Contacts of the strand formed by residues 184 - 192 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A ILE* 3.8 23.1 - - + -
155A ASN* 2.8 38.6 + - - +
156A GLY 3.6 9.7 + - - +
157A VAL* 5.3 2.7 - - + -
66B ALA 3.6 6.3 - - - -
67B ILE* 4.1 6.7 - - + -
86B PHE* 3.8 5.6 - - - -
115B ASN 4.6 0.2 - - - -
116B PHE* 3.1 6.6 - - - +
117B HIS* 2.7 51.6 + - - +
169B LEU* 4.7 0.2 - - - +
182B TYR 3.6 3.6 - - - +
183B SER* 1.3 79.7 - - - +
185B PHE* 1.3 62.5 + - - +
186B SER* 5.8 0.7 - - - -
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Residues in contact with PHE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B PHE* 3.8 34.4 - + - -
65B SER* 3.7 0.9 - - - -
66B ALA* 2.9 32.5 + - + +
86B PHE* 3.4 38.1 - + + -
97B PHE* 4.4 12.3 - + - -
102B SER 4.5 3.8 - - - -
114B PHE* 4.0 20.4 - + + -
115B ASN 3.5 10.3 - - - -
116B PHE* 4.0 2.7 - + + -
131B LEU* 4.2 8.5 - - + -
167B ALA 4.5 4.0 - - - -
168B TYR* 4.0 23.1 - - - -
169B LEU* 3.6 35.9 - - + -
184B THR* 1.3 75.1 - - - +
186B SER* 1.3 66.4 + - - +
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Residues in contact with SER 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A GLY 4.6 4.0 + - - -
157A VAL* 4.4 11.9 + - - -
158A LEU* 4.1 14.1 - - - +
64B PHE* 3.4 15.5 - - - -
65B SER* 3.4 22.7 - - - -
114B PHE* 3.5 3.6 - - - -
115B ASN* 2.8 46.1 + - - +
184B THR* 5.8 0.8 - - - -
185B PHE* 1.3 78.9 + - - +
187B GLY* 1.3 58.7 + - - +
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Residues in contact with GLY 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LEU* 3.5 2.8 - - - +
63B ALA* 3.4 0.3 - - - -
64B PHE* 2.8 50.7 + - - +
104B PHE* 6.0 0.4 - - - -
113B SER 3.0 15.7 - - - -
114B PHE* 4.1 2.5 - - - -
115B ASN* 6.1 0.2 - - - -
186B SER* 1.3 76.3 - - - +
188B PHE* 1.3 69.7 + - - +
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Residues in contact with PHE 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A SER* 5.2 2.2 - - - -
158A LEU* 3.9 24.2 - - + -
188A PHE* 4.1 25.6 - + - -
190A VAL* 3.8 21.8 - - + -
62B VAL* 3.2 14.8 - - - +
63B ALA* 3.5 13.2 - - + +
104B PHE* 6.0 1.1 - - - -
112B TYR* 3.4 9.6 - - - +
113B SER* 2.9 54.5 + - - -
114B PHE* 5.5 0.2 - - - -
115B ASN* 5.4 4.3 - - - -
187B GLY* 1.3 79.5 - - - +
189B LEU* 1.3 70.5 + - - +
190B VAL* 3.4 20.4 + - + -
188C PHE* 4.1 16.4 - + - -
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Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A VAL* 5.3 2.4 - - - +
191A PHE* 5.9 1.9 - - - -
60B ALA* 3.6 34.9 - - - +
62B VAL* 2.8 28.1 + - + +
108B ARG* 4.2 24.0 - - + -
109B LYS 5.2 0.2 - - - +
110B GLY* 3.9 7.4 - - - -
111B ILE 3.6 8.5 - - - +
112B TYR* 3.6 39.0 - - + +
188B PHE* 1.3 78.0 - - - +
190B VAL* 1.3 63.6 + - - +
191B PHE* 3.4 27.6 - - - +
192B PRO* 4.2 11.0 - - + -
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ILE* 2.7 24.2 + - + +
112B TYR 4.1 0.4 - - - -
113B SER* 3.7 31.9 - - - +
158B LEU* 3.9 13.2 - - + -
188B PHE* 4.0 12.8 - - + -
189B LEU* 1.3 74.3 - - - +
191B PHE* 1.3 83.3 + - + +
188C PHE* 3.7 34.1 - - + -
189C LEU 5.2 2.2 - - - +
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Residues in contact with PHE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ALA 6.1 0.2 - - - -
110B GLY* 3.4 0.3 - - - -
111B ILE* 2.8 55.5 + - + -
189B LEU* 3.4 6.5 - - - +
190B VAL* 1.3 95.3 - - + +
192B PRO* 1.3 80.6 - - + +
193B LEU* 3.8 12.6 - - + -
60C ALA 5.1 2.0 - - - -
61C LYS* 3.8 33.9 - - + -
62C VAL 3.7 14.6 - - - -
63C ALA* 3.7 28.5 - - + -
93C ILE* 3.8 21.5 - - + -
189C LEU 5.8 2.2 - - - -
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Residues in contact with PRO 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B ALA* 4.4 15.7 - - + +
108B ARG* 3.4 46.9 - - - +
109B LYS 3.6 6.3 - - - +
110B GLY* 3.8 2.7 - - - -
189B LEU* 4.0 11.4 - - + -
191B PHE* 1.3 92.0 - - + +
193B LEU* 1.3 69.3 + - - +
61C LYS* 2.8 31.3 + - - +
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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