Contacts of the strand formed by residues 206 - 215 (chain E) in PDB entry 3PB1
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 ARG 206 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122E ALA* 4.0 21.5 - - + +
123E LEU 5.0 8.7 + - - -
125E SER* 6.0 3.4 - - - +
201E CYS 3.4 1.4 - - - +
202E SER* 3.6 4.5 + - - -
203E LEU 2.9 26.8 + - - +
204E GLN* 3.2 33.3 + - - +
205E GLY* 1.3 82.7 - - - +
207E MET* 1.3 59.9 + - - +
208E THR* 2.7 24.9 + - - +
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Residues in contact with MET 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ASN 5.7 2.2 - - - +
29E TRP* 3.7 26.7 - - + -
121E ILE* 3.7 11.5 - - + +
122E ALA* 3.3 27.4 + - - +
137E GLU* 5.7 4.7 - - - +
200E VAL* 3.6 24.5 - - - -
201E CYS 4.0 4.3 - - - +
202E SER* 5.1 1.3 - - - +
206E ARG* 1.3 68.2 - - - +
208E THR* 1.3 59.2 + - - +
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Residues in contact with THR 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ILE* 4.1 4.5 - - - -
122E ALA* 3.5 5.3 - - - +
123E LEU 4.0 2.2 - - - +
124E PRO* 3.5 40.6 - - + -
200E VAL* 3.4 6.7 - - - +
201E CYS 2.8 40.5 + - - -
203E LEU* 3.5 27.2 + - + +
206E ARG* 2.7 26.7 + - - +
207E MET* 1.3 73.7 + - - +
209E LEU* 1.3 64.5 + - - +
210E THR* 3.1 8.3 + - - +
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Residues in contact with LEU 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E SER* 3.8 11.0 - - - +
47E ILE* 4.5 2.9 - - + -
53E ILE* 3.5 32.8 - - + -
121E ILE* 3.7 15.5 - - + +
122E ALA 2.8 18.6 + - - +
123E LEU* 4.3 15.9 - - + -
124E PRO* 3.2 20.6 - - - +
198E PRO* 3.5 33.7 - - + -
199E LEU 4.0 3.1 - - - +
200E VAL* 4.9 0.4 - - + -
208E THR* 1.3 69.7 - - - +
210E THR* 1.3 60.8 + - - +
211E GLY 3.6 17.0 - - - +
212E ILE* 4.4 6.3 - - + -
231E VAL* 3.5 20.1 - - + +
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Residues in contact with THR 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E PRO* 5.1 3.9 - - - +
129E ASP* 4.3 6.7 - - - +
130E PRO* 4.0 21.8 - - + +
162E LEU* 4.7 1.8 - - + -
181E LEU* 3.6 26.0 - - + +
199E LEU* 2.9 10.1 + - + -
201E CYS* 3.5 42.0 - - - +
203E LEU* 4.6 3.5 - - - +
208E THR* 3.1 13.3 + - - +
209E LEU* 1.3 74.4 - - - +
211E GLY* 1.3 59.9 + - - +
229E THR 3.9 0.5 - - - +
230E ARG* 4.0 3.3 - - - -
231E VAL* 3.1 23.2 + - - +
232E SER 4.5 1.4 + - - -
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Residues in contact with GLY 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E LEU* 5.3 0.9 - - - -
199E LEU* 2.8 50.8 + - - +
209E LEU* 3.6 11.8 - - - +
210E THR* 1.3 81.5 - - - +
212E ILE* 1.3 62.2 + - - -
228E TYR* 4.2 4.0 - - - -
229E THR 3.2 11.7 - - - -
230E ARG* 5.1 0.2 - - - -
231E VAL* 3.9 1.8 - - - -
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Residues in contact with ILE 212 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E SER* 6.1 0.2 - - - +
53E ILE* 4.2 17.9 - - + -
54E SER 3.8 23.8 - - - +
55E ALA* 4.1 5.4 - - + -
102E ASP 4.7 2.5 - - - +
103E ILE* 4.0 23.1 - - + -
196E GLY* 3.6 32.8 - - - +
197E GLY 3.4 4.7 - - - +
209E LEU* 4.4 8.7 - - + -
211E GLY* 1.3 77.7 - - - +
213E VAL* 1.3 70.9 + - - +
214E SER 3.1 0.7 + - - -
228E TYR* 3.2 4.6 - - - -
229E THR* 3.0 38.4 + - - +
231E VAL* 3.9 21.1 - - + -
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Residues in contact with VAL 213 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE* 6.3 0.2 - - + -
55E ALA* 4.1 2.4 - - - +
138E ILE* 4.8 4.7 - - + -
139E THR 5.2 2.7 - - - +
190E SER* 3.6 29.8 - - - +
194E ASP* 3.3 35.0 - - + +
195E ALA* 3.4 6.9 - - - +
196E GLY 2.9 22.5 + - - -
197E GLY* 2.9 25.0 + - - +
198E PRO 4.6 6.3 - - - +
211E GLY 4.4 0.2 + - - -
212E ILE* 1.3 70.9 - - - +
214E SER* 1.3 60.8 + - - +
227E VAL 5.2 0.2 - - - +
228E TYR* 3.5 26.0 - - + -
346I ARG* 4.1 14.8 - - + -
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Residues in contact with SER 214 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E ALA* 5.6 0.2 - - - -
57E HIS* 3.1 11.1 - - - -
99E HIS* 3.8 2.1 + - - +
102E ASP* 2.5 33.1 + - - +
212E ILE 3.1 7.2 + - - -
213E VAL* 1.3 75.9 - - - +
215E TRP* 1.3 77.7 + - - +
227E VAL* 3.1 17.5 + - - -
228E TYR 4.6 0.2 - - - -
229E THR* 4.1 14.8 - - - -
346I ARG* 3.0 28.8 + - - +
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Residues in contact with TRP 215 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E LEU* 3.9 21.5 - - + -
98E ALA* 3.6 21.8 - - + -
99E HIS* 3.4 39.4 + - + +
172E TYR* 3.5 32.3 - + - -
175E GLU* 3.9 11.4 - - + -
176E VAL* 3.7 23.6 - - + -
180E MET* 3.7 10.0 - - - +
214E SER* 1.3 103.6 - - - +
216E GLY* 1.3 73.0 + - - +
226E GLY 3.8 0.2 - - - -
227E VAL* 2.7 66.5 + - + +
344I SER* 3.3 22.9 - - - +
345I ALA 4.2 0.2 - - - +
346I ARG* 3.8 12.4 + - - +
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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