Contacts of the strand formed by residues 180 - 184 (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 MET 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ALA* 4.8 0.2 - - + -
99B HIS 3.4 24.2 - - - +
100B HIS* 3.6 25.6 - - + +
165B HIS* 5.0 5.9 - - - +
175B GLU 3.5 21.1 - - - +
176B VAL* 3.7 8.7 - - + -
177B THR* 3.0 37.2 + - - +
178B THR* 4.1 2.3 - - - +
179B LYS* 1.3 85.5 - - - +
181B LEU* 1.3 70.7 + - - +
182B CYS* 5.9 0.4 - - - -
214B SER* 6.6 0.2 - - - -
215B TRP* 3.6 20.6 - - - +
227B VAL* 3.7 14.1 - - + -
228B TYR 3.2 11.2 - - - +
229B THR* 5.4 1.6 - - - -
230B ARG* 4.1 7.3 + - - -
305B GOL 4.0 6.1 - - - +
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Residues in contact with LEU 181 (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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129B ASP* 4.2 7.6 - - + +
162B LEU* 5.1 12.6 - - + -
163B ILE 5.7 4.0 - - - +
180B MET* 1.3 75.2 - - - +
182B CYS* 1.3 66.5 + - - +
199B LEU* 4.6 9.9 - - + -
210B THR* 3.6 43.5 - - + +
211B GLY* 4.8 1.3 - - - -
227B VAL* 3.5 2.5 - - - -
228B TYR* 2.7 49.6 + - + +
230B ARG* 3.5 49.1 - - + +
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Residues in contact with CYS 182 (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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162B LEU* 3.6 6.4 - - - +
163B ILE* 2.9 39.0 + - + +
165B HIS* 6.2 0.4 - - - -
168B CYS* 2.0 51.4 - - + -
172B TYR* 4.3 0.2 - - - -
176B VAL* 3.7 19.5 - - - -
180B MET 5.9 0.4 - - - -
181B LEU* 1.3 77.1 - - - +
183B ALA* 1.3 62.9 + - - +
225B PRO* 3.8 10.3 - - + -
226B GLY 3.3 4.3 - - - -
227B VAL* 4.2 10.5 - - - -
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Residues in contact with ALA 183 (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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160B VAL* 3.6 23.5 - - + +
161B LYS 3.2 13.2 - - - +
162B LEU* 4.0 17.0 - - + -
163B ILE* 4.1 2.9 - - - -
182B CYS* 1.3 76.0 - - - +
184B ALA* 1.3 62.0 + - - +
189B ASP* 4.5 2.6 - - - +
199B LEU* 4.6 2.2 - - + -
226B GLY* 2.9 32.8 + - - +
228B TYR* 3.8 16.8 + - + -
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Residues in contact with ALA 184 (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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160B VAL* 3.8 10.2 - - - +
161B LYS* 2.8 37.7 + - - +
163B ILE* 3.7 14.5 - - + +
183B ALA* 1.3 77.2 - - - +
185B ASP* 1.3 64.2 + - - +
186B TRP* 3.5 33.9 - - + -
188B THR 5.2 1.1 - - - -
189B ASP* 5.3 4.3 - - - +
225B PRO* 4.0 4.9 - - + -
226B GLY 4.7 0.7 - - - +
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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