Contacts of the strand formed by residues 214 - 219 (chain I) 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 THR 214 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108H ARG* 2.4 47.2 + - - +
213I ILE* 1.3 82.9 + - - +
215I LEU* 1.3 66.3 + - - +
216I THR* 3.8 15.3 - - + -
243I LYS* 5.9 1.1 - - - +
261I VAL* 3.4 4.7 - - - +
262I TYR* 2.8 57.5 + - + -
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Residues in contact with LEU 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203I CYS* 4.1 6.3 - - - +
205I ALA* 4.0 12.3 - - + +
213I ILE* 4.2 3.6 - - + -
214I THR* 1.3 76.3 - - - +
216I THR* 1.3 69.7 + - - +
228I MET* 4.5 3.3 - - - +
230I LEU* 4.2 16.9 - - + +
243I LYS* 3.8 31.9 - - + +
244I TRP* 3.7 35.4 - - - +
245I ALA* 3.9 15.5 - - + +
259I CYS* 4.9 7.0 - - - -
260I HIS 3.4 2.2 - - - +
261I VAL* 3.2 44.2 - - + -
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Residues in contact with THR 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214I THR* 3.8 20.6 - - + -
215I LEU* 1.3 82.1 - - - +
217I TRP* 1.3 65.8 + - - +
218I GLN* 5.0 2.9 + - - +
223I GLU* 4.0 31.5 + - - +
228I MET* 4.5 4.3 - - - -
245I ALA* 5.3 0.2 - - - +
258I THR 3.5 0.9 - - - +
259I CYS* 3.3 10.1 - - - -
260I HIS* 3.0 49.3 + - - +
262I TYR* 4.1 11.9 + - + -
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Residues in contact with TRP 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189I VAL* 4.4 10.3 - - + -
201I LEU* 3.6 33.7 - - + -
202I ARG 4.4 1.1 - - - -
203I CYS* 3.7 29.0 - - + +
216I THR* 1.3 77.9 - - - +
218I GLN* 1.3 59.7 + - - +
223I GLU* 3.5 3.7 - - - +
224I LEU* 2.8 39.3 + - + +
228I MET* 3.4 33.6 - - + +
245I ALA* 3.1 23.6 + - + -
246I SER* 3.6 13.5 - - - +
247I VAL* 3.8 21.5 - - + -
257I TYR* 3.8 19.7 - - + -
258I THR* 3.3 42.8 - - - -
259I CYS* 3.6 9.0 - - + -
272I LEU 4.8 1.6 - - - -
274I TRP 6.0 1.3 - - - -
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Residues in contact with GLN 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLY* 6.2 0.2 - - - -
53A ASP* 4.8 15.2 + - - +
216I THR* 5.0 3.5 + - - +
217I TRP* 1.3 75.8 - - - +
219I LEU* 1.3 58.5 + - - +
220I ASN 4.0 1.1 + - - +
221I GLY* 4.8 13.1 - - - +
222I GLU 2.3 34.3 - - - +
223I GLU* 3.9 7.5 - - + +
224I LEU* 4.3 5.4 - - - -
256I TYR 4.0 0.7 - - - +
257I TYR* 3.2 5.2 - - - +
258I THR* 2.9 46.6 + - - +
260I HIS* 3.1 36.3 + - + +
262I TYR* 5.5 1.4 + - - -
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Residues in contact with LEU 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLN* 5.0 1.3 - - - +
218I GLN* 1.3 73.6 - - - +
220I ASN* 1.3 99.0 + - - +
221I GLY* 3.0 11.8 + - - +
222I GLU* 3.5 9.4 + - + +
224I LEU* 4.2 16.8 - - + +
253I LYS* 5.6 10.3 - - - +
256I TYR* 3.8 19.1 - - + +
257I TYR* 3.7 42.4 - - + +
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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