Contacts of the strand formed by residues 211 - 216 (chain A) in PDB entry 3DF0
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 ILE 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A GLY 4.7 1.6 - - - +
210A GLY* 1.3 71.2 - - - -
212A ALA* 1.3 60.9 + - - +
213A GLU* 3.3 10.0 + - + +
341A CYS* 4.0 0.9 - - - -
342A ASN* 2.8 34.3 + - + +
343A LEU 5.1 0.2 - - - -
344A THR* 3.3 33.9 - - - +
345A PRO* 3.6 8.3 - - + -
408A LEU* 3.8 25.4 - - + -
472A LEU* 3.9 19.3 - - + -
474A ARG* 4.7 5.4 - - - +
500A ARG* 3.7 11.2 - - - +
502A PHE* 3.3 41.1 - - + -
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Residues in contact with ALA 212 (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 THR* 3.8 31.9 - - + +
205A GLU* 3.2 25.9 + - + +
210A GLY 3.8 0.2 + - - -
211A ILE* 1.3 71.8 - - - +
213A GLU* 1.3 62.5 + - - +
214A TRP* 3.8 10.1 + - - +
340A ILE 3.2 6.7 - - - +
341A CYS* 4.4 2.7 - - + +
470A GLU* 4.5 3.6 - - - +
472A LEU* 4.2 22.6 - - + +
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Residues in contact with GLU 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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211A ILE* 3.3 6.0 + - + +
212A ALA* 1.3 69.9 - - - +
214A TRP* 1.3 65.6 + - - +
215A TYR* 3.8 28.3 + - + +
338A LEU 4.2 0.2 - - - +
340A ILE* 2.9 37.8 + - + +
342A ASN* 3.2 26.9 + - - +
347A THR* 3.6 15.8 + - - -
348A LEU* 3.9 15.1 + - - +
472A LEU* 6.2 1.8 - - + -
474A ARG* 3.2 38.4 + - - +
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Residues in contact with TRP 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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199A ALA* 4.1 4.3 - - + -
201A THR* 3.2 30.3 + - + +
212A ALA* 3.8 15.2 + - - +
213A GLU* 1.3 83.4 - - - +
215A TYR* 1.3 81.8 + - - +
337A ARG* 3.3 46.4 - - + -
338A LEU 3.8 4.0 - - - -
339A GLU* 3.0 30.1 - - + -
466A ILE* 5.7 1.3 - - + -
468A LEU* 3.3 48.5 - - + -
172C LEU* 5.5 2.7 - - + -
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Residues in contact with TYR 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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213A GLU* 3.8 31.1 + - + -
214A TRP* 1.3 96.2 - - - +
216A GLU* 1.3 65.7 + - - +
217A LEU* 3.5 4.0 + - + -
221A PRO* 3.7 37.0 - - + -
224A LEU* 4.2 14.4 - - + -
227A ILE* 4.4 21.9 - - + +
337A ARG* 4.0 2.9 - - - +
338A LEU* 3.1 42.9 + - + +
340A ILE* 3.8 30.3 - - + -
347A THR* 5.5 0.7 + - - -
348A LEU* 5.0 1.4 - - + +
349A THR* 4.7 9.2 + - + +
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Residues in contact with GLU 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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215A TYR* 1.3 72.0 - - - +
217A LEU* 1.3 60.1 + - - +
218A ARG* 3.1 35.1 + - - +
219A LYS* 3.1 54.8 + - + +
220A PRO* 3.8 2.6 - - - +
221A PRO* 5.7 0.2 - - - +
336A SER 4.1 4.0 - - - +
337A ARG* 5.3 4.7 - - + +
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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