Contacts of the helix formed by residues 86 - 96 (chain C) in PDB entry 1KI1
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 SER 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C ALA 6.2 0.2 - - - -
14C VAL* 5.5 1.1 - - - -
83C SER* 2.9 19.4 + - - +
84C VAL 3.5 0.4 - - - -
85C VAL* 1.3 81.6 - - - +
87C PRO* 1.3 67.2 - - - +
88C SER* 3.1 19.9 + - - -
89C SER* 2.7 38.5 + - - -
90C PHE* 3.2 5.6 + - - +
137C ILE* 5.1 1.3 - - - -
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Residues in contact with PRO 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C VAL 3.7 7.6 - - - +
86C SER* 1.3 84.6 - - - +
88C SER* 1.3 62.9 + - - +
90C PHE* 3.0 5.5 + - - +
91C GLU* 3.0 27.6 + - + +
129C LEU* 4.0 11.0 - - + -
134C GLN* 3.6 37.7 - - + +
135C LYS 3.9 21.1 - - - +
137C ILE* 4.4 18.1 - - + -
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Residues in contact with SER 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASP* 4.0 3.5 + - - -
86C SER* 3.1 11.1 + - - -
87C PRO* 1.3 79.8 - - - +
89C SER* 1.3 62.6 + - - +
91C GLU* 3.3 8.4 + - - +
92C ASN* 3.0 34.5 + - - -
134C GLN* 5.1 2.5 - - - +
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Residues in contact with SER 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASP* 3.2 20.3 + - - -
14C VAL* 3.6 25.8 - - - -
81C CYS 4.8 1.4 - - - +
82C PHE* 3.6 4.5 - - - +
83C SER 3.2 21.4 + - - -
86C SER* 2.7 30.5 + - - -
88C SER* 1.3 81.9 + - - +
90C PHE* 1.3 61.1 + - - +
92C ASN* 3.5 3.6 + - - +
93C VAL* 3.4 22.9 + - - +
97C TRP* 5.1 0.7 - - - -
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Residues in contact with PHE 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PHE* 3.5 51.6 - + + -
86C SER 3.2 4.9 + - - +
87C PRO 3.0 10.0 + - - +
89C SER* 1.3 79.3 + - - +
91C GLU* 1.3 78.6 + - + +
93C VAL* 3.1 20.3 + - + +
94C LYS* 4.1 7.8 + - - +
112C LEU* 4.7 1.1 - - + -
137C ILE* 3.8 24.5 - - + -
141C THR* 3.7 40.2 - - + -
142C ALA* 4.0 10.3 - - - -
145C LEU* 3.6 34.6 - - + +
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Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C PRO* 3.0 17.0 + - + +
88C SER* 3.7 10.3 - - - +
90C PHE* 1.3 86.9 - - + +
92C ASN* 1.3 61.9 + - - +
93C VAL 3.2 0.9 + - - -
94C LYS* 3.2 39.6 + - - +
95C GLU* 3.2 33.2 + - + +
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Residues in contact with ASN 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASP* 2.5 44.2 + - - +
88C SER* 3.0 18.8 + - - +
89C SER 3.7 4.0 - - - +
90C PHE 3.3 0.2 - - - -
91C GLU* 1.3 74.3 - - - +
93C VAL* 1.3 59.5 + - - +
95C GLU* 4.5 4.9 - - - +
96C LYS* 2.7 48.8 + - - +
97C TRP* 3.0 13.4 + - - +
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C VAL* 3.8 21.3 - - + -
81C CYS 4.3 3.4 - - - +
82C PHE* 3.7 26.2 - - + -
89C SER 3.4 16.2 - - - +
90C PHE* 3.2 13.0 - - + +
91C GLU 3.1 0.6 - - - -
92C ASN* 1.3 79.1 - - - +
94C LYS* 1.3 59.6 + - - +
97C TRP* 4.1 9.0 - - + -
98C VAL* 2.9 46.5 + - + +
112C LEU* 4.2 10.5 - - + -
145C LEU* 4.0 9.9 - - + -
149C LEU* 3.9 11.7 - - + -
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Residues in contact with LYS 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C PHE* 5.1 5.9 - - - -
91C GLU* 3.2 43.8 + - - +
93C VAL* 1.3 79.2 - - - +
95C GLU* 1.3 77.5 + - - +
96C LYS 3.5 0.2 - - - -
99C PRO* 3.1 22.4 - - - +
145C LEU* 4.0 26.9 - - + +
149C LEU* 3.8 32.6 - - + +
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Residues in contact with GLU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C GLU* 3.2 26.3 + - + +
92C ASN* 4.4 7.4 - - - +
94C LYS* 1.3 100.3 - - + +
96C LYS* 1.3 59.9 + - + +
99C PRO* 3.8 10.3 - - - +
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Residues in contact with LYS 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASP* 4.7 2.1 + - - +
62C GLU* 2.9 26.2 + - - +
63C ASP* 4.6 6.7 + - - +
68C ARG* 3.5 32.7 - - - +
92C ASN* 2.7 36.6 + - - +
94C LYS 3.5 0.2 - - - -
95C GLU* 1.3 76.8 - - + +
97C TRP* 1.3 94.9 + - + +
99C PRO* 3.4 5.5 - - - +
100C GLU* 3.2 25.0 + - - +
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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