Contacts of the strand formed by residues 212 - 217 (chain A) in PDB entry 3MEK
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 CYS 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A LEU* 3.6 28.9 - - - -
204A LEU* 4.9 0.4 - - + -
210A PRO* 3.5 17.8 - - - +
211A ASN* 1.3 95.1 - - - +
213A SER* 1.3 62.7 + - - +
223A LEU* 3.8 16.4 - - + -
224A ARG 3.3 10.3 - - - +
225A ALA* 4.2 0.2 - - - -
226A VAL* 3.9 5.6 - - - +
229A ILE* 3.9 3.1 - - - -
235A LEU* 3.9 22.4 - - - -
236A THR 2.9 18.2 + - - +
237A ILE* 3.7 8.6 - - + +
238A CYS 4.8 0.3 + - - -
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Residues in contact with SER 213 (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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212A CYS* 1.3 75.3 - - - +
214A ILE* 1.3 67.6 + - - +
215A VAL* 4.9 1.4 - - - +
222A LEU 3.7 0.5 - - - +
223A LEU* 3.5 4.6 - - - +
224A ARG* 2.9 33.6 + - - +
226A VAL* 3.6 22.4 - - - -
237A ILE* 4.2 4.0 - - - -
365A SER 5.2 0.9 - - - -
367A PRO* 3.2 35.4 - - - +
403A THR* 4.9 6.9 - - - +
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Residues in contact with ILE 214 (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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183A PHE* 3.7 33.7 - - + -
201A ILE* 4.3 10.3 - - + -
213A SER* 1.3 82.7 + - - +
215A VAL* 1.3 68.6 + - - +
216A PHE* 4.1 21.5 - - + -
221A LEU* 4.2 22.7 - - + -
222A LEU 3.2 5.8 - - - +
223A LEU* 3.8 20.0 - - + -
237A ILE* 4.3 20.2 - - + +
367A PRO* 4.1 5.5 - - - +
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Residues in contact with VAL 215 (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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190A MSE 4.4 6.5 - - + -
213A SER* 4.9 0.2 - - - +
214A ILE* 1.3 78.4 - - - +
216A PHE* 1.3 67.7 + - - +
221A LEU* 3.4 4.7 - - - +
222A LEU* 2.9 53.4 + - + +
224A ARG* 5.2 0.7 - - + -
367A PRO* 3.5 26.9 - - + -
403A THR 3.4 27.8 - - - +
404A HIS* 3.8 15.5 - - + +
408A HIS* 4.0 20.6 - - + -
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Residues in contact with PHE 216 (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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183A PHE* 4.2 10.3 - - + -
184A THR 3.2 24.2 - - - -
185A ILE* 3.9 13.0 - - + -
186A CYS* 3.4 41.1 - - + +
187A ASN 5.0 6.4 - - - +
188A ALA* 5.1 1.4 + - - -
190A MSE 5.7 4.6 - - - +
198A TYR* 3.5 37.2 - + - -
214A ILE* 4.1 24.0 - - + -
215A VAL* 1.3 76.7 - - - +
217A ASN* 1.3 59.8 + - - +
218A GLY 3.5 9.8 + - - +
220A HIS 3.3 6.5 - - - -
221A LEU* 3.7 27.8 - - + -
408A HIS* 2.9 16.7 + - - -
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Residues in contact with ASN 217 (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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188A ALA* 6.1 1.8 - - - +
216A PHE* 1.3 71.8 - - - +
218A GLY* 1.3 65.0 + - - +
220A HIS* 2.7 44.6 + - + +
222A LEU* 5.6 5.4 - - + -
407A GLU 4.0 5.8 - - - +
408A HIS* 3.6 26.1 - - + +
409A SER* 3.2 40.8 + - - -
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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