS 3.2 9.9 - - - -
331H SER* 3.5 25.3 - - - +
335H HIS 3.7 3.2 + - - -
336H PRO* 1.3 69.0 - - - +
338H GLN* 1.3 59.6 + - - +
339H SER* 4.1 4.0 + - - -
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Residues in contact with GLN 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247H ILE* 3.9 16.9 - - + +
248H ASP 5.5 1.8 - - - +
249H LEU* 3.5 19.5 - - + +
253H PRO* 6.0 5.8 - - + -
330H CYS* 2.9 33.6 + - - +
336H PRO 3.1 5.2 + - - +
337H SER* 1.3 70.5 - - - +
339H SER* 1.3 64.7 + - - +
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Residues in contact with SER 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247H ILE* 4.6 4.5 - - - +
257H LEU* 4.4 7.1 - - - -
258H PRO* 3.5 21.1 - - - +
327H TYR* 5.8 4.0 - - - -
328H TYR 3.3 15.0 - - - -
329H THR* 2.7 23.9 + - - -
337H SER 4.3 3.5 + - - -
338H GLN* 1.3 75.8 - - - +
340H ALA* 1.4 63.3 + - - +
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Residues in contact with ALA 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245H PHE* 3.8 33.0 - - + -
247H ILE* 4.1 9.8 - - + +
257H LEU* 4.7 0.9 - - - +
258H PRO* 3.2 19.1 - - + +
260H LEU* 5.6 3.6 - - + -
270H ILE* 5.5 1.6 - - + -
327H TYR* 4.7 1.1 - - - -
328H TYR* 2.9 38.4 + - + +
339H SER* 1.4 74.5 - - - +
341H LEU* 1.4 61.8 + - - +
342H VAL* 4.0 2.2 + - + +
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Residues in contact with LEU 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257H LEU* 4.6 8.1 + - + +
258H PRO 2.9 8.8 + - - +
259H GLN* 3.5 7.5 - - + +
260H LEU* 2.8 26.2 + - - +
326H GLY 3.7 5.8 - - - +
327H TYR* 4.0 17.0 - - + +
340H ALA* 1.4 71.6 - - - +
342H VAL* 1.3 62.7 + - - +
343H THR* 3.9 1.1 + - - -
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Residues in contact with VAL 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260H LEU* 3.4 21.5 - - + +
262H LEU* 3.8 24.7 - - + -
268H LEU* 4.0 21.5 - - + -
270H ILE* 5.4 2.0 - - + -
320H VAL* 5.9 0.4 - - + -
324H ASP 4.4 1.3 - - - +
325H THR* 3.4 11.3 - - - -
326H GLY* 2.8 39.9 + - - +
328H TYR* 3.6 27.8 - - + -
340H ALA* 4.7 3.6 - - + +
341H LEU* 1.3 74.1 - - - +
343H THR* 1.3 60.0 + - - +
344H ILE* 4.3 14.6 - - + -
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Residues in contact with THR 343 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259H GLN* 5.9 2.7 - - - -
260H LEU 2.8 10.5 + - - +
261H PHE* 3.3 37.2 - - - +
262H LEU* 3.1 26.0 + - - +
325H THR* 4.8 0.7 - - - -
341H LEU 3.9 1.9 + - - -
342H VAL* 1.3 71.4 - - - +
344H ILE* 1.3 63.4 + - - +
345H VAL* 3.7 0.8 + - - -
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Residues in contact with ILE 344 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262H LEU* 3.4 11.2 - - + +
264H VAL* 3.8 23.3 - - + -
320H VAL* 3.6 31.2 - - + -
321H ALA 3.2 21.1 - - - +
322H ARG* 3.6 28.3 - - + -
324H ASP 4.6 1.1 - - - -
325H THR* 3.6 27.9 - - - +
342H VAL* 4.3 14.4 - - + -
343H THR* 1.3 72.9 - - - +
345H VAL* 1.3 60.9 + - - +
346H GLU 4.2 0.7 + - - -
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Residues in contact with VAL 345 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261H PHE* 4.0 26.9 - - + -
262H LEU 2.9 29.7 + - - -
263H LYS* 3.3 13.3 - - + +
264H VAL* 3.2 28.5 + - - +
343H THR* 4.3 2.2 - - - +
344H ILE* 1.3 78.7 - - - +
346H GLU* 1.3 63.8 + - - +
347H LYS 3.8 19.1 - - - +
348H GLY* 5.2 0.4 - - - +
349H PHE* 4.3 15.7 - - + -
376H TYR* 3.9 18.4 - - + -
504H NAG 6.1 1.3 - - + -
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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