Contacts of the strand formed by residues 184 - 192 (chain C) in PDB entry 5KC6
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 THR 184 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B ILE* 3.9 22.9 - - + -
155B ASN* 3.0 32.4 + - - +
156B GLY 3.7 9.1 + - - +
157B VAL* 5.5 2.9 - - - -
66C ALA 3.4 7.4 - - - -
67C ILE* 4.1 7.0 - - + -
86C PHE* 3.8 5.6 - - - -
115C ASN 5.3 0.5 + - - -
116C PHE* 3.2 5.6 - - - +
117C HIS* 2.7 46.2 + - - +
182C TYR 3.6 11.2 - - - +
183C SER* 1.3 81.2 - - - +
185C PHE* 1.3 62.4 + - - +
186C SER* 5.5 1.2 + - - -
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Residues in contact with PHE 185 (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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64C PHE* 3.7 35.9 - + - -
65C SER* 3.5 0.9 - - - -
66C ALA* 2.7 41.8 + - + +
86C PHE* 3.5 33.0 - + + -
97C PHE* 4.3 16.4 - + - -
102C SER 4.6 2.7 - - - -
114C PHE* 4.0 19.5 - + + -
115C ASN 3.3 10.8 - - - -
116C PHE* 3.9 8.3 - + + -
131C LEU* 4.2 9.4 - - + -
167C ALA 4.5 4.7 - - - -
168C TYR* 4.2 16.8 - - - -
169C LEU* 3.8 29.8 - - + -
184C THR* 1.3 76.8 - - - +
186C SER* 1.3 72.6 + - - +
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Residues in contact with SER 186 (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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156B GLY 4.4 4.2 + - - -
157B VAL* 4.2 12.8 + - - -
158B LEU* 4.2 14.2 + - - +
64C PHE* 3.3 20.9 - - - -
65C SER* 3.5 17.3 - - - -
114C PHE* 3.5 2.3 - - - -
115C ASN* 3.0 45.7 + - - +
184C THR* 5.5 1.5 + - - -
185C PHE* 1.3 80.7 + - - +
187C GLY* 1.3 60.4 + - - +
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Residues in contact with GLY 187 (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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158B LEU* 3.4 3.6 - - - +
63C ALA* 3.3 0.3 - - - -
64C PHE* 2.8 51.0 + - - +
104C PHE* 5.9 0.4 - - - -
113C SER 3.0 15.9 - - - -
114C PHE* 4.1 1.6 - - - -
115C ASN* 6.0 0.7 - - - -
186C SER* 1.3 76.6 - - - +
188C PHE* 1.3 68.0 + - - +
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Residues in contact with PHE 188 (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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188A PHE* 4.2 14.1 - + - -
113B SER* 5.1 3.1 - - - -
158B LEU* 4.0 22.7 - - + -
188B PHE* 4.1 25.1 - + - -
190B VAL* 3.7 20.9 - - + -
62C VAL* 3.2 14.6 - - - +
63C ALA* 3.6 13.5 - - + +
104C PHE* 5.9 0.9 - - - -
112C TYR* 3.4 10.4 - - - +
113C SER* 2.9 57.0 + - - -
114C PHE* 5.5 0.4 - - - -
115C ASN* 5.5 3.4 - - - -
187C GLY* 1.3 78.2 - - - +
189C LEU* 1.3 72.3 + - - +
190C VAL* 3.4 21.7 + - + -
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Residues in contact with LEU 189 (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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190B VAL* 5.2 2.8 - - - +
191B PHE* 5.8 1.6 - - - -
60C ALA* 3.7 33.4 - - - +
62C VAL* 2.8 28.3 + - + +
108C ARG* 4.1 26.5 - - + -
109C LYS 5.1 0.4 - - - +
110C GLY* 3.9 7.2 - - - -
111C ILE 3.6 9.0 - - - +
112C TYR* 3.7 39.5 - - + +
188C PHE* 1.3 77.5 - - - +
190C VAL* 1.3 63.2 + - - +
191C PHE* 3.5 28.3 - - - +
192C PRO* 4.0 11.2 - - + -
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Residues in contact with VAL 190 (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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188A PHE* 3.7 32.1 - - + -
189A LEU 5.2 2.5 - - - +
111C ILE* 2.8 24.2 + - + +
113C SER* 3.9 8.1 - - - +
158C LEU* 3.8 28.5 - - + -
188C PHE* 3.8 22.4 - - + -
189C LEU* 1.3 74.9 - - - +
191C PHE* 1.3 82.9 + - + +
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Residues in contact with PHE 191 (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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60A ALA 5.1 2.0 - - - -
61A LYS* 3.7 35.4 - - + -
62A VAL 3.7 18.2 - - - -
63A ALA* 3.8 24.5 - - + -
93A ILE* 3.9 20.6 - - + -
189A LEU 5.7 2.5 - - - -
111C ILE* 2.9 46.9 + - + -
189C LEU* 3.5 6.6 - - - +
190C VAL* 1.3 99.0 - - + +
192C PRO* 1.3 80.8 - - + +
193C LEU* 3.9 10.3 - - + -
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Residues in contact with PRO 192 (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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61A LYS* 2.6 37.4 + - - +
60C ALA* 4.4 15.3 - - + -
108C ARG* 3.4 45.5 - - - +
109C LYS 3.4 7.4 - - - +
110C GLY* 3.7 2.0 - - - -
189C LEU* 4.0 14.3 - - + -
191C PHE* 1.3 91.0 - - + +
193C LEU* 1.3 63.9 + - - +
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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