Contacts of the helix formed by residues 87 - 92 (chain F) 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 ALA 87 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27F LEU* 4.8 5.6 - - + -
83F TYR 3.8 4.6 + - - +
84F HIS 3.3 16.5 + - - +
85F SER 3.2 0.2 - - - -
86F LEU* 1.3 77.3 - - - +
88F PRO* 1.3 62.2 - - + +
90F TYR* 2.8 28.9 + - - +
91F TYR* 3.1 32.2 + - + -
115F TRP* 3.8 24.9 - - + -
118F GLU* 4.8 2.2 - - - +
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Residues in contact with PRO 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484E ASP* 4.6 5.2 - - - +
84F HIS 4.2 1.8 - - - +
85F SER* 3.3 18.8 - - - +
86F LEU 3.5 1.1 - - - -
87F ALA* 1.3 93.9 - - + +
89F MET* 1.3 58.9 + - - +
90F TYR 3.0 0.2 - - - -
91F TYR* 3.7 26.9 - - + +
92F ARG* 3.2 34.9 + - + +
118F GLU* 4.9 4.0 - - - +
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Residues in contact with MET 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446E ALA* 3.9 23.3 - - + +
447E HIS* 3.4 30.5 - - + +
450E ALA* 3.7 29.4 - - - -
480E ILE* 4.4 12.0 - - + +
484E ASP* 3.3 36.8 + - + +
23F LYS* 3.8 12.4 + - - -
75F TRP* 5.9 1.3 - - - -
86F LEU* 3.2 20.7 + - + +
87F ALA 3.1 0.2 - - - -
88F PRO* 1.3 79.2 - - - +
90F TYR* 1.3 79.3 + - + +
92F ARG* 4.2 5.5 + - - +
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Residues in contact with TYR 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446E ALA* 4.3 10.9 + - - +
449E GLN* 4.1 4.9 + - - +
450E ALA* 4.9 0.9 - - + -
23F LYS* 3.1 24.0 - - - +
25F VAL* 3.6 31.3 - - + +
27F LEU* 5.5 0.4 - - + -
55F GLY* 3.8 15.0 + - - -
56F ALA* 3.3 33.1 + - + +
75F TRP* 3.4 36.5 - + + +
77F THR* 3.8 15.5 - - + -
83F TYR* 5.6 1.1 - - + -
86F LEU* 3.1 43.1 - - + +
87F ALA* 2.8 11.7 + - - +
89F MET* 1.3 106.0 - - + +
91F TYR* 1.3 58.2 + - + +
92F ARG 3.6 0.7 - - - -
94F ALA* 4.3 0.3 - - - +
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Residues in contact with TYR 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F VAL* 3.7 18.6 - - + -
27F LEU* 4.1 20.4 - - + -
87F ALA* 3.1 41.5 + - + -
88F PRO* 3.7 22.2 - - + +
90F TYR* 1.3 76.4 - - - +
92F ARG* 1.3 68.3 + - - +
93F GLY 3.4 2.0 - - - -
94F ALA* 3.5 18.7 + - + +
115F TRP* 4.8 1.3 - + - -
118F GLU* 3.0 36.0 + - + +
119F LEU* 3.9 16.8 - - + -
122F GLN* 3.8 25.0 - - + +
123F ALA* 3.7 29.0 - - + +
124F SER 4.9 0.7 + - - -
127F ILE* 4.8 0.3 - - - +
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Residues in contact with ARG 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479E ASP* 2.3 43.2 + - - +
480E ILE* 4.9 1.8 - - - +
483E VAL* 3.6 25.1 - - - +
484E ASP* 2.4 43.4 + - - -
23F LYS* 4.4 1.3 - - - +
88F PRO* 3.2 19.0 + - - +
89F MET* 4.2 11.5 + - - +
90F TYR 3.6 1.2 - - - -
91F TYR* 1.3 84.6 - - - +
93F GLY* 1.3 60.0 + - - +
94F ALA 3.7 0.3 + - - -
123F ALA* 5.6 2.2 - - - +
124F SER* 4.6 16.8 + - - -
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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