Contacts of the helix formed by residues 86 - 92 (chain D) in PDB entry 4KYI
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 LEU 86 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442C PHE* 3.5 36.6 - - + -
443C GLU* 4.0 27.4 - - + +
446C ALA* 3.6 31.9 - - + -
447C HIS* 4.8 4.0 - - - +
55D GLY* 4.8 2.2 - - - -
83D TYR* 3.3 25.3 + - + +
84D HIS 3.2 1.2 - - - -
85D SER* 1.3 80.5 - - - +
87D ALA* 1.3 64.6 + - - +
88D PRO* 3.4 1.3 - - - -
89D MET* 3.1 30.5 + - + +
90D TYR* 3.6 23.8 - - + +
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Residues in contact with ALA 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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27D LEU* 4.8 5.8 - - + -
83D TYR 3.6 4.4 + - - +
84D HIS 3.2 17.8 + - - +
86D LEU* 1.3 77.4 - - - +
88D PRO* 1.4 67.1 - - + +
90D TYR* 2.9 24.1 + - - +
91D TYR* 3.0 30.7 + - + -
115D TRP* 3.7 25.6 - - + -
118D GLU* 4.3 2.9 - - - +
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Residues in contact with PRO 88 (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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484C ASP* 5.1 2.7 - - - +
84D HIS 4.3 1.3 - - - +
85D SER* 3.4 17.3 - - - +
86D LEU 3.5 1.8 - - - -
87D ALA* 1.4 93.5 - - + +
89D MET* 1.3 59.8 + - - +
91D TYR* 3.6 28.5 - - + +
92D ARG* 3.2 36.9 + - + +
118D GLU* 4.5 4.0 - - - +
122D GLN* 4.6 7.0 - - - +
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Residues in contact with MET 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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446C ALA* 3.6 22.7 - - + +
447C HIS* 3.6 28.3 - - + +
450C ALA* 4.1 19.7 - - + -
480C ILE* 4.5 8.3 - - + -
484C ASP* 3.1 34.5 + - + +
23D LYS* 3.6 13.5 + - - -
86D LEU* 3.1 19.4 + - + +
87D ALA 3.0 0.4 + - - -
88D PRO* 1.3 79.3 - - - +
90D TYR* 1.3 96.4 + - + +
92D ARG* 4.3 5.0 - - - +
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Residues in contact with TYR 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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446C ALA* 4.4 3.1 + - - +
449C GLN* 4.2 3.7 + - - -
450C ALA* 5.1 3.8 - - + -
23D LYS* 3.2 24.5 - - - +
25D VAL* 3.9 28.4 - - + +
27D LEU* 5.6 0.9 - - + -
55D GLY* 3.6 30.6 + - - -
56D ALA* 3.6 21.5 - - + +
75D TRP* 4.3 25.4 - + + +
77D THR* 3.5 21.1 - - + -
83D TYR* 5.4 3.4 - - + -
86D LEU* 3.6 34.2 - - + +
87D ALA* 2.9 12.2 + - - +
89D MET* 1.3 115.1 - - + +
91D TYR* 1.3 59.1 + - + +
92D ARG 3.4 2.5 - - - -
94D ALA* 4.1 1.2 - - - +
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Residues in contact with TYR 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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25D VAL* 3.9 16.8 - - + -
27D LEU* 4.1 16.2 - - + -
87D ALA* 3.0 43.9 + - + -
88D PRO* 3.5 18.1 - - + +
90D TYR* 1.3 78.0 - - + +
92D ARG* 1.3 70.9 + - + +
93D GLY 3.8 0.2 - - - -
94D ALA* 3.7 16.7 + - + +
115D TRP* 5.4 0.2 - + - -
118D GLU* 2.6 33.0 + - + +
119D LEU* 3.7 19.3 - - + -
122D GLN* 3.0 21.0 + - + -
123D ALA* 3.6 41.1 - - + +
127D ILE* 4.7 3.2 - - + +
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Residues in contact with ARG 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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479C ASP* 3.1 27.3 + - - -
483C VAL* 4.4 26.0 - - - +
484C ASP* 4.7 7.2 - - - +
23D LYS* 4.4 2.8 - - - +
88D PRO* 3.2 24.8 + - + +
89D MET 4.3 7.9 - - - +
90D TYR 3.4 3.0 - - - -
91D TYR* 1.3 86.0 - - + +
93D GLY* 1.3 87.3 + - - +
94D ALA 3.2 2.4 + - - -
123D ALA* 5.4 0.6 - - - +
124D SER* 4.3 18.0 + - - -
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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