Contacts of the strand formed by residues 84 - 90 (chain C) in PDB entry 4GKH
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 ILE 84 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C MSE 3.5 35.2 - - + +
72C LEU* 3.8 23.1 - - + -
73C ASN* 3.7 28.7 - - + +
82C PRO 3.9 0.6 + - - +
83C THR* 1.3 80.9 - - - +
85C LYS* 1.3 62.7 + - - +
86C HIS* 3.8 16.8 - - - +
87C PHE* 4.6 6.1 - - + -
96C LEU* 4.2 16.8 - - + -
97C LEU 3.9 3.4 - - - -
98C THR* 4.4 1.3 - - - -
89D ARG* 4.9 13.5 - - + +
90D THR 5.9 2.0 - - - -
91D PRO* 3.7 20.4 - - + +
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Residues in contact with LYS 85 (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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22C ASP* 4.6 6.6 - - + +
26C TYR* 5.2 1.8 + - - -
50C PRO* 4.7 14.3 - - - +
52C LEU* 4.2 27.1 - - + +
83C THR* 3.3 3.3 + - + +
84C ILE* 1.3 75.3 - - - +
86C HIS* 1.3 66.1 + - + +
97C LEU* 2.8 27.5 + - + +
99C THR* 3.9 29.6 - - + +
89D ARG 4.6 0.2 - - - -
90D THR* 4.0 3.8 - - - +
91D PRO* 3.4 24.4 - - + +
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Residues in contact with HIS 86 (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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17C SER* 3.3 22.7 + - - -
18C ASN* 3.6 10.9 - - - -
19C LEU* 3.7 22.7 - - + -
22C ASP* 3.0 29.4 - - - +
84C ILE* 3.6 4.0 - - - +
85C LYS* 1.3 80.0 - - - +
87C PHE* 1.3 74.1 + - - +
88C ILE* 3.9 19.5 - - + +
95C TRP 3.9 0.6 - - - +
96C LEU* 3.8 1.7 - - - +
97C LEU* 2.8 36.0 + - + +
88D ILE* 3.6 29.8 - - + -
89D ARG 3.3 9.3 + - - -
90D THR* 4.2 11.9 - - + +
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Residues in contact with PHE 87 (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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65C VAL* 4.2 6.5 - - + -
66C THR* 3.6 34.8 - - - -
69C MSE 3.6 52.5 - - + -
84C ILE* 4.6 2.0 - - + -
86C HIS* 1.3 78.6 + - - +
88C ILE* 1.3 73.5 + - - +
89C ARG* 3.8 22.2 - - + -
94C ALA* 4.1 11.2 - - + -
95C TRP 3.1 23.1 - - - -
96C LEU* 4.0 10.1 - - + -
69D MSE 4.0 3.4 - - + -
87D PHE* 3.7 18.6 - + - -
88D ILE* 3.3 5.5 - - - -
89D ARG* 2.9 38.5 + - + -
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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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18C ASN* 3.7 22.4 - - - +
19C LEU* 3.9 31.4 - - + +
86C HIS* 3.9 14.6 - - + +
87C PHE* 1.3 84.6 - - - +
89C ARG* 1.3 67.5 + - - +
90C THR* 4.4 6.3 - - + +
93C ASP 4.0 0.4 - - - +
94C ALA* 3.2 5.9 - - - +
95C TRP* 2.8 49.7 + - + +
15D LEU* 5.5 3.8 - - + -
16D ASN* 4.7 11.0 - - + +
86D HIS* 3.9 25.8 - - + +
87D PHE 3.4 3.6 - - - +
88D ILE* 4.3 6.3 - - + -
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Residues in contact with ARG 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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59C GLY 4.9 1.6 + - - -
62C ALA* 3.7 14.4 - - - +
63C ASN* 3.0 29.1 + - - -
66C THR* 3.6 22.8 + - - +
87C PHE* 3.8 16.1 - - + -
88C ILE* 1.3 74.7 - - - +
90C THR* 1.3 92.3 + - - +
91C PRO* 3.0 20.8 + - - -
93C ASP 3.3 17.4 + - - +
94C ALA* 4.0 5.6 - - - -
69D MSE 4.7 11.4 - - - -
73D ASN* 3.1 21.4 + - - +
84D ILE* 4.8 11.2 - - + +
86D HIS* 3.3 6.4 - - - -
87D PHE* 2.8 48.3 + - + +
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Residues in contact with THR 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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88C ILE* 4.3 4.2 - - + -
89C ARG* 1.3 113.5 + - - +
91C PRO* 1.4 64.6 - - + +
92C ASP 4.2 0.7 + - - -
93C ASP* 2.8 19.0 + - - +
16D ASN* 2.6 38.8 + - - +
17D SER* 5.5 3.1 - - - -
84D ILE* 5.0 2.7 - - - -
85D LYS 4.1 2.5 - - - +
86D HIS* 3.7 31.4 - - + +
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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