Contacts of the strand formed by residues 179 - 186 (chain B) in PDB entry 1K86
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 LYS 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137B PHE* 3.5 9.0 - - + -
166B PHE* 3.3 33.4 - - + +
168B GLY* 5.0 4.9 - - - +
174B LEU* 2.8 40.9 + - + +
175B LEU* 4.6 1.8 - - - +
176B GLU 4.6 2.6 - - - +
177B LYS 2.7 28.4 + - - +
178B PRO* 1.3 71.8 - - - +
180B LEU* 1.3 62.3 + - - +
181B PHE* 3.8 19.2 - - + -
216B GLU* 5.5 0.7 - - - -
217B ALA 4.1 4.4 + - - -
218B ASP* 2.8 18.4 + - - +
219B PHE* 3.3 37.5 - - + -
220B LEU 3.1 24.4 + - - +
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Residues in contact with LEU 180 (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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101B PHE* 6.1 0.2 - - + -
106B PHE* 4.7 0.9 - - + -
136B CYS* 4.5 12.3 - - - -
137B PHE 2.7 18.0 + - - +
138B ALA* 3.2 9.6 - - + -
139B CYS* 2.7 32.2 + - - +
178B PRO* 3.8 21.3 - - + -
179B LYS* 1.3 78.1 - - - +
181B PHE* 1.3 63.0 + - - +
182B PHE* 3.7 25.4 - - + -
220B LEU* 3.7 25.4 - - + +
258B ILE* 5.3 2.5 - - + -
295B LEU* 4.8 2.2 - - + -
299B LEU* 3.8 24.5 - - + -
301B PHE* 4.3 20.4 - - + -
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Residues in contact with PHE 181 (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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123B LEU* 5.5 2.2 - - + -
137B PHE* 4.2 9.9 - + - -
139B CYS* 3.3 37.2 - - + +
141B LEU* 5.4 4.0 - - + -
162B LEU 5.1 0.7 - - - -
163B THR* 3.3 36.6 - - + -
166B PHE* 4.0 25.6 - + - -
179B LYS* 3.8 20.2 - - + -
180B LEU* 1.3 74.8 - - - +
182B PHE* 1.3 63.8 + - - +
183B ILE* 3.8 7.4 + - + +
219B PHE* 3.7 25.1 - + - -
220B LEU* 2.9 11.9 + - - +
221B PHE* 3.3 30.1 - + + +
222B ALA 2.9 24.7 + - - +
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Residues in contact with PHE 182 (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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101B PHE* 3.7 28.0 - + - -
138B ALA* 4.3 3.4 - - + -
139B CYS 2.8 18.2 + - - +
140B ILE* 3.2 27.7 - - + +
141B LEU* 3.0 24.8 + - - +
180B LEU* 3.7 36.1 - - + -
181B PHE* 1.3 73.2 - - - +
183B ILE* 1.3 62.6 + - - +
184B GLN 4.2 0.2 - - - -
220B LEU* 5.1 4.0 - - + -
222B ALA* 3.6 20.6 - - + +
241B PHE* 5.0 5.2 - + + -
245B LEU* 4.0 31.2 - - + -
249B LEU* 6.2 0.4 - - + -
258B ILE* 5.5 4.5 - - + -
262B LEU* 4.3 22.9 - - + -
301B PHE* 5.5 5.6 - + - -
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Residues in contact with ILE 183 (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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141B LEU* 3.7 28.0 - - + +
150B ILE* 5.3 1.3 - - + -
159B ILE* 4.0 33.0 - - + -
181B PHE* 4.2 10.8 - - + +
182B PHE* 1.3 78.1 - - - +
184B GLN* 1.3 60.4 + - - +
185B ALA* 4.0 21.3 + - + +
221B PHE* 4.1 16.8 - - + -
222B ALA 2.7 14.1 + - - +
223B TYR* 3.3 34.6 - - + -
224B SER* 2.9 26.7 + - - -
241B PHE* 4.5 4.0 - - - -
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Residues in contact with GLN 184 (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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87B ARG* 4.0 15.5 + - - +
93B ASP* 5.0 2.7 - - - +
140B ILE* 6.1 0.2 - - + -
141B LEU 2.9 17.8 + - - +
142B LEU* 3.5 19.4 - - + -
143B SER 3.3 15.9 + - - +
182B PHE 4.2 0.4 - - - -
183B ILE* 1.3 71.6 - - - +
185B ALA* 1.3 58.2 + - - +
186B CYS* 3.7 12.7 - - - -
224B SER* 3.2 21.1 + - - -
231B SER* 2.8 36.3 + - - -
233B ARG* 5.5 1.4 - - - +
239B SER* 2.8 36.1 + - - +
241B PHE* 3.5 13.0 - - + +
242B VAL* 3.9 8.5 - - + +
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Residues in contact with ALA 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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87B ARG* 5.5 0.2 - - - +
143B SER 3.2 14.1 - - - +
144B HIS 4.0 2.2 - - - +
145B GLY* 3.8 22.3 - - - +
150B ILE* 4.6 9.0 - - + -
159B ILE* 6.1 1.8 - - + -
183B ILE* 3.8 18.8 + - + +
184B GLN* 1.3 76.5 - - - +
186B CYS* 1.3 68.1 + - - +
224B SER* 3.6 10.6 + - - -
225B THR* 4.2 6.9 + - - -
229B TYR 5.6 0.5 - - - +
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Residues in contact with CYS 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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87B ARG* 5.6 2.1 - - - +
143B SER 3.6 5.3 + - - -
144B HIS* 3.3 11.8 + - + +
145B GLY 2.6 29.1 + - - -
184B GLN* 3.7 7.4 - - - -
185B ALA* 1.3 77.7 - - - +
187B ARG* 1.3 66.1 + - - +
229B TYR 5.3 1.3 - - - -
230B TYR* 3.6 28.5 - - + +
231B SER* 3.1 54.7 - - - +
233B ARG* 5.9 2.9 - - - -
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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