Contacts of the strand formed by residues 335 - 342 (chain D) in PDB entry 3RIK
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 MET 335 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D LYS* 5.0 1.8 - - + -
228D TRP* 3.7 34.3 - - + -
279D LEU* 4.4 4.9 - - + -
306D HIS* 3.6 36.6 + - + +
307D GLY* 3.3 8.7 - - - -
308D ILE* 2.9 26.3 + - - +
328D HIS* 6.6 0.2 - - - -
332D PRO 5.6 0.4 - - - -
333D ASN 3.9 3.4 + - - -
334D THR* 1.3 73.3 - - - +
336D LEU* 1.3 58.6 + - - +
337D PHE* 3.8 21.1 - - + -
376D VAL* 3.8 36.6 - - + -
504D SO4 4.6 4.3 - - - +
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Residues in contact with LEU 336 (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 LEU* 4.4 3.4 - - + -
308D ILE* 3.4 25.4 - - + +
310D VAL* 4.6 2.5 - - + -
324D LEU* 3.7 44.9 - - + +
327D THR* 3.9 22.0 - - + -
328D HIS* 4.5 12.8 - - + +
334D THR 3.4 6.0 + - - +
335D MET* 1.3 72.4 - - - +
337D PHE* 1.3 60.9 + - - +
373D TYR 4.0 16.8 - - - +
374D HIS* 4.4 14.2 + - + +
375D VAL* 4.1 16.6 - - + -
376D VAL* 2.8 33.5 + - - +
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Residues in contact with PHE 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D LYS* 4.4 3.6 - - + -
118D ILE* 3.7 25.4 - - + -
175D LEU* 3.8 22.7 - - + -
228D TRP* 4.2 23.6 - + - -
279D LEU* 4.4 13.2 - - + -
308D ILE 3.0 8.9 + - - +
309D ALA* 3.1 8.0 - - + -
310D VAL* 2.7 31.7 + - - +
335D MET* 3.8 16.2 - - + -
336D LEU* 1.3 76.1 - - - +
338D ALA* 1.3 61.6 + - - +
339D SER* 3.4 9.1 + - - -
375D VAL* 4.0 3.8 - - - +
376D VAL* 4.1 9.2 - - + -
377D GLY* 3.7 29.8 - - - -
379D THR* 3.1 29.2 - - - -
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Residues in contact with ALA 338 (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 VAL* 3.3 14.1 - - + +
337D PHE* 1.3 71.8 - - - +
339D SER* 1.3 58.4 + - - +
340D GLU 3.5 4.0 - - - +
370D ASN* 4.0 13.7 - - - +
375D VAL* 3.5 3.4 - - + +
377D GLY 3.0 17.7 + - - +
378D TRP* 3.4 32.7 - - + +
379D THR* 2.9 27.0 + - - +
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Residues in contact with SER 339 (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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120D ARG* 3.3 27.8 + - - +
175D LEU* 4.5 7.0 - - - -
231D THR* 5.3 0.2 - - - -
282D ASP* 2.4 29.8 + - - -
309D ALA* 3.4 19.0 - - - +
310D VAL 2.8 7.4 + - - -
311D HIS* 3.1 14.3 + - - -
337D PHE* 3.4 15.9 + - - -
338D ALA* 1.3 72.9 - - - +
340D GLU* 1.3 63.4 + - - +
379D THR* 3.4 15.4 - - - +
380D ASP 4.7 1.2 - - - +
381D TRP* 5.8 0.2 - - - -
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Residues in contact with GLU 340 (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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120D ARG* 2.8 24.7 + - - +
179D TRP* 3.8 5.5 - - - -
234D ASN* 3.6 2.6 - - - +
310D VAL 3.7 1.5 + - - +
311D HIS* 3.3 21.8 - - + +
312D TRP 3.1 23.0 + - - -
338D ALA* 3.5 3.7 - - - +
339D SER* 1.3 83.4 + - - +
341D ALA* 1.3 62.4 + - - +
379D THR 3.3 7.6 + - - -
380D ASP 4.9 0.7 - - - -
381D TRP* 3.9 30.8 - - + -
501D 3RI 2.8 64.4 + - - +
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Residues in contact with ALA 341 (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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312D TRP* 3.5 9.2 - - + +
314D LEU* 4.0 13.5 - - + -
338D ALA* 6.4 0.4 - - + -
340D GLU* 1.3 74.9 - - - +
342D CYS* 1.3 66.7 + - - +
363D TYR* 4.5 0.7 - - - -
378D TRP* 3.1 46.0 - - + -
379D THR 3.6 5.0 + - - +
380D ASP* 3.3 19.1 - - - +
381D TRP* 3.4 8.8 + - - +
501D 3RI 4.3 0.9 - - - -
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Residues in contact with CYS 342 (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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312D TRP 3.6 5.7 + - - +
313D TYR* 4.2 12.4 - - - -
314D LEU* 3.1 26.1 + - - +
315D ASP 4.4 0.5 + - - -
341D ALA* 1.3 78.0 - - - +
343D VAL* 1.3 67.0 + - - +
363D TYR* 4.0 8.5 - - - +
381D TRP* 4.2 17.5 - - + -
398D VAL* 4.2 17.3 - - + -
399D ASP 5.0 2.9 - - - +
501D 3RI 3.7 46.2 + - - -
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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