Contacts of the helix formed by residues 86 - 95 (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 THR 86 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84D ALA* 3.1 8.6 + - + -
85D MET* 1.3 78.4 - - - +
87D ASP* 1.3 65.6 + - - +
88D ALA 3.4 3.8 + - - -
89D ALA* 2.9 19.7 + - - +
90D ALA* 2.9 23.1 + - - +
122D PRO* 4.2 14.1 - - + -
126D CYS* 4.3 1.6 - - - -
128D PHE* 3.9 8.7 - - + -
157D LYS* 4.6 1.1 - - - -
381D TRP* 3.4 38.6 - - + -
382D ASN* 2.6 31.3 + - - +
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Residues in contact with ASP 87 (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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86D THR* 1.3 73.4 - - - +
88D ALA* 1.3 64.0 + - - +
90D ALA* 4.0 4.8 - - - +
91D LEU* 2.9 29.9 + - - +
122D PRO* 5.5 1.0 - - - +
124D ALA 5.1 2.6 - - - +
125D SER* 4.4 0.3 - - - -
126D CYS* 5.7 0.8 - - - -
128D PHE 3.3 10.4 + - - +
129D SER* 2.8 31.2 + - - -
130D ILE* 4.9 4.0 + - + +
133D TYR* 2.6 31.7 + - - -
152D GLU* 3.5 18.6 - - + +
156D LEU* 5.0 4.3 - - + +
157D LYS* 3.4 22.4 + - - +
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Residues in contact with ALA 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D THR* 3.1 1.7 - - - +
87D ASP* 1.3 77.0 - - - +
89D ALA* 1.3 61.5 + - - +
91D LEU* 3.7 1.6 - - - +
92D ASN* 3.0 31.2 + - - -
128D PHE* 3.0 32.8 + - + +
129D SER* 5.6 0.2 - - - +
384D ALA 4.2 0.4 - - - -
385D LEU* 4.0 6.5 - - + -
391D PRO* 3.4 45.1 - - + +
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Residues in contact with ALA 89 (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 3.9 15.7 - - - +
85D MET* 4.5 3.8 - - - -
86D THR* 2.9 23.3 + - - +
88D ALA* 1.3 73.4 - - - +
90D ALA* 1.3 67.4 + - - +
92D ASN* 3.0 4.5 + - - +
93D ILE* 2.9 30.5 + - + +
383D LEU* 3.9 7.9 - - + +
384D ALA 3.3 33.8 + - - +
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Residues in contact with ALA 90 (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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85D MET* 4.1 7.9 - - - -
86D THR 2.9 16.6 + - - +
87D ASP* 4.0 3.1 - - - +
89D ALA* 1.3 77.7 - - - +
91D LEU* 1.3 62.8 + - - +
93D ILE 3.4 0.2 + - - -
94D LEU* 3.0 30.6 + - - +
156D LEU* 3.8 26.5 - - + -
157D LYS* 4.2 6.1 - - + -
160D LEU* 3.4 26.0 - - + +
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Residues in contact with LEU 91 (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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130A ILE 3.5 25.6 - - - +
131A ARG* 4.0 15.9 - - + -
132A THR* 5.0 2.7 - - + +
393A TRP* 4.0 29.4 - - + +
87D ASP 2.9 18.8 + - - +
88D ALA* 3.7 1.8 - - - +
90D ALA* 1.3 77.1 - - - +
92D ASN* 1.3 64.3 + - - +
94D LEU* 3.3 1.8 + - - +
95D ALA* 3.0 25.6 + - + +
130D ILE* 4.0 17.3 - - + -
156D LEU* 4.5 15.2 - - + +
391D PRO* 3.7 30.5 - - + -
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Residues in contact with ASN 92 (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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88D ALA 3.0 23.4 + - - +
89D ALA 3.0 5.0 + - - +
91D LEU* 1.3 80.7 - - - +
93D ILE* 1.3 61.2 + - - +
95D ALA* 3.4 12.5 + - - +
96D LEU* 3.9 1.7 + - - +
384D ALA* 4.6 5.8 - - + +
385D LEU* 3.5 7.9 - - - +
386D ASN* 3.4 25.6 + - - +
390D GLY 3.0 26.5 + - - -
391D PRO* 3.5 8.3 - - - +
404D VAL* 3.5 32.8 - - + +
406D ILE* 3.6 20.0 - - - +
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Residues in contact with ILE 93 (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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85D MET* 4.7 5.2 - - + -
89D ALA* 2.9 30.0 + - + +
90D ALA 3.8 3.6 - - - +
92D ASN* 1.3 74.2 - - - +
94D LEU* 1.3 60.6 + - - +
96D LEU* 3.3 17.6 + - - +
101D GLN* 3.2 36.6 - - + +
104D LEU* 3.7 32.5 - - + -
105D LEU* 4.5 16.6 - - + -
160D LEU* 3.7 32.3 - - + -
383D LEU* 4.7 10.1 - - + -
384D ALA* 4.1 16.8 - - + -
404D VAL* 5.0 0.2 - - - -
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Residues in contact with LEU 94 (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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132A THR* 3.8 11.6 + - - +
90D ALA 3.0 18.2 + - - +
91D LEU 4.1 2.7 - - - +
93D ILE* 1.3 72.2 - - - +
95D ALA* 1.3 63.7 + - - +
96D LEU 3.1 3.8 + - - +
101D GLN* 3.4 36.5 + - - +
155D LYS 3.9 6.1 - - - +
156D LEU* 3.5 52.0 - - + +
159D PRO* 5.9 3.6 - - + -
160D LEU* 3.9 14.8 - - + +
163D ARG* 3.7 14.8 - - - +
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Residues in contact with ALA 95 (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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132A THR* 3.7 28.9 + - + +
190A ALA* 5.9 0.9 - - - -
191A VAL* 4.6 12.6 + - - +
393A TRP* 4.9 4.0 - - + -
91D LEU* 3.0 16.9 + - + +
92D ASN 3.8 1.6 - - - +
93D ILE 3.3 1.2 - - - -
94D LEU* 1.3 77.3 - - - +
96D LEU* 1.3 60.8 + - - +
406D ILE* 3.7 46.6 - - + +
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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