Contacts of the helix formed by residues 87 - 98 (chain C) 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 ASP 87 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C GLY 3.7 2.6 + - - -
86C MET* 1.3 79.5 - - - +
88C ILE* 1.3 80.4 + - - +
89C LYS* 3.2 22.8 - - - +
90C ASP* 3.2 21.9 + - - +
91C ILE* 3.0 20.7 + - - +
129C GLN* 4.3 5.0 - - - +
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Residues in contact with ILE 88 (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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54C ILE* 5.2 11.0 - - + -
55C GLN* 4.7 20.2 - - + +
58C GLN* 3.5 47.3 - - + +
86C MET 3.8 1.2 + - - -
87C ASP* 1.3 87.0 + - - +
89C LYS* 1.3 67.0 + - + +
91C ILE* 3.3 11.1 + - + +
92C LYS* 3.3 22.9 + - + +
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Residues in contact with LYS 89 (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 ASP* 3.2 16.7 + - - +
88C ILE* 1.3 85.9 - - + +
90C ASP* 1.3 69.9 + - - +
92C LYS* 3.7 4.8 + - - +
93C LYS* 3.2 47.8 + - + +
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Residues in contact with ASP 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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86C MET* 3.6 19.7 - - + -
87C ASP* 3.2 23.9 + - - +
89C LYS* 1.3 88.9 - - - +
91C ILE* 1.3 60.8 + - - +
93C LYS* 3.4 12.7 + - - +
94C LEU* 2.8 30.1 + - - +
129C GLN* 4.1 10.4 + - - +
132C LYS* 4.4 12.5 + - - -
173C VAL* 3.5 32.8 - - + +
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Residues in contact with ILE 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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51C LEU* 4.3 7.2 - - + -
54C ILE* 4.2 28.3 - - + -
81C ILE* 4.4 15.9 - - + +
82C LEU* 3.7 29.6 - - + -
86C MET* 3.9 32.8 - - + +
87C ASP 3.0 17.2 + - - +
88C ILE* 3.7 11.7 - - + +
89C LYS 3.3 0.6 - - - -
90C ASP* 1.3 73.4 - - - +
92C LYS* 1.3 57.9 + - - +
94C LEU* 3.1 3.1 + - - +
95C ILE* 2.7 51.5 + - + +
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Residues in contact with LYS 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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51C LEU* 3.8 19.5 - - + -
55C GLN* 3.7 27.1 - - + +
88C ILE* 3.3 13.2 + - + +
89C LYS* 4.1 5.8 - - - +
90C ASP 3.4 0.2 - - - -
91C ILE* 1.3 78.6 - - - +
93C LYS* 1.3 59.7 + - + +
96C GLU* 2.9 77.1 + - - +
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Residues in contact with LYS 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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89C LYS* 3.2 38.8 - - + +
90C ASP* 3.4 12.8 + - - +
91C ILE 3.2 0.8 - - - -
92C LYS* 1.3 77.9 - - + +
94C LEU* 1.3 60.0 + - - +
96C GLU* 4.8 4.0 - - - -
97C GLY 2.9 24.4 + - - +
172C ASN* 5.0 1.6 + - - +
173C VAL* 4.7 13.8 - - + +
174C ASP* 2.4 41.3 + - - +
177C ILE* 3.2 23.2 - - + +
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Residues in contact with LEU 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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77C MET* 4.7 12.5 - - - +
81C ILE* 4.8 16.2 - - + -
86C MET* 4.3 13.5 - - + -
90C ASP 2.8 20.5 + - - +
91C ILE* 3.6 5.8 - - - +
93C LYS* 1.3 76.9 - - - +
95C ILE* 1.3 61.1 + - + +
98C LEU* 3.1 54.7 + - + +
125C ILE* 3.7 35.2 - - + -
173C VAL* 3.9 21.1 - - + +
176C ILE* 4.4 8.7 - - + -
177C ILE* 4.5 6.5 - - + +
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Residues in contact with ILE 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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47C GLY* 3.6 28.5 - - - +
48C ILE* 3.6 25.1 - - + +
50C TYR* 6.0 0.4 - - + -
51C LEU* 3.8 33.7 - - + -
54C ILE* 5.7 1.3 - - + -
77C MET* 4.8 12.8 - - - -
78C THR* 4.3 14.6 - - + +
81C ILE* 3.9 22.0 - - + -
91C ILE* 2.7 37.6 + - + +
94C LEU* 1.3 75.2 - - - +
96C GLU* 1.3 65.3 + - - +
98C LEU 4.1 7.8 - - - +
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Residues in contact with GLU 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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48C ILE* 5.0 5.3 - - + +
51C LEU* 4.8 13.8 - - + +
92C LYS* 2.9 60.5 + - + +
93C LYS* 4.4 3.1 - - - +
95C ILE* 1.3 79.6 - - + +
97C GLY* 1.3 65.1 + - - +
98C LEU 4.5 1.4 - - - -
99C ASP* 4.3 6.1 - - - +
391C ARG* 3.4 31.3 + - - +
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Residues in contact with GLY 97 (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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93C LYS 2.9 22.4 + - - -
96C GLU* 1.3 73.0 - - - +
98C LEU* 1.3 52.1 + - - +
99C ASP* 2.7 30.8 + - - +
177C ILE* 4.3 24.9 - - - +
180C THR* 5.0 3.9 + - - -
181C LYS* 5.1 4.8 + - - -
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Residues in contact with LEU 98 (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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48C ILE* 5.1 2.1 - - - +
77C MET* 4.6 21.2 - - + +
93C LYS 4.3 0.2 + - - -
94C LEU* 3.1 51.4 + - + +
95C ILE 4.1 7.7 - - - +
96C GLU 3.5 3.1 - - - -
97C GLY* 1.3 70.3 - - - +
99C ASP* 1.3 64.4 + - - +
100C ILE* 3.3 12.4 + - - +
103C LEU* 4.6 12.8 - - + -
121C ILE* 3.8 27.6 - - + -
122C LEU* 5.9 0.7 - - + -
125C ILE* 3.8 5.8 - - + -
176C ILE* 4.4 9.6 - - + +
177C ILE* 4.8 7.4 - - + +
180C THR* 4.1 26.5 - - + +
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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