Contacts of the strand formed by residues 170 - 177 (chain A) in PDB entry 3QFR
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 5.3 0.8 - - - +
134A ALA* 3.7 22.4 + - - +
135A LEU* 3.7 4.5 - - + -
136A VAL* 3.0 29.2 + - - +
168A GLY* 3.6 21.7 + - - +
169A VAL* 1.3 78.3 - - - +
171A PHE* 1.3 61.4 + - - +
201A GLN* 3.4 31.6 + - + +
203A ILE* 3.7 14.1 - - + -
233A HIS* 3.2 28.4 + - + -
234A PHE* 4.0 19.2 - - + -
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Residues in contact with PHE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 4.4 2.7 - - - -
136A VAL* 3.1 21.8 - - + +
138A PHE* 4.5 2.0 - - + -
169A VAL* 5.3 0.9 - - + -
170A LYS* 1.3 74.6 - - - +
172A ALA* 1.3 64.3 + - - +
173A VAL* 3.8 9.0 - - + -
192A ASP* 3.5 39.7 - - - -
195A LEU* 3.5 43.7 - - + -
196A GLU* 4.0 5.6 - - - -
200A ALA* 3.4 34.1 - - + -
201A GLN 3.0 12.8 + - - -
202A ARG* 3.5 33.7 - - + -
203A ILE* 2.8 33.9 + - - +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 5.2 0.7 - - + -
136A VAL 3.2 4.1 + - - +
137A VAL* 3.3 12.5 - - + +
138A PHE* 3.0 23.0 + - - -
171A PHE* 1.3 78.0 - - - +
173A VAL* 1.3 66.1 + - - +
203A ILE* 5.2 1.3 - - + -
204A PHE* 4.3 17.0 - - + +
222A TRP* 4.3 8.1 - - + -
226A PHE* 3.3 36.3 - - + -
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Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A PHE* 3.5 29.8 - - + +
140A MET* 5.0 1.8 - - + -
171A PHE* 3.8 21.0 - - + -
172A ALA* 1.3 82.0 - - - +
174A PHE* 1.3 63.2 + - - +
188A GLY* 3.6 31.6 - - - +
191A VAL* 4.2 7.0 - - + -
192A ASP* 4.1 20.7 + - + +
204A PHE 4.9 3.8 + - - -
205A GLU 5.2 0.2 + - - -
206A LEU* 3.5 17.0 - - + +
207A GLY 2.8 23.4 + - - -
222A TRP* 4.1 7.0 - - - -
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Residues in contact with PHE 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A PHE* 3.8 29.8 - + - -
137A VAL* 5.4 0.4 - - + +
138A PHE 2.8 11.4 + - - +
139A CYS* 3.3 16.0 - - - -
140A MET 3.0 22.1 + - - -
173A VAL* 1.3 75.0 - - - +
175A GLY* 1.3 65.8 + - - +
176A LEU* 3.8 15.3 - - + +
207A GLY* 3.7 10.8 - - - -
208A LEU 4.4 1.1 - - - -
209A GLY* 3.8 28.0 - - - -
215A LEU* 4.7 1.6 - - + -
218A ASP* 3.8 17.5 - - + -
219A PHE* 3.7 26.0 - + + -
222A TRP* 3.6 46.5 - + + -
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Residues in contact with GLY 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A MET 3.3 8.7 - - - -
173A VAL* 4.0 3.4 - - - +
174A PHE* 1.3 77.9 - - - +
176A LEU* 1.3 59.7 + - - -
185A ASN* 2.9 16.8 - - - -
188A GLY* 4.3 13.7 - - - -
206A LEU* 4.6 0.6 - - - +
207A GLY 2.8 16.2 + - - +
208A LEU* 6.0 0.2 - - - -
209A GLY* 2.8 29.1 + - - -
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A THR* 3.7 20.2 - - + -
94A ALA* 3.5 42.8 - - + +
97A PHE* 4.1 12.8 - - + -
139A CYS* 4.2 2.9 - - + -
140A MET 2.7 21.3 + - - +
141A ALA* 3.9 6.5 - - - -
142A THR 3.2 23.2 + - - -
174A PHE* 3.8 23.1 - - + +
175A GLY* 1.3 74.4 - - - -
177A GLY* 1.3 59.2 + - - +
185A ASN* 2.9 7.8 + - - +
209A GLY 4.3 0.9 - - - -
215A LEU* 3.9 11.0 - - + -
751A FMN 3.3 28.8 + - - +
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Residues in contact with GLY 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 1.3 74.1 - - - +
178A ASN* 1.3 54.7 + - - -
184A PHE* 3.9 1.6 - - - -
185A ASN* 3.1 10.6 - - - +
209A GLY 2.9 19.6 + - - +
211A ASP* 2.6 37.1 + - - +
215A LEU* 4.6 1.1 - - - +
751A FMN 3.1 22.7 - - - -
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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