Contacts of the strand formed by residues 208 - 219 (chain E) in PDB entry 3SGB
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 208 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124E ILE* 4.1 2.5 - - - -
126E SER* 3.4 17.7 - - - +
128E ALA* 4.0 29.1 - - + +
134E MET* 3.9 27.8 - - - +
200E TYR* 3.1 5.0 - - - +
201E SER* 2.6 72.3 + - - +
202E GLY 3.3 0.2 - - - -
207E THR* 1.3 86.9 - - - +
209E ALA* 1.3 60.4 + - - +
210E ILE* 3.6 4.3 + - + +
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Residues in contact with ALA 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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46E PHE* 3.6 38.1 - - + -
124E ILE* 3.9 10.0 - - + +
126E SER 2.8 17.0 + - - +
127E ALA* 3.3 5.4 - - - -
128E ALA 3.0 24.8 + - - -
199E LEU 4.2 0.2 - - - -
207E THR 3.9 1.2 + - - -
208E ARG* 1.3 70.1 - - - +
210E ILE* 1.3 60.7 + - - +
231E VAL* 3.4 13.0 - - + +
241E VAL* 4.2 9.4 - - + -
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Residues in contact with ILE 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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46E PHE* 4.2 0.2 - - - -
128E ALA* 3.7 32.3 - - + +
129E ASN 4.6 0.4 - - - +
130E ALA* 3.8 30.9 + - + +
134E MET* 3.9 22.9 - - + -
136E VAL* 4.6 2.7 - - + -
181E ILE* 4.1 3.7 - - + +
199E LEU* 2.8 34.3 + - + +
200E TYR 4.0 1.8 - - - +
201E SER* 3.9 18.8 - - - +
208E ARG* 3.7 17.3 - - + +
209E ALA* 1.3 80.4 - - - +
211E GLY* 1.4 58.6 + - - +
230E PRO* 3.7 6.4 - - - +
231E VAL* 2.9 24.9 + - - +
232E THR 4.7 0.2 + - - -
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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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46E PHE* 3.3 14.0 - - - -
181E ILE* 4.8 0.9 - - - -
198E PRO* 3.6 0.2 - - - +
199E LEU* 2.8 40.9 + - - +
210E ILE* 1.4 79.0 - - - +
212E LEU* 1.3 62.6 - - - -
228E PHE* 4.4 5.4 - - - -
229E GLN 3.1 13.5 - - - -
230E PRO* 4.4 0.2 - - - -
231E VAL* 3.7 4.8 - - - +
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Residues in contact with LEU 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 GLY* 3.9 7.9 - - - -
46E PHE* 3.8 23.6 - - + -
53E LEU* 4.2 19.5 - - + -
54E THR 3.8 20.6 - - - +
55E ALA* 5.1 0.7 - - - +
102E ASP 4.8 3.1 - - - +
103E TYR* 3.8 22.2 - - + -
196E GLY* 3.9 21.8 - - - +
197E GLY 3.4 3.8 - - - +
211E GLY* 1.3 81.4 - - - +
213E THR* 1.3 66.4 - - - +
214E SER 3.3 0.2 + - - -
228E PHE* 3.1 5.8 - - - +
229E GLN* 2.7 48.2 + - + +
231E VAL* 4.3 7.2 - - + -
234E ALA* 4.5 8.3 - - + -
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Residues in contact with THR 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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55E ALA* 3.9 7.4 - - - +
102E ASP 6.2 0.2 - - - -
138E ARG* 3.6 17.5 - - - +
192E ALA* 4.3 1.1 - - + -
194E ASP 3.4 29.3 + - - +
195E SER* 3.8 2.7 - - - -
196E GLY* 2.9 26.3 + - - -
197E GLY 2.7 22.5 + - - -
212E LEU* 1.3 73.5 - - - +
214E SER* 1.3 60.3 + - - +
226E THR* 3.9 22.7 - - + -
228E PHE* 3.2 21.1 - - - -
18I LEU* 4.2 14.4 - - + -
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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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57E HIS* 3.0 23.6 - - - -
102E ASP* 2.6 29.4 + - - +
171E TYR* 2.6 23.9 + - - -
180E MET* 3.3 32.6 - - - +
195E SER* 3.8 0.6 + - - -
212E LEU 3.3 3.5 + - - -
213E THR* 1.3 78.7 - - - +
215E GLY* 1.3 61.3 - - - +
227E PHE 2.9 10.1 + - - -
229E GLN* 4.6 0.4 - - - -
17I THR* 3.5 8.8 - - - -
18I LEU* 3.6 3.6 + - - -
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Residues in contact with GLY 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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171E TYR* 3.2 13.4 + - - -
213E THR* 4.7 0.4 - - - +
214E SER* 1.3 84.6 - - - +
216E GLY* 1.3 59.5 - - - -
226E THR* 3.4 3.8 - - - +
227E PHE* 2.7 30.4 + - - -
16I CYS 3.0 15.3 - - - -
18I LEU* 3.8 14.0 - - - +
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Residues in contact with GLY 216 (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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192E ALA 5.9 2.0 - - - -
215E GLY* 1.3 75.8 - - - -
217E SER* 1.3 62.2 + - - -
225E THR 2.9 14.6 - - - -
226E THR* 4.1 3.4 - - - -
227E PHE* 4.3 4.3 - - - -
15I ALA* 3.5 14.1 - - - +
16I CYS* 2.9 33.4 + - - +
18I LEU* 4.0 9.9 - - - +
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Residues in contact with SER 217 (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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192E ALA 5.2 3.0 + - - +
216E GLY* 1.3 74.2 - - - -
218E GLY* 1.3 67.5 + - - +
224E GLY* 3.1 4.0 - - - -
225E THR* 2.8 40.4 + - - +
226E THR* 5.3 0.3 + - - -
227E PHE* 5.7 1.2 - - - -
13I LYS 5.7 0.4 - - - -
14I PRO 3.2 27.0 + - - -
15I ALA* 4.5 0.8 - - - +
39I ASN* 6.0 3.4 - - - +
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Residues in contact with GLY 218 (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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192E ALA* 4.2 9.1 - - - +
217E SER* 1.3 82.8 - - - +
219E ASN* 1.3 69.6 - - - +
222E SER* 6.1 0.4 - - - -
223E GLY 3.4 11.9 - - - -
224E GLY* 3.9 0.7 - - - -
36I ASN* 5.1 8.8 + - - -
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Residues in contact with ASN 219 (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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191E CYS* 3.6 7.4 - - - +
192E GLU* 3.4 25.6 - - + +
218E GLY* 1.3 79.6 - - - +
220E CYS* 1.3 55.4 + - - +
221E SER* 2.8 16.7 + - - -
222E SER* 2.8 39.9 + - - -
223E GLY* 2.8 36.9 + - - -
224E GLY* 3.5 1.3 + - - -
29I LYS* 6.0 2.4 - - - +
36I ASN* 6.3 0.2 - - - +
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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