Contacts of the strand formed by residues 184 - 192 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ALA 3.5 6.7 - - - -
67A ILE* 4.1 7.2 - - + -
86A PHE* 3.8 4.8 - - - -
115A ASN 5.8 0.2 - - - -
116A PHE* 3.2 4.8 - - - +
117A HIS* 2.6 51.8 + - - +
182A TYR 3.6 4.0 - - - +
183A SER* 1.3 80.9 - - - +
185A PHE* 1.3 62.4 + - - +
186A SER* 5.7 1.3 + - - -
139C ILE* 3.7 23.6 - - + -
155C ASN* 2.8 40.8 + - - +
156C GLY 3.7 9.8 + - - -
157C VAL* 5.6 2.2 - - - -
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Residues in contact with PHE 185 (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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64A PHE* 3.8 32.9 - + - -
65A SER* 3.7 0.7 - - - -
66A ALA* 2.8 36.4 + - + +
86A PHE* 3.5 31.0 - + + -
97A PHE* 4.4 9.0 - + - -
102A SER 4.5 7.9 - - - -
114A PHE* 4.1 19.1 - + + -
115A ASN 3.3 13.0 - - - -
116A PHE* 3.9 8.3 - + + -
131A LEU* 4.2 13.7 - - + -
167A ALA 4.6 4.5 - - - -
168A TYR* 4.2 17.5 - - - -
169A LEU* 3.8 33.7 - - + -
184A THR* 1.3 75.5 - - - +
186A SER* 1.3 65.7 + - - +
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Residues in contact with SER 186 (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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64A PHE* 3.4 17.3 - - - -
65A SER* 3.5 23.6 - - - -
114A PHE* 3.6 1.9 - - - -
115A ASN* 2.9 45.4 + - - +
184A THR* 5.7 1.2 + - - -
185A PHE* 1.3 78.3 + - - +
187A GLY* 1.3 58.8 - - - +
156C GLY 4.3 5.2 + - - -
157C VAL* 4.2 13.1 + - - -
158C LEU* 4.4 12.0 + - - +
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Residues in contact with GLY 187 (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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64A PHE* 2.8 53.0 + - - +
104A PHE* 5.9 0.4 - - - -
113A SER 3.0 15.7 - - - -
114A PHE* 4.2 1.3 - - - -
115A ASN* 6.0 0.7 - - - -
186A SER* 1.3 75.9 - - - +
188A PHE* 1.3 68.4 + - - +
158C LEU* 3.5 2.5 - - - +
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Residues in contact with PHE 188 (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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62A VAL* 3.2 15.0 - - - +
63A ALA* 3.6 12.3 - - + +
64A PHE* 5.4 0.2 - - - -
104A PHE* 5.9 0.9 - - - -
112A TYR* 3.5 9.3 - - - -
113A SER* 2.9 54.7 + - - -
114A PHE* 5.5 0.4 - - - -
115A ASN* 5.5 3.4 - - - -
187A GLY* 1.3 80.4 - - - +
189A LEU* 1.3 70.9 + - - +
190A VAL* 3.4 21.0 + - + -
188B PHE* 4.1 23.6 - + - -
113C SER* 5.2 2.7 - - - -
158C LEU* 3.9 22.4 - - + -
188C PHE* 4.2 17.0 - + - -
190C VAL* 3.7 23.8 - - + -
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Residues in contact with LEU 189 (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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60A ALA* 3.7 32.0 - - - +
62A VAL* 2.8 30.2 + - + +
108A ARG* 4.2 22.9 - - + -
109A LYS 5.2 0.4 - - - +
110A GLY* 4.0 6.5 - - - -
111A ILE 3.5 9.0 - - - +
112A TYR* 3.6 39.4 - - + +
188A PHE* 1.3 76.9 - - - +
190A VAL* 1.3 63.7 + - - +
191A PHE* 3.5 27.8 - - - +
192A PRO* 4.2 13.2 - - + -
190C VAL* 5.2 3.3 - - - +
191C PHE* 5.7 2.6 - - - -
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Residues in contact with VAL 190 (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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111A ILE* 2.8 25.1 + - + +
112A TYR 4.2 0.4 - - - -
113A SER* 3.9 24.9 - - - +
158A LEU* 4.0 12.8 - - + -
188A PHE* 3.9 19.7 - - + -
189A LEU* 1.3 73.7 - - - +
191A PHE* 1.3 83.0 + - + +
63B ALA* 5.1 1.1 - - + -
188B PHE* 3.8 33.0 - - + -
189B LEU 5.3 1.8 - - - +
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Residues in contact with PHE 191 (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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60A ALA 6.1 0.2 - - - -
111A ILE* 2.9 49.7 + - + -
189A LEU* 3.5 6.9 - - - +
190A VAL* 1.3 96.9 - - + +
192A PRO* 1.3 80.7 - - + +
193A LEU* 3.9 11.7 - - + -
60B ALA 5.4 0.9 - - - -
61B LYS* 3.8 35.0 - - + -
62B VAL 3.9 14.8 - - - -
63B ALA* 3.8 30.7 - - + -
93B ILE* 3.9 21.5 - - + -
189B LEU 5.9 1.8 - - - -
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Residues in contact with PRO 192 (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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60A ALA* 4.5 16.2 - - + -
108A ARG* 3.4 44.6 - - - +
109A LYS 3.5 7.4 - - - +
110A GLY* 3.7 2.2 - - - -
189A LEU* 4.0 13.0 - - + -
191A PHE* 1.3 91.9 - - + +
193A LEU* 1.3 65.8 + - - +
61B LYS* 2.7 37.2 + - - +
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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