Contacts of the strand formed by residues 195 - 206 (chain A) in PDB entry 6A3V
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 SER 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A GLU* 5.8 5.8 - - - -
149A LEU 3.4 6.5 + - - -
150A ARG* 5.4 2.6 - - - +
186A PRO* 4.6 8.1 - - - +
193A ARG* 2.8 36.3 + - - +
194A ASN* 1.3 83.1 + - - +
196A ALA* 1.3 63.7 + - - +
226A TRP* 4.6 2.2 - - - -
182E THR* 4.7 17.3 + - - +
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Residues in contact with ALA 196 (chain A).
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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147A LEU 3.9 0.3 - - - +
148A GLU* 3.3 5.5 - - - +
149A LEU* 2.9 35.6 + - + +
183A VAL* 3.6 14.6 - - + -
184A ASP 3.4 26.0 - - - +
185A LEU* 4.2 12.3 - - + -
186A PRO* 4.6 3.6 - - + -
193A ARG* 4.8 2.0 - - - +
195A SER* 1.3 77.1 - - - +
197A PHE* 1.3 62.3 + - - +
226A TRP* 4.5 3.4 - - + -
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Residues in contact with PHE 197 (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 19.7 - - + -
147A LEU 3.3 24.5 - - - -
148A GLU* 3.8 24.7 - - + -
183A VAL* 4.0 10.7 - - - +
196A ALA* 1.3 76.1 - - - +
198A GLY* 1.3 88.3 + - - +
199A PHE* 4.0 2.7 - - + -
232A ALA* 4.9 2.2 - - + -
180E ALA 5.5 0.4 - - - -
181E LEU* 5.5 6.5 - - + -
182E THR* 5.4 13.9 - - - +
199E PHE 3.2 26.7 - - - -
200E GLN* 3.1 42.8 - - + -
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Residues in contact with GLY 198 (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* 3.7 1.0 - - - -
147A LEU 3.0 30.0 + - - -
181A LEU* 3.6 24.8 - - - +
183A VAL* 3.8 2.6 - - - +
197A PHE* 1.3 88.8 - - - +
199A PHE* 1.3 60.7 - - - +
197C PHE* 5.7 2.2 - - - -
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Residues in contact with PHE 199 (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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142A TYR* 4.2 1.8 - - - -
144A PHE* 3.5 27.4 - + + -
145A PHE 3.0 20.4 - - - -
146A GLN* 3.8 10.5 - - + -
181A LEU* 3.7 4.4 - - - +
197A PHE* 4.0 2.7 - - + -
198A GLY* 1.3 72.9 - - - +
200A GLN* 1.3 63.9 + - - +
197C PHE* 3.0 22.3 - - - -
199C PHE* 3.4 56.9 - + + +
142E TYR* 3.2 23.3 - - - -
199E PHE* 3.6 33.7 - + + +
200E GLN* 4.5 0.7 - - - -
201E GLY 3.1 29.2 - - - -
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Residues in contact with GLN 200 (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 VAL 4.0 0.2 - - - +
144A PHE* 3.2 1.6 - - - +
145A PHE* 2.5 50.9 + - + +
179A LEU* 3.8 23.9 - - + +
180A ALA* 2.9 30.6 + - - +
181A LEU* 3.9 15.5 - - + +
199A PHE* 1.3 79.9 - - - +
201A GLY* 1.3 62.7 + - - +
202A ARG* 4.6 3.7 - - - +
146C GLN* 2.7 38.3 + - - +
148C GLU* 5.3 1.6 + - - -
197C PHE* 3.1 25.3 - - + -
199C PHE* 4.0 1.4 - - - -
232C ALA* 6.2 1.6 - - - +
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Residues in contact with GLY 201 (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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142A TYR* 4.2 11.2 - - - -
