Contacts of the strand formed by residues 181 - 186 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176G VAL* 3.7 0.9 - - - -
177G ARG* 2.9 53.6 + - - +
179G ASP* 2.5 34.9 + - - +
180G ASN* 1.3 81.9 - - - +
182G TYR* 1.3 64.1 + - - +
194G GLY 3.3 9.2 - - - +
195G SER* 3.9 15.7 - - - +
196G LEU* 4.2 2.4 - - - +
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Residues in contact with TYR 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146G VAL* 5.4 0.2 - - + -
148G PHE* 5.7 0.4 - - + -
157G ILE* 3.5 28.7 - - + +
159G LYS* 3.8 1.0 + - - +
174G LEU* 4.6 6.3 - - + -
175G ILE 3.0 14.8 - - - +
176G VAL* 4.6 7.6 - - + -
177G ARG* 4.3 6.6 + - - +
181G THR* 1.3 76.6 - - - +
183G GLU* 1.3 69.4 + - - +
184G VAL* 4.1 17.7 - - + -
192G GLU* 3.8 11.8 - - + +
193G SER* 3.4 18.4 + - - -
194G GLY 2.9 49.2 + - - +
195G SER 3.8 4.3 - - - -
196G LEU* 4.2 9.6 - - + -
199G ASP* 2.5 32.3 + - - -
200G TRP* 3.5 29.6 - + + -
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Residues in contact with GLU 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173G THR 3.9 0.7 - - - +
174G LEU* 3.7 2.8 - - - +
175G ILE* 2.8 46.0 + - + +
177G ARG* 2.8 30.5 + - - +
182G TYR* 1.3 76.9 - - - +
184G VAL* 1.3 72.9 + - - +
185G LYS* 3.7 27.3 - - + -
190G GLN* 3.0 39.4 + - + +
192G GLU 3.4 9.0 - - - +
193G SER* 4.4 2.8 - - - -
336G GLU* 4.4 2.2 - - - +
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Residues in contact with VAL 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G PHE* 4.0 14.4 - - + -
144G VAL* 4.5 11.4 - - + -
146G VAL* 4.0 19.1 - - + -
161G ILE* 4.2 9.2 - - + -
172G TYR* 5.8 0.4 - - + -
173G THR 3.4 7.9 - - - +
174G LEU* 4.0 19.3 - - + -
182G TYR* 4.1 13.9 - - + -
183G GLU* 1.3 78.5 - - - +
185G LYS* 1.3 69.1 + - - +
186G ILE* 5.0 2.7 - - + -
190G GLN* 3.6 2.8 - - - -
191G VAL* 2.8 38.1 + - + +
192G GLU* 2.8 22.9 + - + +
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Residues in contact with LYS 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171G LEU 3.7 0.4 - - - +
172G TYR* 3.6 3.3 - - - -
173G THR* 2.9 59.6 + - + +
175G ILE* 4.3 16.4 - - + +
183G GLU* 3.7 23.6 + - + +
184G VAL* 1.3 81.6 - - - +
186G ILE* 1.3 67.3 + - - +
188G ASN* 4.3 26.5 + - - +
189G SER 3.4 11.9 - - - +
190G GLN* 3.9 15.0 - - - +
336G GLU* 5.2 7.5 + - - +
340G GLU* 4.0 24.9 + - - +
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Residues in contact with ILE 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G VAL* 4.2 6.1 - - + -
162G ARG 3.5 25.4 - - - +
163G CYS* 4.4 2.9 - - - -
164G LYS* 3.9 36.3 - - + +
170G HIS* 4.7 0.9 - - + -
171G LEU 3.2 7.6 - - - +
172G TYR* 3.7 29.4 - - + -
184G VAL* 5.0 2.2 - - + -
185G LYS* 1.3 77.9 - - - +
187G ASP* 1.3 78.9 + - - +
188G ASN 3.2 0.9 - - - -
189G SER* 3.0 21.9 + - - +
191G VAL* 4.0 30.2 - - + +
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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