Contacts of the helix formed by residues 76 - 87 (chain F) in PDB entry 1KYO
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 ASP 76 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196D THR* 5.7 0.7 - - - +
227D ARG* 5.7 0.3 + - - -
231D ASP* 3.6 23.8 + - - +
243D THR* 3.7 2.3 - - - -
244D THR* 3.9 17.1 + - + +
245D SER* 2.9 37.3 + - - -
74F ASP 3.9 1.2 + - - -
75F THR* 1.3 73.6 + - - +
77F GLN* 1.3 63.7 + - - +
78F LEU* 3.9 11.8 - - - +
79F GLU* 3.0 38.5 + - + +
80F ASP* 2.9 27.9 + - - +
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Residues in contact with GLN 77 (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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241D PRO* 4.9 4.2 - - - +
243D THR* 2.6 44.3 + - - +
245D SER* 3.4 9.3 + - - -
246D GLN* 4.3 4.2 - - - +
74F ASP* 5.0 4.8 - - - +
75F THR* 3.4 5.5 + - - +
76F ASP* 1.3 69.7 + - - +
78F LEU* 1.3 59.9 + - - +
80F ASP* 3.7 7.7 - - - +
81F LEU* 3.3 27.9 + - - +
142F LEU* 4.0 16.4 - - + -
145F LYS* 3.6 35.9 - - + +
146F LEU* 3.3 16.7 - - + +
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Residues in contact with LEU 78 (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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74D TYR* 4.4 7.4 - - - +
192D PHE* 5.1 0.4 - - + -
196D THR* 3.8 28.0 - - + +
245D SER* 4.1 6.5 + - - -
76F ASP* 3.2 12.4 + - - +
77F GLN* 1.3 75.7 - - - +
79F GLU* 1.3 62.1 + - + +
81F LEU* 3.2 3.8 + - + +
82F ARG* 2.8 71.9 + - + +
138F THR* 3.9 28.5 - - - +
142F LEU* 3.7 34.1 - - + +
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Residues in contact with GLU 79 (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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227D ARG* 5.8 4.8 + - - +
244D THR* 6.0 1.1 - - + -
75F THR* 4.9 3.6 - - - +
76F ASP* 3.0 33.9 + - + +
78F LEU* 1.3 79.1 - - + +
80F ASP* 1.3 55.4 + - - +
82F ARG* 3.2 20.8 + - - +
83F GLU* 2.9 35.2 + - - +
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Residues in contact with ASP 80 (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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75F THR* 2.9 38.2 + - - +
76F ASP 2.9 12.6 + - - +
77F GLN* 3.7 9.2 - - - +
79F GLU* 1.3 77.0 - - - +
81F LEU* 1.3 58.4 + - + +
83F GLU* 3.4 5.1 + - - +
84F HIS* 3.1 27.9 + - - +
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Residues in contact with LEU 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F GLN 3.3 19.2 + - - +
78F LEU* 3.2 5.9 + - - +
80F ASP* 1.3 80.6 - - + +
82F ARG* 1.3 61.6 + - - +
84F HIS* 3.5 10.0 + - + -
85F PHE* 3.0 47.7 + - + -
138F THR* 3.8 17.3 - - + +
141F ARG* 4.4 18.2 - - + -
142F LEU* 3.7 40.2 - - + +
145F LYS* 4.0 27.6 - - + +
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Residues in contact with ARG 82 (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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74D TYR* 4.7 4.6 + - - -
196D THR* 3.9 17.6 + - - -
197D GLY* 4.1 15.4 - - - +
217D TYR* 4.1 9.5 + - - -
78F LEU* 2.8 53.7 + - + +
79F GLU* 3.7 21.0 + - - +
81F LEU* 1.3 74.9 - - - +
83F GLU* 1.3 61.3 + - - +
85F PHE 3.6 1.0 + - - -
86F LYS* 3.1 42.6 + - + +
131F GLN* 3.7 26.6 - - - +
134F LEU* 4.0 24.8 - - + +
135F ASP* 4.3 7.1 + - - -
138F THR* 4.3 17.1 + - + -
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Residues in contact with GLU 83 (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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79F GLU* 2.9 20.0 + - - +
80F ASP* 3.9 5.2 - - - +
82F ARG* 1.3 74.6 - - - +
84F HIS* 1.3 66.3 + - - +
86F LYS* 3.3 31.5 + - - +
87F ASN* 3.4 43.5 + - - +
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Residues in contact with HIS 84 (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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80F ASP 3.1 17.1 + - - +
81F LEU* 3.6 14.6 - - + +
83F GLU* 1.3 77.0 - - - +
85F PHE* 1.3 86.9 + + - +
87F ASN* 3.0 28.4 + - - +
88F THR* 3.9 17.0 - - + +
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Residues in contact with PHE 85 (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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81F LEU* 3.0 33.6 + - + +
82F ARG 3.6 0.2 + - - -
83F GLU 3.5 0.2 - - - -
84F HIS* 1.3 103.0 - + - +
86F LYS* 1.3 61.9 + - - +
87F ASN 3.1 1.3 - - - -
88F THR* 3.0 24.6 + - + -
91F GLY* 3.3 2.4 - - - -
133F TYR* 3.2 39.7 - + + +
134F LEU* 4.0 12.6 - - + -
137F ALA* 3.6 28.9 - - + -
138F THR* 4.5 3.6 - - + -
141F ARG* 3.6 44.2 - - - -
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Residues in contact with LYS 86 (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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82F ARG* 3.1 29.9 + - - +
83F GLU* 3.3 38.4 + - - +
84F HIS 3.2 0.2 - - - -
85F PHE* 1.3 77.5 - - - +
87F ASN* 1.3 60.6 + - - +
91F GLY* 3.4 5.7 - - - -
92F LYS* 3.3 28.6 + - - +
95F VAL* 4.3 18.1 - - + +
130F LEU* 4.9 11.1 - - + +
134F LEU* 4.1 23.5 - - + +
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Residues in contact with ASN 87 (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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83F GLU* 3.4 31.7 + - - +
84F HIS* 3.0 12.4 + - - +
86F LYS* 1.3 79.2 - - - +
88F THR* 1.3 66.1 + - - +
92F LYS* 4.2 16.0 - - - +
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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