Contacts of the strand formed by residues 211 - 216 (chain A) in PDB entry 3ATF
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 ALA 211 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A HIS* 1.3 74.6 - - - +
212A VAL* 1.3 59.7 + - - +
222A LEU* 3.9 20.9 - - + -
223A MET 3.3 13.7 - - - +
224A PHE* 4.3 7.9 - - + -
306A ILE* 5.4 0.9 - - + -
327A TYR* 3.8 16.7 - - + -
331A GLU 2.9 5.9 + - - +
332A ILE* 3.2 16.7 - - + -
333A LEU* 2.7 32.9 + - - +
338A PHE* 4.6 0.2 - - - -
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Residues in contact with VAL 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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210A HIS 5.4 0.4 - - - -
211A ALA* 1.3 78.9 - - - +
213A ILE* 1.3 61.5 + - - +
221A CYS 3.5 0.3 - - - +
222A LEU* 3.4 5.4 - - - +
223A MET* 2.8 64.3 + - + +
333A LEU* 3.3 10.5 - - + +
336A TYR* 3.6 34.8 - - + +
337A ARG* 4.2 5.2 - - - +
338A PHE* 3.9 17.7 - - + -
359A THR* 3.8 28.9 - - + -
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Residues in contact with ILE 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 VAL* 1.3 78.5 - - - +
214A SER* 1.3 69.8 + - - +
220A LEU* 3.8 31.2 - - + -
221A CYS 3.1 8.7 - - - +
222A LEU* 3.8 13.0 - - + -
285A ILE* 4.1 12.3 - - + -
291A PHE* 5.4 7.6 - - + -
294A ILE* 6.4 0.2 - - + -
299A LEU* 4.9 8.5 - - + -
332A ILE* 3.6 25.6 - - + -
333A LEU 3.2 6.2 + - - +
334A TRP* 3.6 39.3 - - + -
335A GLY* 2.8 29.5 + - - -
336A TYR 3.4 1.6 + - - -
364A THR* 4.4 0.3 - - - +
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Residues in contact with SER 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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213A ILE* 1.3 77.6 - - - +
215A MET* 1.3 66.6 + - - +
216A ARG 3.6 0.2 + - - -
220A LEU* 3.7 12.8 - - - -
221A CYS* 2.9 31.2 + - - +
223A MET* 3.2 17.5 - - - +
336A TYR 2.7 25.3 + - - -
337A ARG* 3.9 8.7 - - - +
362A THR* 4.3 8.1 - - - -
364A THR* 3.8 17.7 - - - -
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Residues in contact with MET 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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214A SER* 1.3 79.1 + - - +
216A ARG* 1.3 66.3 - - - +
217A ASP 4.2 0.2 - - - -
218A GLY* 3.1 38.1 - - - +
219A LYS 3.4 5.2 - - - -
220A LEU* 3.6 29.2 - - + -
337A ARG* 4.7 14.0 + - - -
362A THR* 5.9 0.2 - - - +
363A SER 5.6 2.0 - - - +
364A THR* 4.6 4.7 + - + +
365A PRO* 3.9 25.1 - - + -
372A LEU* 4.0 22.4 - - + -
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Residues in contact with ARG 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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214A SER* 3.6 0.6 + - - +
215A MET* 1.3 79.2 - - - +
217A ASP* 1.3 75.7 + - + +
218A GLY 3.2 0.2 - - - -
219A LYS* 2.8 26.6 + - - +
221A CYS* 4.2 18.1 - - - -
223A MET* 3.4 33.2 - - + -
280A ILE* 3.9 32.7 + - - +
282A SER* 3.9 22.5 - - - -
337A ARG* 6.1 5.1 - - - +
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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