Contacts of the strand formed by residues 170 - 177 (chain B) in PDB entry 3QFC
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 LYS 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU* 5.9 0.2 - - - +
134B ALA 4.4 12.7 + - - +
135B LEU* 3.2 10.4 - - + +
136B VAL* 3.1 24.6 + - - +
168B GLY* 3.8 14.1 + - - +
169B VAL* 1.3 79.8 - - - +
171B PHE* 1.3 60.3 + - - +
201B GLN* 3.2 25.1 + - + -
203B ILE* 3.5 22.2 - - + -
233B HIS* 2.8 40.0 + - + +
234B PHE* 4.2 13.3 - - + -
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Residues in contact with PHE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU* 4.3 3.6 - - - -
136B VAL* 3.1 24.0 - - + +
138B PHE* 4.6 0.9 - - + -
169B VAL* 5.0 1.1 - - + -
170B LYS* 1.3 75.0 - - - +
172B ALA* 1.3 66.1 + - - +
173B VAL* 3.9 9.0 - - + -
192B ASP* 3.6 45.3 - - - -
195B LEU* 3.7 29.6 - - + -
196B GLU* 4.0 6.1 - - + -
200B ALA* 3.4 34.1 - - + -
201B GLN 2.8 28.2 + - - -
202B ARG* 3.5 24.5 - - + -
203B ILE* 2.8 31.5 + - - +
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU* 5.2 0.4 - - + -
136B VAL 3.3 3.1 + - - +
137B VAL* 3.3 11.5 - - + -
138B PHE* 3.0 23.0 + - - -
171B PHE* 1.3 79.9 - - - +
173B VAL* 1.3 66.3 + - - +
203B ILE* 5.1 1.6 - - + -
204B PHE* 4.3 17.3 - - + +
222B TRP* 4.2 9.0 - - + -
226B PHE* 3.6 35.7 - - + -
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Residues in contact with VAL 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B PHE* 3.3 31.6 - - + +
140B MET* 4.6 4.9 - - + -
171B PHE* 3.9 19.5 - - + -
172B ALA* 1.3 83.3 - - - +
174B PHE* 1.3 65.8 + - - +
188B GLY* 4.0 16.8 - - - +
191B VAL* 4.2 12.8 - - + -
192B ASP* 4.2 12.0 + - + +
204B PHE 4.7 3.4 + - - -
206B LEU* 3.3 29.6 - - + +
207B GLY 2.8 21.8 + - - -
222B TRP* 3.6 8.2 - - - -
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Residues in contact with PHE 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE* 3.9 18.2 - + - -
138B PHE 2.8 10.1 + - - +
139B CYS* 3.3 14.3 - - - -
140B MET 3.1 21.8 + - - -
173B VAL* 1.3 74.8 - - - +
175B GLY* 1.3 61.0 + - - +
176B LEU* 3.5 26.8 - - + +
207B GLY* 3.8 8.5 - - - -
209B GLY* 3.9 26.0 - - - -
215B LEU* 4.2 3.8 - - + -
218B ASP* 4.1 3.6 - - + -
219B PHE* 3.6 44.2 - + + -
222B TRP* 3.6 51.4 - + + -
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Residues in contact with GLY 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B MET 3.3 8.3 - - - -
173B VAL 4.0 1.6 - - - -
174B PHE* 1.3 75.5 - - - +
176B LEU* 1.3 58.0 + - - -
185B ASN* 3.0 14.5 + - - -
188B GLY* 4.5 14.4 - - - -
206B LEU* 4.3 1.8 - - - +
207B GLY 2.6 18.3 + - - -
208B LEU* 5.7 0.2 - - - -
209B GLY* 2.7 34.0 + - - -
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B THR* 3.5 24.2 - - + -
94B ALA* 3.4 43.7 - - + +
97B PHE* 3.6 14.6 - - + -
139B CYS* 4.3 3.1 - - + -
140B MET 2.7 18.8 + - - +
141B ALA* 3.2 6.2 - - - -
142B THR 3.2 23.7 + - - -
174B PHE* 3.5 36.6 - - + +
175B GLY* 1.3 71.0 - - - -
177B GLY* 1.3 58.8 + - - +
185B ASN* 2.8 8.6 + - - +
209B GLY 4.1 1.3 - - - -
215B LEU* 3.8 7.4 - - + -
751B FMN 3.2 16.7 + - - +
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Residues in contact with GLY 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LEU* 1.3 76.0 - - - +
178B ASN* 1.3 54.9 + - - -
184B PHE* 3.8 2.2 - - - -
185B ASN* 3.1 6.3 - - - +
209B GLY 2.9 16.7 + - - +
210B ASP* 3.3 0.2 - - - -
211B ASP* 2.7 33.8 + - - +
215B LEU* 4.8 0.8 - - - +
751B FMN 3.3 28.7 + - - -
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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