Contacts of the strand formed by residues 191 - 196 (chain F) in PDB entry 5IJ7
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 191 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F PHE* 3.5 5.9 - - - -
185F HIS* 2.9 62.9 + - + +
188F ASP* 3.3 28.0 + - + +
190F ASN* 1.3 76.8 - - - +
192F LEU* 1.3 59.5 + - - +
203F LEU* 4.0 15.7 - - + -
204F TRP 3.4 9.9 - - - +
205F ASN* 4.1 25.4 - - + +
212F VAL* 4.5 9.2 - - + -
230F TYR* 3.6 2.9 + - - -
260F ILE* 3.9 37.9 - - + -
264F TYR* 4.8 0.2 - - - +
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Residues in contact with LEU 192 (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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150F ALA* 4.4 0.9 - - + -
158F ILE* 3.7 39.9 - - + -
160F ILE* 4.0 9.0 - - + -
182F LEU* 3.8 23.3 - - + -
183F LYS 3.6 16.8 - - - +
184F PHE* 3.7 35.4 - - + -
190F ASN 3.6 0.6 + - - -
191F LEU* 1.3 73.4 - - - +
193F LEU* 1.3 62.1 + - - +
202F ARG 3.4 2.6 - - - +
203F LEU* 3.5 1.9 - - - -
204F TRP* 2.8 40.7 + - + +
206F ILE* 3.7 26.7 - - + -
230F TYR* 4.2 2.0 - - - -
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Residues in contact with LEU 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181F GLU 3.9 0.5 - - - +
182F LEU* 3.2 5.4 - - - -
183F LYS* 2.8 45.3 + - + +
192F LEU* 1.3 74.9 - - - +
194F SER* 1.3 61.1 + - - +
195F VAL* 4.6 3.3 - - + +
201F LEU* 4.1 25.6 - - + -
202F ARG 3.3 19.1 - - - +
203F LEU* 4.5 2.9 - - + +
215F PHE* 4.4 6.5 - - + -
228F ALA* 3.9 16.4 - - + -
229F ASP 5.0 1.6 - - - +
230F TYR* 3.4 23.9 + - + +
237F ILE* 3.6 49.6 - - + -
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Residues in contact with SER 194 (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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158F ILE* 3.8 13.5 - - - -
175F HIS* 2.7 33.5 - - - -
179F ILE* 4.1 3.8 - - - -
181F GLU 3.4 4.9 - - - -
182F LEU* 3.8 20.0 - - - -
192F LEU 4.1 0.4 + - - -
193F LEU* 1.3 74.9 - - - +
195F VAL* 1.3 62.5 + - - +
201F LEU* 3.3 5.0 - - - +
202F ARG 2.8 30.7 + - - -
204F TRP* 2.9 16.4 + - - -
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Residues in contact with VAL 195 (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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179F ILE* 3.4 4.1 - - - -
180F ASN* 2.8 27.2 + - - +
181F GLU* 2.8 26.6 + - + +
183F LYS* 6.2 0.9 - - + -
193F LEU* 4.6 5.2 - - + +
194F SER* 1.3 75.5 - - - +
196F SER* 1.3 60.4 + - - +
200F ALA 4.0 2.7 - - - -
201F LEU* 3.4 23.3 - - + +
225F VAL* 3.3 44.2 - - + +
226F LEU 4.0 2.7 - - - +
227F SER 3.8 12.1 - - - +
228F ALA* 3.4 19.5 - - + -
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Residues in contact with SER 196 (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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175F HIS* 3.1 33.1 + - - -
177F ASN 3.4 9.2 + - - -
178F ALA 2.9 14.1 + - - -
179F ILE* 4.6 0.7 - - - -
195F VAL* 1.3 75.8 - - - +
197F LYS* 1.4 70.0 + - - +
198F ASP* 2.9 27.5 + - - +
199F HIS 3.2 7.8 + - - -
200F ALA 2.9 10.9 + - - -
225F VAL* 3.0 29.0 + - - +
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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