Contacts of the strand formed by residues 204 - 211 (chain X) in PDB entry 1M6E
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 204 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X ALA* 4.6 4.0 - - - +
39X ALA* 3.5 41.7 + - + +
42X ALA* 3.9 19.0 - - - +
43X LEU* 3.7 18.7 - - + +
142X PHE* 3.0 30.5 + - + +
143X ILE* 2.9 24.1 + - - +
199X VAL* 5.2 1.3 - - - +
202X GLY 4.2 2.5 - - - +
203X GLY* 1.3 75.0 - - - -
205X MET* 1.3 64.8 + - - +
206X VAL* 5.3 0.2 - - + -
272X PHE* 6.2 0.2 - - - -
275X ASP* 3.9 20.0 + - - +
353X SER* 3.4 20.0 + - - -
354X LEU 3.4 12.1 + - - -
355X ILE* 3.1 43.0 - - - +
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Residues in contact with MET 205 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143X ILE* 3.3 34.1 - - + +
191X PHE* 4.7 1.3 - - + -
192X LEU* 4.2 6.1 - - + -
195X ARG* 3.3 34.8 - - + -
199X VAL* 4.3 7.9 - - + -
204X ARG* 1.3 75.9 - - - +
206X VAL* 1.3 63.1 + - - +
207X LEU* 3.8 22.1 + - + -
272X PHE* 4.1 29.6 - - + -
352X VAL 3.6 1.9 - - - +
353X SER* 3.6 1.7 - - - -
354X LEU* 3.0 60.3 + - + +
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Residues in contact with VAL 206 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32X THR* 5.0 5.4 - - + +
35X ILE* 4.4 17.0 - - + -
36X THR* 4.0 22.0 - - + +
39X ALA* 3.7 22.0 - - + -
142X PHE* 3.6 27.1 - - + -
143X ILE 3.0 8.7 + - - -
144X HIS* 3.7 11.2 + - + -
145X SER* 3.1 22.5 + - - +
205X MET* 1.3 76.0 - - - +
207X LEU* 1.3 60.2 + - - +
208X THR* 4.0 4.2 + - - +
351X ILE* 4.6 9.4 - - + -
352X VAL 3.4 8.7 - - - +
353X SER* 3.9 7.9 - - - +
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Residues in contact with LEU 207 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143X ILE* 4.3 18.4 - - + +
145X SER* 3.4 28.7 - - - +
149X LEU* 3.8 14.4 - - + -
188X HIS* 5.2 9.6 - - + +
191X PHE* 3.6 29.4 - - + -
192X LEU* 5.5 0.4 - - + -
205X MET* 4.0 24.2 - - + +
206X VAL* 1.3 77.9 - - - +
208X THR* 1.3 61.0 + - - +
209X ILE* 4.0 9.3 + - + +
350X VAL 4.0 0.9 - - - +
351X ILE* 3.5 2.6 - - - +
352X VAL* 2.9 39.9 + - + +
354X LEU* 4.5 9.4 - - + -
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Residues in contact with THR 208 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28X VAL* 3.6 30.5 - - + -
32X THR* 3.6 21.0 + - - +
144X HIS* 5.0 1.2 + - - -
145X SER 2.8 9.6 + - - +
146X SER* 3.3 21.8 + - - +
147X TYR* 2.9 34.1 + - + -
148X SER 4.5 0.7 + - - -
149X LEU 5.2 0.5 + - - -
206X VAL* 4.7 4.3 + - - +
207X LEU* 1.3 73.8 + - - +
209X ILE* 1.3 59.8 + - - +
349X ASN* 4.3 7.0 - - + -
350X VAL 3.6 3.4 - - - -
351X ILE* 4.2 19.4 - - + +
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Residues in contact with ILE 209 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147X TYR* 5.1 1.6 - - - +
149X LEU* 3.4 31.2 - - + +
150X MET* 3.7 25.1 - - + +
184X PHE* 4.8 3.8 - - + -
188X HIS* 3.7 31.0 - - + +
207X LEU* 4.0 7.2 - - + -
208X THR* 1.3 78.1 - - - +
210X LEU* 1.3 75.8 + - - +
211X GLY* 3.2 1.2 + - - +
256X THR 4.6 4.7 - - - +
257X PRO 4.6 7.2 - - - +
258X SER 5.5 0.7 - - - +
262X VAL* 4.5 19.3 - - + -
349X ASN* 3.5 2.6 - - - -
350X VAL* 2.9 39.8 + - + +
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Residues in contact with LEU 210 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147X TYR* 3.5 32.5 - - + +
150X MET* 3.2 38.6 - - + +
208X THR 4.0 1.6 + - - -
209X ILE* 1.3 79.5 - - - +
211X GLY* 1.3 60.9 + - - +
221X GLU 6.1 0.4 - - - +
222X CYS* 5.9 3.6 - - + +
255X TYR* 3.9 23.3 - - + +
257X PRO* 3.5 19.2 - - + +
347X PHE* 3.4 45.8 - - + -
348X ILE 3.5 8.3 - - - +
2000X SAL 4.5 8.1 - - + -
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Residues in contact with GLY 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209X ILE 3.2 5.2 + - - -
210X LEU* 1.3 77.6 - - - +
212X ARG* 1.3 64.7 + - - +
221X GLU 4.1 8.1 - - - +
222X CYS* 4.1 2.3 - - - +
257X PRO* 3.4 26.9 - - - +
258X SER 3.6 7.0 - - - -
348X ILE* 2.9 29.0 + - - +
350X VAL* 4.3 1.7 - - - +
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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