Contacts of the strand formed by residues 257 - 261 (chain H) in PDB entry 1MWA
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 TYR 257 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201H LEU* 3.9 6.9 - - + +
217H TRP* 3.5 20.9 - + + -
218H GLN 3.2 7.6 - - - -
219H LEU* 3.7 30.6 - - + +
224H LEU* 3.4 34.5 - - + -
247H VAL* 4.5 5.8 - - + -
248H VAL 5.2 0.7 + - - -
249H VAL* 3.1 37.3 - - + +
250H PRO* 4.2 9.5 - - - +
253H LYS* 2.9 27.3 - - + +
254H GLU* 2.7 28.1 + - - +
255H GLN 3.2 1.0 - - - -
256H TYR* 1.3 82.7 - - + +
258H THR* 1.3 66.2 + - - +
272H LEU 4.1 2.9 - - - +
273H ARG* 4.1 12.1 + - - +
274H TRP 4.6 2.6 + - - -
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Residues in contact with THR 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C ASP* 2.9 30.5 + - - +
54C PRO* 5.9 0.9 - - + -
216H THR 3.8 0.2 - - - +
217H TRP* 3.3 5.9 - - - -
218H GLN* 2.6 57.9 + - - +
257H TYR* 1.3 78.7 - - - +
259H CYS* 1.3 60.7 + - - +
260H HIS* 3.5 16.8 - - - -
271H THR* 4.5 8.3 - - - +
272H LEU 3.3 8.1 - - - +
273H ARG* 3.6 23.6 - - + +
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Residues in contact with CYS 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203H CYS* 2.0 54.7 - - + -
215H LEU* 4.9 4.9 - - - -
216H THR 3.3 13.0 - - - -
217H TRP* 3.4 16.7 - - + -
245H ALA* 5.8 0.2 - - - -
258H THR* 1.3 73.8 - - - +
260H HIS* 1.3 68.4 + - - +
261H VAL* 4.2 9.9 - - - -
271H THR* 3.3 4.9 + - - -
272H LEU* 2.6 47.3 + - + +
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Residues in contact with HIS 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214H THR 3.4 2.1 - - - +
215H LEU* 3.2 5.5 - - - -
216H THR* 2.8 43.7 + - - +
218H GLN* 2.6 50.6 + - - +
258H THR* 3.5 16.2 - - - -
259H CYS* 1.3 74.1 - - - +
261H VAL* 1.3 63.3 + - - +
262H TYR* 3.7 22.0 - + + +
269H PRO* 5.0 4.3 - - + -
270H LEU 3.4 14.4 - - - +
271H THR* 2.8 30.8 + - - -
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Residues in contact with VAL 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185H PRO* 3.9 19.3 - - + -
187H ALA* 4.1 22.9 - - + -
203H CYS* 4.3 2.2 - - - -
205H ALA* 4.2 4.0 - - + -
213H ILE* 3.7 19.3 - - + -
214H THR 3.4 2.7 - - - -
215H LEU* 3.4 29.2 - - + -
259H CYS* 4.2 13.5 - - - -
260H HIS* 1.3 74.5 - - - +
262H TYR* 1.3 63.9 + - - +
266H LEU* 3.9 5.0 - - + +
269H PRO* 3.6 4.9 - - - +
270H LEU* 3.2 36.7 + - + -
272H LEU* 4.3 6.5 - - + -
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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