Contacts of the helix formed by residues 86 - 92 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432G LEU* 4.7 2.0 - - + -
442G PHE* 3.9 17.9 - - + -
443G GLU* 4.1 30.3 - - + +
446G ALA* 3.6 33.7 - - + -
447G HIS* 5.0 2.2 - - + -
55H GLY* 5.0 2.5 - - - -
83H TYR* 3.0 41.3 + - + +
85H SER* 1.3 80.1 - - - +
87H ALA* 1.3 64.4 + - - +
88H PRO* 3.3 2.2 - - - -
89H MET* 3.0 34.0 + - + +
90H TYR* 4.0 24.8 + - + +
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Residues in contact with ALA 87 (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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27H LEU* 5.0 4.9 - - + -
83H TYR 3.5 4.6 + - - +
84H HIS* 3.4 14.5 + - + +
86H LEU* 1.3 76.9 - - - +
88H PRO* 1.4 69.5 - - + +
90H TYR* 2.8 27.3 + - - +
91H TYR* 3.1 29.4 + - + -
115H TRP* 3.9 26.9 - - + -
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Residues in contact with PRO 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484G ASP* 4.4 5.2 - - - +
84H HIS 3.9 5.4 - - - +
85H SER* 3.7 12.8 - - - +
86H LEU 3.4 4.5 - - - -
87H ALA* 1.4 93.4 - - + +
89H MET* 1.3 61.1 + - - +
90H TYR 3.2 0.7 + - - -
91H TYR* 3.5 28.4 - - + +
92H ARG* 3.1 33.5 + - - +
118H GLU* 5.3 3.4 - - - +
122H GLN* 5.5 4.3 - - - +
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Residues in contact with MET 89 (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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446G ALA* 4.3 12.3 - - + -
447G HIS* 3.3 40.2 - - + +
450G ALA* 3.8 28.7 - - - -
480G ILE* 4.3 15.4 - - + +
484G ASP* 3.2 36.1 + - - +
23H LYS* 3.5 13.9 + - - -
86H LEU* 3.0 21.7 + - + +
88H PRO* 1.3 79.4 - - - +
90H TYR* 1.3 78.4 + - + +
92H ARG* 4.4 10.0 + - - +
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Residues in contact with TYR 90 (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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446G ALA* 4.9 4.9 + - - +
449G GLN* 4.3 3.8 + - - -
450G ALA* 4.8 1.9 - - + +
23H LYS* 3.2 30.2 + - - +
25H VAL* 3.9 23.7 - - + +
27H LEU* 5.8 0.7 - - + -
55H GLY 3.8 13.6 + - - -
56H ALA* 3.3 29.8 + - + +
75H TRP* 4.1 27.5 - + + -
77H THR* 3.5 25.4 - - + -
83H TYR* 5.5 2.9 - - + -
86H LEU* 4.0 27.3 - - + +
87H ALA* 2.8 22.0 + - - +
89H MET* 1.3 109.1 - - + +
91H TYR* 1.3 58.3 + - + +
92H ARG 3.3 2.5 - - - -
94H ALA* 4.1 3.5 - - - +
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Residues in contact with TYR 91 (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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25H VAL* 4.1 15.7 - - + -
27H LEU* 4.6 10.8 - - + -
87H ALA* 3.1 41.0 + - + -
88H PRO* 3.5 26.5 - - + +
90H TYR* 1.3 77.1 - - + +
92H ARG* 1.3 67.6 + - + +
93H GLY 3.5 0.7 - - - -
94H ALA* 3.7 19.3 + - + +
115H TRP* 5.2 2.2 - + - -
118H GLU* 3.5 32.0 + - + +
119H LEU* 4.0 24.2 - - + -
122H GLN* 3.5 31.7 + - - +
123H ALA* 3.9 24.3 - - + +
124H SER* 4.8 2.9 + - - -
127H ILE* 4.7 5.3 - - + +
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Residues in contact with ARG 92 (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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479G ASP* 2.6 47.0 + - - +
480G ILE* 4.5 2.2 - - - +
483G VAL* 3.7 29.4 - - - +
484G ASP* 2.4 36.2 + - - -
23H LYS* 5.7 0.2 - - - +
88H PRO* 3.1 21.6 + - - +
89H MET* 4.4 10.1 + - - +
90H TYR 3.3 1.8 - - - -
91H TYR* 1.3 85.5 - - + +
93H GLY* 1.3 60.3 + - - +
94H ALA 3.4 0.7 + - - -
123H ALA* 6.2 0.4 - - - +
124H SER* 4.7 13.3 + - - +
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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