Contacts of the strand formed by residues 183 - 187 (chain F) in PDB entry 1KQN
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F LEU* 3.2 44.4 - - + +
155F CYS* 4.3 15.0 - - - -
160F LEU* 3.7 31.9 - - + -
163F PHE* 4.0 17.0 - - + -
177F ILE* 3.8 14.1 - - + -
178F VAL* 4.2 14.1 - - + -
182F GLY* 1.3 74.1 - - - -
184F ILE* 1.3 63.5 + - - +
185F CYS* 3.8 2.9 - - + +
209F ASN 3.1 6.1 + - - +
210F ILE* 3.3 16.1 - - + +
211F HIS* 2.8 31.2 + - - -
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Residues in contact with ILE 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F LEU* 3.4 29.6 - - + -
31F ALA* 3.8 24.2 - - + -
35F MET* 3.3 44.0 - - + -
152F LYS* 4.2 14.6 - - + -
153F LEU 2.9 9.5 + - - +
154F LEU* 3.6 6.4 - - + +
155F CYS 3.0 26.5 + - - +
183F LEU* 1.3 76.4 - - - +
185F CYS* 1.3 58.5 + - - +
186F VAL* 3.9 2.9 + - + -
211F HIS* 3.3 10.5 - - + +
213F VAL* 3.8 22.4 - - + -
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Residues in contact with CYS 185 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F CYS* 3.3 13.7 - - - -
156F GLY 3.6 5.4 - - - -
157F ALA* 3.6 37.5 - - - -
160F LEU* 4.2 22.2 - - + -
183F LEU* 3.8 6.5 - - + -
184F ILE* 1.3 72.9 - - - +
186F VAL* 1.3 63.2 + - - +
187F THR* 3.9 0.8 + - - -
193F ALA* 4.6 9.4 - - - -
210F ILE* 5.4 2.7 - - + -
211F HIS 2.8 11.2 + - - +
212F VAL* 3.3 11.7 - - + +
213F VAL* 2.8 24.3 + - - +
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Residues in contact with VAL 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F LEU* 3.5 47.1 - - + +
30F LEU* 4.1 25.1 - - + -
31F ALA* 4.6 5.4 - - + +
154F LEU* 4.3 8.1 - - + -
155F CYS 2.8 11.1 + - - +
156F GLY* 3.3 21.1 - - - -
157F ALA 3.5 1.4 + - - -
184F ILE 4.9 1.1 - - - +
185F CYS* 1.3 71.5 - - - +
187F THR* 1.3 71.1 + - - +
213F VAL* 3.3 27.6 - - + +
215F GLU* 4.1 11.4 - - + +
756F XE 4.6 0.2 - - - -
782F NAD 3.6 5.2 - - - -
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Residues in contact with THR 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F ALA* 3.4 22.7 - - - +
185F CYS* 4.6 1.8 - - - +
186F VAL* 1.3 81.3 - - - +
188F ARG* 1.3 62.2 + - - +
189F ALA* 3.1 34.2 + - - +
190F GLY* 3.6 11.1 + - - -
193F ALA* 4.2 7.4 - - + -
212F VAL* 4.1 15.7 - - + -
213F VAL 3.0 5.8 + - - +
214F ASN* 3.4 7.2 - - - +
215F GLU* 2.8 36.3 + - - -
782F NAD 4.9 1.1 - - - -
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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