Contacts of the strand formed by residues 206 - 215 (chain B) in PDB entry 4MNY
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B ALA* 3.8 21.0 - - + +
123B LEU 4.0 18.4 + - - -
124B PRO* 5.8 0.2 - - - +
125B SER 5.9 1.2 - - - +
201B CYS 3.5 0.7 - - - +
202B SER* 4.0 1.2 + - - -
203B LEU 3.0 26.4 + - - +
204B GLN* 4.0 10.6 + - - +
205B GLY* 1.3 78.8 - - - +
207B MET* 1.3 70.7 + - - +
208B THR* 2.9 23.5 + - - +
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Residues in contact with MET 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B TRP* 3.8 33.0 - - + -
121B ILE* 3.8 8.7 - - + +
122B ALA* 3.7 18.2 + - - +
137B GLU* 4.7 13.0 - - - +
200B VAL* 3.7 17.3 - - + -
201B CYS 4.3 0.9 - - - +
202B SER* 3.4 39.7 - - - +
205B GLY 4.3 1.5 + - - +
206B ARG* 1.3 72.9 - - - +
208B THR* 1.3 59.6 + - - +
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Residues in contact with THR 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 4.0 4.0 - - - -
122B ALA* 3.6 9.1 - - - +
123B LEU 4.0 2.0 - - - +
124B PRO* 3.6 40.6 - - + -
200B VAL* 3.3 5.9 - - - +
201B CYS 2.9 36.7 + - - -
203B LEU* 3.9 27.7 + - + +
206B ARG* 2.9 22.8 + - - +
207B MET* 1.3 72.5 + - - +
209B LEU* 1.3 61.3 + - - +
210B THR* 3.1 7.9 + - - +
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B SER* 3.6 13.2 - - - +
47B ILE* 4.4 3.1 - - + -
53B ILE* 3.5 32.3 - - + -
121B ILE* 3.8 16.4 - - + +
122B ALA 3.0 18.8 + - - +
123B LEU* 4.2 15.0 - - + -
124B PRO* 3.2 21.3 - - - +
197B GLY 5.4 0.2 - - - -
198B PRO* 3.4 33.9 - - + -
199B LEU 3.9 2.9 - - - +
208B THR* 1.3 68.8 - - - +
210B THR* 1.3 61.3 + - - +
211B GLY 3.5 17.0 - - - +
212B ILE* 4.5 4.0 - - + -
231B VAL* 3.4 19.9 - - + +
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Residues in contact with THR 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B PRO* 4.7 7.2 - - - +
129B ASP* 4.4 9.0 - - - +
130B PRO* 3.8 22.7 - - + -
162B LEU* 4.9 1.1 - - + -
181B LEU* 3.6 27.5 - - + +
199B LEU* 3.0 11.3 + - + -
201B CYS* 3.5 34.8 - - - +
203B LEU* 4.1 14.0 - - - +
208B THR* 3.1 7.1 + - - +
209B LEU* 1.3 74.2 - - - +
211B GLY* 1.3 57.4 + - - +
230B ARG* 4.9 0.5 - - - +
231B VAL* 3.3 21.6 + - - +
232B SER 4.7 1.7 + - - -
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B LEU* 4.8 0.9 - - - -
198B PRO* 3.8 0.2 - - - +
199B LEU* 2.9 44.1 + - - +
209B LEU* 3.5 14.9 - - - +
210B THR* 1.3 80.1 - - - +
212B ILE* 1.3 64.5 + - - -
228B TYR* 4.1 4.7 - - - -
229B THR 3.2 10.3 - - - -
231B VAL* 4.0 1.6 - - - -
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Residues in contact with ILE 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ILE* 3.9 25.8 - - + -
54B SER 3.7 24.5 - - - +
55B ALA* 4.2 4.9 - - + +
102B ASP 4.6 2.2 - - - +
103B ILE* 4.0 15.5 - - + -
196B GLY* 3.5 33.4 - - - +
197B GLY 3.4 3.6 - - - +
209B LEU* 4.5 7.6 - - + -
211B GLY* 1.3 78.4 - - - +
213B VAL* 1.3 73.6 + - - +
214B SER* 3.0 2.1 + - - -
228B TYR* 3.1 4.6 - - - -
229B THR* 2.9 38.9 + - - +
231B VAL* 3.8 20.9 - - + -
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Residues in contact with VAL 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ILE* 6.5 0.2 - - + -
55B ALA* 3.9 4.0 - - - +
138B ILE* 4.9 4.0 - - + -
139B THR 5.2 2.7 - - - +
190B SER* 3.7 20.0 - - - +
194B ASP* 3.2 36.1 - - + +
195B SER* 3.5 5.7 - - - +
196B GLY 2.9 21.9 + - - +
197B GLY* 2.9 26.4 + - - +
198B PRO 4.7 5.4 - - - +
212B ILE* 1.3 74.5 - - - +
214B SER* 1.3 61.5 + - - +
228B TYR* 3.6 25.2 - - + -
6D TYR* 3.5 24.2 - - + -
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Residues in contact with SER 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B HIS* 3.1 13.1 - - - -
99B HIS* 2.9 23.4 + - - +
102B ASP* 2.7 33.7 + - - +
180B MET* 6.6 0.4 - - - -
212B ILE 3.0 7.8 + - - -
213B VAL* 1.3 74.5 - - - +
215B TRP* 1.3 73.9 + - - +
227B VAL 3.0 17.2 + - - -
228B TYR 4.3 0.2 - - - -
229B THR* 3.7 17.4 + - - -
6D TYR* 3.7 6.5 - - - -
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Residues in contact with TRP 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 3.5 34.5 - - + -
98B ALA* 3.6 17.9 - - + +
99B HIS* 3.4 30.7 + - + +
172B TYR* 3.7 37.7 - + - -
175B GLU* 3.7 24.7 - - + -
176B VAL* 3.8 8.1 - - + -
180B MET* 3.6 12.7 - - + -
214B SER* 1.3 102.3 - - - +
216B GLY* 1.3 73.8 + - - +
227B VAL* 2.7 69.3 + - + +
6D TYR* 3.2 25.5 - - - +
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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