Contacts of the helix formed by residues 87 - 97 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A GLY 3.5 3.9 + - - -
86A MET* 1.3 78.2 - - - +
88A ILE* 1.3 69.8 + - - +
89A LYS* 2.9 34.5 + - - +
90A ASP* 3.1 20.1 + - - +
91A ILE* 3.0 20.8 + - - +
129A GLN* 4.8 4.0 - - - +
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 5.6 2.7 - - + -
54A ILE* 4.1 18.8 - - + -
55A GLN* 4.1 39.5 - - + +
58A GLN* 4.0 43.5 - - + +
63A ILE* 5.6 1.8 - - + -
86A MET 3.6 1.6 + - - -
87A ASP* 1.3 79.1 + - - +
89A LYS* 1.3 64.6 + - + +
91A ILE* 4.0 11.4 - - + -
92A LYS* 3.3 21.4 + - + +
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Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ASP* 2.9 15.1 + - - +
88A ILE* 1.3 83.3 - - + +
90A ASP* 1.3 68.9 + - - +
92A LYS* 3.6 9.0 + - - +
93A LYS* 3.3 46.6 + - + +
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Residues in contact with ASP 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A MET* 3.6 16.3 - - + +
87A ASP* 3.1 23.2 + - - +
89A LYS* 1.3 84.4 - - - +
91A ILE* 1.3 53.1 + - - +
93A LYS* 3.0 22.1 + - - +
94A LEU* 2.6 37.2 + - - +
129A GLN* 4.2 11.3 + - - +
132A LYS* 4.4 9.7 + - - -
173A VAL* 3.5 31.9 - - + +
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Residues in contact with ILE 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 4.6 7.4 - - + -
54A ILE* 4.4 21.3 - - + -
81A ILE* 3.8 26.7 - - + +
82A LEU* 3.8 23.1 - - + -
86A MET* 3.5 33.7 - - + +
87A ASP 3.0 13.2 + - - +
88A ILE* 4.0 12.1 - - + +
90A ASP* 1.3 75.4 - - - +
92A LYS* 1.3 54.7 + - - +
94A LEU* 4.0 6.5 - - - -
95A ILE* 2.6 52.2 + - + +
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Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 4.0 14.8 - - + +
55A GLN* 3.7 26.7 - - - +
88A ILE* 3.3 17.5 + - + +
89A LYS* 3.6 7.9 - - - +
90A ASP 3.2 0.4 - - - -
91A ILE* 1.3 78.3 - - - +
93A LYS* 1.3 60.8 + - + +
96A GLU* 3.1 61.6 + - - +
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Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LYS* 3.3 37.9 + - + +
90A ASP* 3.0 24.2 + - - +
92A LYS* 1.3 80.7 - - + +
94A LEU* 1.3 63.9 + - - +
96A GLU* 5.0 2.2 - - - -
97A GLY* 3.4 14.0 + - - -
172A ASN* 5.0 4.6 + - - -
173A VAL* 5.0 7.4 - - + +
174A ASP* 3.1 35.2 + - - +
177A ILE* 3.3 24.7 - - + +
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A MET* 4.1 10.8 - - + -
81A ILE* 4.4 15.0 - - + -
86A MET* 4.4 15.5 - - + -
90A ASP 2.6 21.0 + - - +
91A ILE* 3.6 8.3 - - - +
93A LYS* 1.3 74.5 - - - +
95A ILE* 1.3 66.6 + - + +
97A GLY 3.7 0.5 - - - -
98A LEU* 3.1 51.8 + - + +
125A ILE* 3.8 30.7 - - + -
173A VAL* 4.1 17.7 - - + +
176A ILE* 5.0 8.7 - - + -
177A ILE* 4.5 13.0 - - + -
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Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLY* 3.2 36.8 - - - +
48A ILE* 3.3 21.3 - - + +
50A TYR 6.3 0.4 - - - -
51A LEU* 3.7 27.1 - - + -
54A ILE* 5.8 0.7 - - + -
77A MET* 4.8 10.8 - - + -
78A THR* 4.4 15.7 - - + +
81A ILE* 3.6 22.2 - - + -
91A ILE* 2.6 39.4 + - + +
94A LEU* 1.3 80.3 - - + +
96A GLU* 1.3 61.7 + - - +
98A LEU* 3.9 7.9 + - - +
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Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ILE* 4.8 7.9 - - + -
51A LEU* 3.6 27.1 - - + +
92A LYS* 3.1 48.3 + - - +
93A LYS* 4.7 2.2 - - - +
95A ILE* 1.3 79.3 - - - +
97A GLY* 1.3 57.6 + - - +
98A LEU 3.5 2.1 + - - -
99A ASP* 5.4 0.9 - - - +
391A ARG* 2.8 44.6 + - - +
395A VAL* 5.5 3.7 - - + +
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Residues in contact with GLY 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LYS 3.4 13.3 + - - -
94A LEU 3.7 2.5 - - - -
95A ILE 3.4 0.2 - - - -
96A GLU* 1.3 78.7 - - - +
98A LEU* 1.3 63.2 + - - +
99A ASP* 4.2 3.6 - - - -
177A ILE* 3.5 33.4 - - - +
180A THR* 5.3 1.0 + - - -
181A LYS* 5.0 6.4 + - - -
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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