Contacts of the strand formed by residues 217 - 222 (chain A) in PDB entry 1I7M
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 VAL 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A GLY 4.4 0.2 + - - -
216A SER* 1.3 72.1 - - - +
218A ILE* 1.3 65.2 + - - +
231A ASN 3.7 1.4 - - - +
232A GLY* 3.3 3.3 - - - -
233A MSE 2.7 55.5 + - + +
55B THR* 4.4 16.7 - - + +
57B THR* 4.1 12.3 - - + +
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Residues in contact with ILE 218 (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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201A LYS* 4.0 24.6 + - + +
204A THR* 3.9 19.5 - - + -
210A ARG* 3.7 41.3 - - + +
216A SER* 3.5 11.7 + - - +
217A VAL* 1.3 85.4 - - - +
219A ASP* 1.3 68.1 + - - +
220A ALA* 4.3 4.9 - - + +
230A MSE 3.8 33.9 - - + -
231A ASN 3.3 2.2 - - - +
232A GLY* 4.3 0.7 - - - -
240A TRP* 3.9 20.6 - - + -
55B THR* 5.4 0.8 + - - -
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Residues in contact with ASP 219 (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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218A ILE* 1.3 74.5 - - - +
220A ALA* 1.3 69.2 + - - +
230A MSE 3.1 2.4 - - - -
231A ASN* 2.8 44.0 + - + +
53B SER* 2.7 41.1 + - - -
54B VAL 4.0 0.7 + - - -
55B THR* 3.0 33.1 + - - +
62B ALA* 4.9 2.0 - - + +
64B VAL* 4.0 14.3 - - + +
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Residues in contact with ALA 220 (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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200A ALA* 4.0 13.3 - - + +
201A LYS* 5.4 0.9 - - - +
204A THR* 3.6 24.0 - - - +
218A ILE* 4.1 6.3 + - + +
219A ASP* 1.3 84.7 + - - +
221A THR* 1.3 64.9 + - - +
228A TYR* 3.6 13.0 - - + +
229A SER 3.2 14.6 - - - +
230A MSE 3.9 3.1 - - + -
64B VAL* 5.2 0.9 - - - -
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Residues in contact with THR 221 (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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200A ALA* 3.9 5.4 - - - -
220A ALA* 1.3 78.0 - - - +
222A MSE 1.3 74.9 + - - +
223A PHE* 4.0 10.9 - - + -
228A TYR* 3.6 4.2 - - - -
229A SER* 3.1 29.1 + - - +
52B ILE* 3.9 20.0 - - + +
53B SER* 5.9 4.9 - - - -
64B VAL* 3.5 33.7 - - + -
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Residues in contact with MSE 222 (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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191A GLN 4.4 2.0 - - - +
192A PHE* 3.6 32.3 - - + +
193A TYR 5.1 1.8 - - - +
194A MSE 3.9 36.1 - - + +
198A VAL 5.4 2.9 - - - +
199A THR 4.6 2.2 - - - +
200A ALA* 3.6 23.7 - - + +
203A VAL* 3.7 33.0 - - - -
221A THR* 1.3 86.3 + - - +
223A PHE* 1.3 66.0 + - - +
224A ASN 4.1 0.3 + - - -
227A GLY 3.3 10.8 - - - +
228A TYR* 3.5 32.1 - - + -
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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