Contacts of the strand formed by residues 200 - 208 (chain A) in PDB entry 3MIB
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 LEU 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A PRO* 6.1 0.4 - - + -
152A LYS 4.7 5.8 - - - +
153A GLY* 3.0 16.1 + - - +
154A VAL* 3.3 25.7 - - + -
155A GLY 3.1 23.4 + - - -
198A GLN* 3.7 5.7 - - - +
199A PRO* 1.3 93.4 - - + +
201A ILE* 1.3 62.8 + - - +
322A TYR* 4.0 29.2 - - + -
323A MET 3.5 9.6 - - - +
324A GLU* 3.5 30.3 - - - +
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Residues in contact with ILE 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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93A PHE* 3.6 35.7 - - + -
155A GLY 3.3 6.1 - - - +
157A ARG* 3.9 24.9 - - - +
198A GLN* 3.7 17.5 - - + +
200A LEU* 1.3 74.3 - - - +
202A ALA* 1.3 72.8 + - - +
321A TYR* 4.6 2.4 - - - -
322A TYR* 3.3 3.6 - - - -
323A MET* 2.9 32.3 + - - +
325A ALA* 3.7 23.8 - - + -
328A ALA* 3.5 22.8 - - + +
329A LEU 5.4 1.3 - - - +
330A SER* 4.3 15.9 - - - +
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Residues in contact with ALA 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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150A LEU* 4.5 4.9 - - + -
154A VAL* 3.5 24.4 - - + +
155A GLY 2.8 18.1 + - - +
156A PHE* 3.6 39.1 - - + -
201A ILE* 1.3 85.6 - - - +
203A GLY* 1.3 59.0 + - - +
237A PHE* 4.5 3.1 - - + -
321A TYR* 3.2 10.5 - - - +
330A SER* 4.4 2.6 + - - +
361A GOL 4.1 5.5 + - - -
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Residues in contact with GLY 203 (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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156A PHE* 4.3 8.2 - - - -
202A ALA* 1.3 75.1 - - - +
204A MET* 1.3 60.3 + - - +
320A MET* 3.5 12.1 - - - +
321A TYR* 2.8 47.9 + - - +
330A SER* 3.2 15.7 - - - -
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Residues in contact with MET 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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136A ASN* 5.9 4.5 - - + +
137A ILE* 3.6 34.8 - - + +
156A PHE* 4.9 2.2 - - + -
203A GLY* 1.3 74.1 - - - +
205A TYR* 1.3 62.7 + - - +
206A LEU* 3.8 5.1 - - + +
274A PHE* 3.6 9.0 - - + -
318A TYR* 3.6 35.0 - - + -
319A ILE 3.6 16.2 - - - +
320A MET* 3.6 40.8 - - + -
321A TYR* 3.2 5.9 - - - -
330A SER 3.2 9.5 + - - +
331A PHE* 3.3 7.5 - - + +
332A MET 2.9 27.0 + - - +
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Residues in contact with TYR 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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204A MET* 1.3 73.5 - - - +
206A LEU* 1.3 59.5 + - - +
207A MET* 3.6 27.1 - - + -
227A CYS* 3.3 21.0 - - - +
229A TYR* 4.0 6.5 - + - -
234A MET* 4.0 8.1 - - + -
289A LEU* 3.3 33.5 - - + +
317A LEU 3.5 3.8 - - - +
319A ILE* 2.8 51.0 + - + +
321A TYR* 3.4 11.1 - - + -
332A MET* 3.3 39.0 - - + -
333A THR 4.5 0.4 - - - -
334A CYS* 3.5 16.8 - - + +
362A GOL 2.6 33.5 + - - -
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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 ALA 5.9 3.4 - - - +
204A MET* 3.8 6.0 - - + +
205A TYR* 1.3 72.0 - - - +
207A MET* 1.3 69.4 + - - +
208A MET* 3.8 24.5 - - + -
316A ASN* 4.3 12.3 - - + +
317A LEU 3.6 5.2 - - - +
318A TYR* 3.6 44.2 - - + +
332A MET 2.8 14.0 + - - +
333A THR* 3.1 20.1 - - + +
334A CYS 2.7 31.5 + - - -
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Residues in contact with MET 207 (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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205A TYR* 3.6 21.3 - - + -
206A LEU* 1.3 73.7 - - - +
208A MET* 1.3 61.0 + - - +
225A ILE* 3.5 40.5 - - + +
226A SER* 4.3 1.6 - - - +
252A GLY* 5.8 0.2 - - - -
253A TYR 5.8 0.4 - - - +
289A LEU* 3.5 42.0 - - + +
290A ALA 4.5 2.0 - - - -
291A ALA* 3.8 17.7 - - + +
315A CYS 3.4 1.2 - - - +
316A ASN* 3.3 4.2 - - - -
317A LEU* 2.8 50.3 + - + +
319A ILE* 3.9 21.1 - - + -
334A CYS* 3.4 10.3 - - + -
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Residues in contact with MET 208 (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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206A LEU* 3.8 27.1 - - + -
207A MET* 1.3 75.2 - - - +
209A SER* 1.3 71.4 + - - +
210A VAL* 4.8 7.2 - - + -
225A ILE* 3.7 7.6 - - - +
306A ILE* 5.4 6.5 - - + -
314A MET* 5.8 7.6 - - + -
315A CYS 3.1 4.0 - - - -
316A ASN* 3.2 31.4 - - - +
333A THR* 4.6 2.9 - - + -
334A CYS 3.0 8.3 + - - +
335A THR* 3.3 44.6 - - + -
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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