Contacts of the strand formed by residues 183 - 187 (chain A) in PDB entry 1KKU
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 LEU 183 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 3.4 33.7 - - + +
155A CYS* 4.3 14.1 - - - -
159A LEU* 4.3 7.4 - - + -
160A LEU* 4.0 20.0 - - + -
163A PHE* 4.0 24.5 - - + -
177A ILE* 3.9 15.7 - - + -
178A VAL* 4.9 11.1 + - + -
182A GLY* 1.3 81.9 - - - +
184A ILE* 1.3 62.8 + - - +
185A CYS* 3.9 2.2 - - + +
203A LEU* 5.1 0.2 - - + -
209A ASN 3.1 8.7 + - - +
210A ILE* 3.3 23.8 - - + +
211A HIS* 2.8 32.4 + - - +
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Residues in contact with ILE 184 (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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9A VAL* 5.0 0.4 - - + -
11A LEU* 3.5 31.2 - - + -
31A ALA* 4.0 14.4 - - + -
35A MET* 3.8 34.1 - - + -
152A LYS* 4.1 16.8 - - + -
153A LEU 2.8 12.8 + - - +
154A LEU* 3.3 23.4 - - + +
155A CYS* 3.0 27.9 + - - +
183A LEU* 1.3 77.0 - - - +
185A CYS* 1.3 59.3 + - - +
186A VAL* 4.8 0.9 - - + -
211A HIS* 3.6 12.1 - - + +
213A VAL* 4.1 19.3 - - + -
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Residues in contact with CYS 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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155A CYS* 3.4 11.7 - - - -
156A GLY 3.4 32.5 - - - -
157A ALA* 3.6 10.1 - - - -
160A LEU* 3.9 21.5 - - + -
183A LEU* 3.9 2.0 - - + -
184A ILE* 1.3 70.2 - - - +
186A VAL* 1.3 57.9 + - - +
187A THR* 3.8 13.6 + - - +
193A ALA* 4.4 4.0 - - - -
210A ILE* 5.2 5.4 - - + -
211A HIS 2.9 13.4 + - - +
212A VAL* 3.5 9.2 - - + -
213A VAL* 2.6 33.3 + - - +
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Residues in contact with VAL 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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27A LEU* 3.3 42.1 - - + +
30A LEU* 3.8 26.7 - - + -
31A ALA* 3.9 29.2 - - + +
154A LEU* 4.1 9.9 - - + -
155A CYS 3.1 8.1 + - - +
156A GLY* 3.6 14.6 - - - -
184A ILE* 3.7 0.6 + - + -
185A CYS* 1.3 71.6 - - - +
187A THR* 1.3 69.5 + - - +
213A VAL* 3.4 22.9 - - + +
215A GLU* 4.6 4.3 - - + -
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Residues in contact with THR 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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27A LEU* 5.8 0.4 - - - -
156A GLY* 5.0 0.2 - - - -
157A ALA* 4.3 19.5 - - + +
185A CYS* 4.2 11.7 - - - +
186A VAL* 1.3 80.8 - - - +
188A ARG* 1.3 67.5 + - - +
189A ALA* 2.8 19.6 + - - +
190A GLY* 3.8 23.6 - - - -
193A ALA* 4.1 15.0 - - + -
212A VAL* 4.6 1.6 - - + -
213A VAL 2.8 16.1 + - - +
214A ASN* 3.5 5.7 - - - +
215A GLU* 2.9 25.3 + - - -
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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