Contacts of the strand formed by residues 181 - 186 (chain E) in PDB entry 5LK5
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 181 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E VAL* 3.8 0.7 - - - -
177E ARG* 2.9 53.8 + - - +
179E ASP* 2.5 33.5 + - - +
180E ASN* 1.3 83.8 - - - +
182E TYR* 1.3 63.2 + - - +
194E GLY 3.3 8.5 - - - +
195E SER* 3.9 10.3 - - - +
196E LEU* 4.2 2.6 - - - +
198J ASP* 3.9 21.3 - - + +
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Residues in contact with TYR 182 (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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146E VAL* 5.5 0.4 - - + -
148E PHE* 5.6 1.1 - - + -
157E ILE* 3.5 22.9 - - + +
159E LYS* 3.5 13.2 - - - +
174E LEU* 4.6 5.8 - - + -
175E ILE 3.0 13.9 - - - +
176E VAL* 4.6 7.2 - - + -
177E ARG* 4.3 7.2 + - - +
181E THR* 1.3 77.0 - - - +
183E GLU* 1.3 71.4 + - - +
184E VAL* 4.1 17.5 - - + -
192E GLU* 3.8 6.2 - - + +
193E SER* 3.4 16.1 + - - -
194E GLY 2.9 48.4 + - - +
195E SER 3.8 5.2 - - - -
196E LEU* 4.1 9.6 - - + -
199E ASP* 2.5 32.8 + - - -
200E TRP* 3.4 28.7 - + + -
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Residues in contact with GLU 183 (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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173E THR 3.9 0.5 - - - +
174E LEU* 3.7 2.8 - - - +
175E ILE* 2.9 49.6 + - + +
177E ARG* 2.9 27.0 + - - +
182E TYR* 1.3 78.0 - - - +
184E VAL* 1.3 70.4 + - - +
185E LYS* 3.6 27.7 + - + -
190E GLN* 3.0 39.8 + - + +
192E GLU 3.4 9.4 - - - +
193E SER* 4.4 3.0 - - - -
336E GLU* 4.4 2.4 - - - +
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Residues in contact with VAL 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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132E PHE* 4.0 14.8 - - + -
144E VAL* 4.5 11.4 - - + -
146E VAL* 4.0 19.3 - - + -
161E ILE* 4.2 9.2 - - + -
173E THR 3.4 8.1 - - - +
174E LEU* 4.0 18.4 - - + -
182E TYR* 4.1 13.7 - - + -
183E GLU* 1.3 77.5 - - - +
185E LYS* 1.3 70.4 + - - +
186E ILE* 5.0 2.7 - - + -
190E GLN* 3.6 2.8 - - - +
191E VAL* 2.9 38.2 + - + +
192E GLU* 2.8 23.9 + - + +
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Residues in contact with LYS 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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171E LEU 3.7 0.4 - - - +
172E TYR* 3.6 2.4 - - - +
173E THR* 2.9 59.2 + - + +
175E ILE* 4.4 15.7 - - + +
183E GLU* 3.6 23.2 + - + +
184E VAL* 1.3 82.2 - - - +
186E ILE* 1.3 67.3 + - - +
187E ASP 4.3 0.2 - - - -
188E ASN* 4.3 26.9 + - - +
189E SER 3.4 12.1 - - - +
190E GLN* 3.9 15.7 - - - +
191E VAL* 4.4 0.2 - - - -
336E GLU* 5.3 7.1 + - - +
340E GLU* 3.7 24.7 + - - +
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Residues in contact with ILE 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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144E VAL* 4.2 6.1 - - + -
162E ARG 3.5 24.9 - - - +
163E CYS* 4.4 3.1 - - - -
164E LYS* 3.9 37.9 - - + +
170E HIS* 4.7 0.9 - - + -
171E LEU 3.2 7.6 - - - +
172E TYR* 3.8 30.7 - - + -
184E VAL* 5.0 2.2 - - + -
185E LYS* 1.3 75.9 - - - +
187E ASP* 1.3 76.8 + - - +
188E ASN 3.2 1.1 - - - -
189E SER* 3.0 21.7 + - - +
191E VAL* 4.0 32.4 - - + +
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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