143A VAL 3.2 12.8 - - - -
144A PHE* 4.0 4.0 - - - -
179A LEU* 5.1 0.9 - - - -
199A PHE* 4.8 0.2 - - - -
200A GLN* 1.3 82.5 + - - +
202A ARG* 1.3 63.6 + - - -
144C PHE* 3.7 1.8 - - - -
146C GLN* 2.9 18.7 - - - +
199C PHE* 3.0 23.4 - - - -
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Residues in contact with ARG 202 (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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142A TYR* 4.1 8.7 - - - -
143A VAL 3.4 22.6 + - - +
178A ALA 3.1 23.6 + - - -
179A LEU* 3.6 22.6 - - + +
200A GLN* 4.6 2.5 - - - +
201A GLY* 1.3 73.2 - - - +
203A LEU* 1.3 65.5 + - - +
204A LEU* 3.6 18.7 + - + +
94C GLN* 3.8 20.4 - - - +
96C VAL* 4.9 0.8 - - - +
117C GLY* 4.7 11.5 - - - -
144C PHE* 3.6 14.4 - - + -
146C GLN* 3.1 36.9 + - - +
231C GLY 3.4 14.4 + - - -
232C ALA* 5.8 0.9 - - - -
234C VAL* 3.3 25.7 - - - +
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Residues in contact with LEU 203 (chain A).
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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140A VAL* 4.1 10.3 - - + -
141A TYR 3.4 3.6 - - - +
142A TYR* 3.6 33.7 - - + -
202A ARG* 1.3 72.0 - - - +
204A LEU* 1.3 68.2 + - - +
240A VAL* 4.2 11.9 - - + -
92C PHE* 4.1 23.1 - - + -
93C ALA 3.6 25.8 - - - +
94C GLN* 2.9 35.8 + - + +
117C GLY* 4.6 3.1 - - - +
119C SER* 5.2 6.1 + - - +
144C PHE* 4.2 7.0 - - + -
237C LEU 3.7 15.7 - - - +
238C PHE* 4.0 13.7 - - + -
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Residues in contact with LEU 204 (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 VAL* 3.3 5.7 - - - -
141A TYR* 2.7 43.8 + - - +
143A VAL* 3.8 28.9 - - + -
165A LEU* 4.3 17.7 - - + -
167A LEU* 5.8 4.5 - - + -
178A ALA* 4.3 18.4 - - + +
179A LEU* 4.5 8.1 - - + -
202A ARG* 3.8 31.9 - - + +
203A LEU* 1.3 83.2 - - - +
205A HIS* 1.3 61.2 + - - +
206A LEU* 3.8 18.5 + - + +
212A LEU* 5.4 1.1 - - + -
94C GLN* 5.8 0.2 - - - +
117C GLY* 6.5 1.6 - - - -
119C SER* 5.8 0.7 - - - -
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Residues in contact with HIS 205 (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 ALA* 5.3 4.1 - - + +
139A GLY* 3.4 23.3 + - - -
140A VAL* 3.7 20.0 - - + +
167A LEU* 5.2 4.2 - - - +
204A LEU* 1.3 70.9 - - - +
206A LEU* 1.3 74.4 + - - +
207A SER* 5.3 1.2 - - - -
210A GLN* 4.2 5.7 + - - -
119C SER* 5.4 7.2 + - - +
39D ASN* 4.7 23.2 + - + -
60D ARG* 4.0 25.3 + - - +
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Residues in contact with LEU 206 (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 VAL* 3.7 27.1 - - + -
138A ALA* 3.3 2.8 - - - +
139A GLY 2.8 33.0 + - - +
141A TYR* 3.7 29.8 - - + -
143A VAL* 4.9 1.3 - - + -
167A LEU* 4.1 26.5 - - + -
204A LEU* 4.1 21.3 - - + +
205A HIS* 1.3 86.3 - - - +
207A SER* 1.3 66.8 + - - +
210A GLN* 3.7 8.3 - - + +
212A LEU* 4.1 12.6 - - + -
237A LEU* 3.8 17.0 - - + -
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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