Contacts of the strand formed by residues 190 - 198 (chain F) in PDB entry 6PI7
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 TYR 190 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44F PRO* 6.0 1.4 - - - +
94F THR* 5.7 4.9 - - - +
158F ASP* 2.9 23.9 + - - -
159F TYR* 2.8 46.4 + - + +
160F PHE* 3.8 30.3 - + - -
161F PRO* 4.7 0.2 - - + -
162F GLU* 3.5 51.0 - - + +
182F ALA* 3.9 9.9 - - + -
183F VAL 3.4 15.3 - - - -
184F LEU* 4.0 33.3 - - + +
185F GLN* 3.9 0.2 - - - -
189F LEU* 1.3 73.0 - - - +
191F SER* 1.3 59.8 + - - +
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Residues in contact with SER 191 (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 LEU* 5.2 4.7 - - - -
156F VAL 3.2 13.0 - - - -
157F LYS* 4.0 14.4 - - - -
159F TYR* 4.1 3.4 - - - -
182F ALA* 3.4 1.6 - - - -
183F VAL* 2.9 41.7 + - - +
185F GLN* 3.7 25.1 - - - -
190F TYR* 1.3 74.5 - - - +
192F LEU* 1.3 63.1 + - - +
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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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155F LEU* 3.7 8.0 - - - +
156F VAL* 2.8 57.4 + - + +
159F TYR* 3.5 12.1 - - - +
164F VAL* 3.4 29.6 - - + +
166F VAL* 4.3 11.0 - - + -
179F THR* 4.3 10.8 - - + -
180F PHE* 3.7 22.9 - - - +
181F PRO 4.4 2.9 - - - +
182F ALA* 3.9 11.9 - - + +
183F VAL* 5.8 0.2 - - - -
191F SER* 1.3 74.9 - - - +
193F SER* 1.3 74.2 + - - +
194F SER 4.1 1.1 - - - +
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Residues in contact with SER 193 (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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134E VAL* 4.3 10.2 - - - +
177E SER* 4.8 7.9 - - - -
179E THR* 5.2 2.2 + - - -
138F LEU* 3.7 22.1 - - - +
154F CYS 3.4 6.7 + - - -
155F LEU* 3.9 13.7 - - - +
180F PHE* 3.0 51.1 + - - +
192F LEU* 1.3 79.2 - - - +
194F SER* 1.3 58.5 + - - +
195F VAL* 4.6 2.9 - - - -
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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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153F GLY* 3.1 2.6 - - - -
154F CYS* 2.8 36.7 + - - +
156F VAL* 5.8 0.4 - - - -
166F VAL* 3.6 25.5 - - - +
168F TRP* 3.1 24.7 + - - -
177F VAL* 4.1 1.7 - - - +
178F HIS 3.4 5.4 + - - -
179F THR* 2.8 28.1 + - - +
192F LEU* 4.1 1.6 - - - +
193F SER* 1.3 72.5 - - - +
195F VAL* 1.3 61.9 + - - +
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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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119E PHE* 5.1 5.8 - - + -
134E VAL* 5.7 2.7 - - + -
136E LEU* 4.2 26.2 - - + -
138E ASN* 5.4 2.5 - - - -
138F LEU* 4.1 19.7 - - + -
151F ALA* 5.9 1.8 - - + -
152F LEU 3.3 12.8 - - - +
153F GLY* 3.9 0.7 - - - -
168F TRP* 4.8 1.6 - - - -
177F VAL* 3.3 7.6 - - - +
178F HIS* 2.8 56.4 + - + +
180F PHE* 3.9 24.2 - - + -
193F SER* 4.6 3.6 - - - -
194F SER* 1.3 78.8 - - - +
196F VAL* 1.3 62.4 + - - +
197F THR* 6.0 0.4 - - - +
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Residues in contact with VAL 196 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150F ALA 3.9 0.5 - - - +
151F ALA* 3.5 4.4 - - - +
152F LEU* 2.8 62.7 + - + +
168F TRP* 4.5 11.9 - - + -
173F LEU* 3.9 18.2 - - + -
175F SER 4.1 4.7 - - - +
176F GLY 3.3 11.7 - - - +
177F VAL* 3.6 26.2 - - + -
195F VAL* 1.3 78.5 - - - +
197F THR* 1.3 69.4 + - - +
198F VAL* 3.8 20.3 + - + -
208F TYR* 5.2 0.2 - - + -
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Residues in contact with THR 197 (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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117E PHE* 5.1 7.4 - - + -
138E ASN* 3.9 22.7 - - + -
139E ASN* 5.0 5.7 + - - +
149F THR* 3.6 32.3 - - + +
150F ALA 3.4 7.9 - - - +
151F ALA* 4.6 3.9 - - - +
173F LEU* 6.0 0.2 - - - +
175F SER 4.7 2.1 - - - +
176F GLY* 3.0 25.3 + - - -
195F VAL* 6.0 0.5 - - - +
196F VAL* 1.3 76.2 - - - +
198F VAL* 1.3 64.2 + - - +
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Residues in contact with VAL 198 (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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149F THR* 3.7 3.7 - - - -
150F ALA* 2.8 43.2 + - + +
152F LEU* 3.8 23.3 - - + -
173F LEU* 4.6 4.7 - - + -
196F VAL* 3.8 25.4 - - + -
197F THR* 1.3 78.2 - - - +
199F PRO* 1.4 77.6 - - + +
202F SER* 4.0 0.2 - - - +
203F LEU* 5.9 1.3 - - + +
208F TYR* 3.4 37.5 - - + +
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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