Contacts of the strand formed by residues 183 - 187 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153E LEU* 3.3 43.1 - - + -
155E CYS* 4.1 15.9 - - - -
159E LEU* 5.1 0.4 - - + -
160E LEU* 3.7 30.1 - - + -
163E PHE* 4.0 19.5 - - + -
177E ILE* 4.3 8.5 - - + -
178E VAL* 4.2 17.7 - - + -
182E GLY* 1.3 74.1 - - - -
184E ILE* 1.3 68.1 + - - +
185E CYS* 3.8 3.1 - - + +
209E ASN 3.1 7.3 + - - +
210E ILE* 3.3 18.3 - - + +
211E HIS* 2.8 27.8 + - - +
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Residues in contact with ILE 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LEU* 3.3 32.8 - - + -
31E ALA* 3.9 20.6 - - + -
35E MET* 3.4 38.6 - - + -
152E LYS* 4.0 12.8 - - + -
153E LEU 2.8 11.7 + - - +
154E LEU* 3.2 10.6 - - + +
155E CYS* 2.9 27.1 + - - -
182E GLY 5.5 0.2 - - - -
183E LEU* 1.3 76.9 - - - +
185E CYS* 1.3 59.3 + - - +
186E VAL* 4.0 0.7 - - + -
211E HIS* 3.4 13.2 - - + +
213E VAL* 3.8 25.1 - - + -
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Residues in contact with CYS 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E CYS* 3.4 10.8 - - - -
156E GLY 3.7 6.1 - - - -
157E ALA* 3.7 37.0 - - - -
160E LEU* 4.0 25.6 - - + -
183E LEU* 3.8 5.4 - - + -
184E ILE* 1.3 71.0 - - - +
186E VAL* 1.3 62.6 + - - +
187E THR* 3.9 0.8 + - - -
193E ALA* 4.4 9.0 - - - -
210E ILE* 5.4 2.9 - - + -
211E HIS 2.8 12.8 + - - +
212E VAL* 3.4 12.0 - - + +
213E VAL* 2.8 25.9 + - - +
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Residues in contact with VAL 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E LEU* 3.4 50.3 - - + +
30E LEU* 3.8 24.5 - - + -
31E ALA* 4.3 10.5 - - + +
154E LEU* 4.2 12.3 - - + -
155E CYS 2.8 6.9 + - - -
156E GLY* 3.1 23.9 - - - -
157E ALA 3.4 0.9 + - - -
184E ILE* 5.0 0.4 - - + +
185E CYS* 1.3 72.8 - - - +
187E THR* 1.3 70.6 + - - +
213E VAL* 3.3 24.5 - - + +
215E GLU* 4.3 6.3 - - + -
758E XE 4.5 0.7 - - - -
781E NAD 3.4 5.1 - - + -
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Residues in contact with THR 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E ALA* 3.4 23.6 - - + +
185E CYS* 4.2 2.5 - - - +
186E VAL* 1.3 82.4 - - - +
188E ARG* 1.3 63.8 + - - +
189E ALA* 2.9 30.9 + - - +
190E GLY* 4.1 4.5 + - - +
193E ALA* 4.2 8.1 - - + -
212E VAL* 4.2 19.7 - - + -
213E VAL 3.1 10.9 + - - +
214E ASN* 3.6 4.5 - - - +
215E GLU* 3.0 23.3 + - - -
781E NAD 4.4 8.1 - - - -
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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