Contacts of the strand formed by residues 161 - 171 (chain A) in PDB entry 4FQP
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 VAL 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A VAL* 3.3 35.4 - - + -
157A THR* 3.5 17.7 - - + +
159A GLU* 3.2 21.0 + - + +
160A PRO* 1.3 77.4 - - - +
162A PRO* 1.3 81.5 - - + +
163A MET* 3.3 2.5 + - + +
207A ILE* 3.9 4.3 - - - -
208A LEU 3.1 30.6 + - - +
210A PRO* 4.5 1.3 - - + -
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Residues in contact with PRO 162 (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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152A GLN* 3.6 25.9 - - + +
154A VAL* 3.8 8.8 - - - +
160A PRO 4.8 0.2 - - - +
161A VAL* 1.3 90.2 - - + +
163A MET* 1.3 59.2 + - - +
164A ALA 3.7 1.3 - - - +
165A ARG* 5.4 0.4 - - + -
205A LEU* 3.4 35.4 - - + -
206A TRP 3.8 2.0 - - - +
207A ILE* 3.7 17.2 - - + -
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Residues in contact with MET 163 (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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151A VAL* 3.5 8.8 - - - +
152A GLN* 2.9 31.8 + - - +
154A VAL* 3.6 21.3 - - + -
161A VAL* 3.5 15.9 - - + +
162A PRO* 1.3 72.3 - - - +
164A ALA* 1.3 63.6 + - - +
206A TRP* 3.0 15.0 + - + +
208A LEU* 3.9 27.8 - - + +
210A PRO* 3.8 26.5 - - - -
214A VAL* 4.3 2.9 - - + -
238A LEU* 3.5 28.9 - - + +
239A THR 4.0 2.9 - - - +
240A VAL* 3.4 32.1 - - + -
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Residues in contact with ALA 164 (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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150A GLU 3.6 8.5 - - - +
151A VAL* 4.5 0.7 - - - -
152A GLN* 4.1 2.7 - - - +
162A PRO 3.7 0.2 - - - -
163A MET* 1.3 82.2 - - - +
165A ARG* 1.3 60.9 + - - +
179A TRP* 3.8 13.3 - - + -
205A LEU* 3.5 2.3 - - - +
206A TRP* 2.8 45.8 + - + +
219A VAL* 4.9 1.1 - - + -
236A VAL* 3.6 31.6 - - + -
238A LEU* 4.8 3.8 - - + -
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Residues in contact with ARG 165 (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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149A ALA* 3.1 26.6 - - - +
150A GLU* 3.0 46.0 + - - +
152A GLN* 3.1 37.0 + - + +
164A ALA* 1.3 74.4 - - - +
166A CYS* 1.3 62.0 + - - +
167A VAL* 4.4 11.5 - - - +
179A TRP* 3.8 3.1 - - - -
203A THR* 4.1 21.1 - - + +
204A SER 3.8 2.7 - - - +
205A LEU* 3.7 32.9 - - + +
236A VAL* 4.9 0.2 - - - +
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Residues in contact with CYS 166 (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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148A THR 3.3 11.9 - - - -
149A ALA* 4.4 1.8 - - - -
165A ARG* 1.3 74.2 - - - +
167A VAL* 1.3 68.0 + - - +
177A ILE* 4.2 9.2 - - + -
179A TRP* 3.4 16.8 - - + -
202A VAL 4.6 0.2 - - - -
203A THR* 3.4 3.7 - - - +
204A SER 2.7 35.5 + - - +
221A CYS* 2.0 49.4 - - - -
223A VAL* 4.0 13.0 - - - -
234A LEU* 4.3 5.8 - - - -
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Residues in contact with VAL 167 (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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146A GLN 4.1 0.2 - - - +
147A ASN* 3.1 5.7 - - - -
148A THR* 2.8 59.2 + - - +
150A GLU* 4.6 3.4 - - - +
165A ARG* 4.4 18.6 - - - +
166A CYS* 1.3 80.1 - - - +
168A SER* 1.3 60.0 + - - +
169A THR* 3.7 28.4 + - + +
177A ILE* 4.6 0.7 - - - -
201A THR* 5.3 1.6 - - - +
202A VAL 3.2 10.1 - - - +
203A THR* 3.7 19.1 - - + +
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Residues in contact with SER 168 (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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145A PRO* 3.3 15.8 - - - +
146A GLN 3.8 0.2 - - - -
147A ASN* 2.9 29.8 + - - -
167A VAL* 1.3 70.9 - - - +
169A THR* 1.3 61.2 + - - +
170A GLY 3.7 0.2 + - - -
171A GLY* 4.3 1.0 + - - -
175A ALA* 3.3 26.1 - - - +
177A ILE* 4.1 11.9 - - - +
200A VAL 3.8 3.3 - - - +
201A THR* 3.3 3.7 - - - -
202A VAL* 2.8 31.8 + - - +
223A VAL* 4.0 4.9 - - - -
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Residues in contact with THR 169 (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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145A PRO* 3.3 15.2 - - - +
146A GLN 3.0 26.1 + - - -
147A ASN* 4.9 0.5 - - - -
148A THR* 5.1 3.1 + - - -
167A VAL* 3.7 20.9 + - + +
168A SER* 1.3 71.3 - - - +
170A GLY* 1.3 60.0 - - - +
171A GLY 3.6 0.2 - - - -
201A THR* 3.5 23.1 - - + +
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Residues in contact with GLY 170 (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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143A ALA* 3.7 12.5 - - - +
144A LYS 4.4 1.2 - - - +
145A PRO* 3.7 6.2 - - - +
168A SER 3.7 0.4 + - - -
169A THR* 1.3 74.1 - - - +
171A GLY* 1.3 64.5 + - - +
194A GLY* 5.0 0.9 - - - -
195A PHE* 5.1 3.6 - - - -
196A LEU* 5.2 4.0 - - - +
199A THR* 3.5 27.3 - - - +
201A THR* 3.1 18.7 - - - +
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Residues in contact with GLY 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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143A ALA 3.9 0.2 - - - -
145A PRO* 3.5 24.2 - - - +
168A SER 4.3 0.6 + - - -
169A THR 3.6 0.2 - - - -
170A GLY* 1.3 73.1 - - - +
172A ARG* 1.3 61.3 + - - -
173A PRO 3.5 11.4 - - - -
174A PRO* 4.6 2.9 - - - -
175A ALA 4.7 2.0 - - - -
198A GLY 4.0 0.3 - - - +
199A THR* 2.9 5.0 - - - -
200A VAL* 2.5 47.9 + - - +
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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