Contacts of the strand formed by residues 375 - 382 (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 VAL 375 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D GLN* 2.9 19.2 + - - -
310D VAL* 5.2 1.6 - - + -
324D LEU* 3.8 21.8 - - + -
336D LEU* 3.5 22.2 - - + +
337D PHE* 4.0 0.2 - - - -
338D ALA* 3.5 17.0 - - + +
370D ASN* 3.1 47.6 + - + +
371D LEU* 3.7 10.5 - - + +
373D TYR 3.9 3.8 - - - +
374D HIS* 1.3 76.3 - - - +
376D VAL* 1.3 61.5 + - - +
377D GLY 3.2 25.6 - - - +
378D TRP* 5.1 0.4 - - + -
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Residues in contact with VAL 376 (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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76D GLN* 3.9 9.9 - - + -
77D LYS 3.2 25.4 - - - +
78D VAL* 3.3 10.6 - - - +
79D LYS* 2.5 41.7 + - + +
80D GLY 3.5 1.4 + - - -
81D PHE* 6.3 0.2 - - - -
335D MET* 3.8 43.3 - - + -
336D LEU 2.8 21.4 + - - +
337D PHE* 4.1 3.4 - - + -
371D LEU* 5.5 1.8 - - - -
374D HIS 3.6 14.1 - - - +
375D VAL* 1.3 73.5 - - - +
377D GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 377 (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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78D VAL* 5.4 0.4 - - - -
80D GLY 3.2 14.1 - - - -
81D PHE* 5.1 3.4 - - - -
337D PHE* 3.7 21.4 - - - -
338D ALA* 3.0 23.1 + - - +
371D LEU* 5.7 1.1 - - - +
375D VAL* 3.2 11.8 + - - +
376D VAL* 1.3 83.4 - - - +
378D TRP* 1.3 61.2 + - - +
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Residues in contact with TRP 378 (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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80D GLY 3.0 7.5 + - - +
81D PHE* 3.3 28.5 - - + -
82D GLY 3.3 20.3 + - - +
118D ILE* 5.0 0.2 - - - +
312D TRP* 6.2 0.4 - - + -
314D LEU* 4.3 2.9 - - + -
337D PHE* 4.4 0.4 - - - -
338D ALA* 3.4 25.7 - - + +
341D ALA* 3.1 35.4 - - + -
363D TYR* 3.7 40.4 - + - -
366D SER* 3.4 32.7 + - - -
367D ILE* 3.4 27.4 - - + +
370D ASN* 3.8 25.2 - - + +
377D GLY* 1.3 72.1 - - - -
379D THR* 1.3 68.5 + - - +
380D ASP* 4.1 9.1 + - - -
420D LEU* 3.9 17.3 - - + +
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Residues in contact with THR 379 (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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82D GLY 3.3 18.8 - - - +
83D GLY 4.0 2.9 - - - +
118D ILE* 4.0 17.5 - - + +
120D ARG* 4.0 18.4 - - + -
175D LEU* 5.4 0.4 - - + -
337D PHE* 3.1 24.3 - - + -
338D ALA* 2.9 19.3 + - - +
339D SER* 3.5 12.3 - - - +
340D GLU* 3.3 22.2 + - - -
341D ALA* 3.6 3.1 + - - +
378D TRP* 1.3 79.5 + - - +
380D ASP* 1.3 71.9 + - - +
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Residues in contact with ASP 380 (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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82D GLY 2.7 16.3 + - - +
83D GLY* 3.3 14.7 - - - -
84D ALA* 3.4 5.4 + - - +
108D TYR* 4.9 1.0 + - - -
116D TYR* 4.4 9.7 + - - +
120D ARG* 5.4 0.2 - - - +
339D SER 4.7 2.1 - - - +
340D GLU* 4.9 0.4 - - - -
341D ALA 3.3 8.5 - - - +
363D TYR* 2.7 38.0 + - + -
378D TRP* 4.1 11.4 - - + -
379D THR* 1.3 80.8 - - - +
381D TRP* 1.3 88.4 + - - +
382D ASN 4.0 1.4 - - - +
383D LEU* 5.3 1.6 - - - +
401D PRO* 3.0 33.5 - - - +
420D LEU* 4.3 4.3 - - + +
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Residues in contact with TRP 381 (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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83D GLY* 3.9 2.1 - - - -
84D ALA* 3.0 34.7 + - + -
86D THR* 3.4 24.7 - - + -
120D ARG* 3.7 17.5 - - + -
122D PRO* 4.6 2.5 - - + -
126D CYS* 3.9 7.4 - - - -
128D PHE* 3.4 17.4 - + - -
179D TRP* 3.2 26.9 - + - -
340D GLU* 3.9 21.1 - - + -
341D ALA 3.4 18.1 + - - +
342D CYS* 4.2 15.0 - - + -
380D ASP* 1.3 88.4 + - - +
382D ASN* 1.3 94.2 + - - +
383D LEU 3.1 0.3 + - - -
398D VAL* 4.2 5.2 - - + -
399D ASP 6.0 0.9 - - - +
501D 3RI 3.1 50.5 + - - -
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Residues in contact with ASN 382 (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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84D ALA* 3.7 7.2 - - - -
86D THR* 2.6 34.9 + - - +
128D PHE* 3.3 30.6 - - - -
380D ASP* 4.0 0.5 - - - +
381D TRP* 1.3 105.8 - - - +
383D LEU* 1.4 59.1 + - - +
384D ALA 3.8 6.1 - - - +
385D LEU* 3.7 33.8 - - + +
398D VAL* 4.0 1.6 - - - +
399D ASP 5.2 1.2 + - - +
400D SER* 2.9 21.5 + - - -
401D PRO* 3.9 8.5 - - - +
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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