Contacts of the strand formed by residues 251 - 258 (chain A) in PDB entry 3AEF
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 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A TYR* 4.1 1.3 - - + +
221A TYR* 4.0 21.3 - - + +
248A LEU 3.7 15.9 - - - +
249A GLU 3.4 6.3 + - - +
250A PHE* 1.3 75.0 - - - +
252A GLN* 1.3 66.5 + - - +
253A PHE* 3.4 20.7 - - + -
364A VAL* 3.7 34.3 - - + -
366A TYR 3.9 3.4 - - - +
367A ASN* 3.9 20.2 - - - +
368A MET* 4.1 3.5 - - - +
485A ARG* 4.4 7.2 + - - +
536A THR* 3.9 17.5 - - + -
549A ALA* 3.6 10.9 - - - +
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Residues in contact with GLN 252 (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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251A VAL* 1.3 73.9 - - - +
253A PHE* 1.3 73.0 + - - +
254A HIS 4.0 2.2 - - - +
298A ARG* 2.7 44.4 + - + +
364A VAL* 3.6 4.0 - - - -
365A HIS* 2.9 32.6 + - + -
366A TYR* 2.9 24.4 + - + +
368A MET* 3.7 18.9 - - + +
408A ASN* 3.1 21.6 - - - +
409A ARG* 3.1 40.8 + - - +
549A ALA* 4.6 2.5 - - - -
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Residues in contact with PHE 253 (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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221A TYR* 4.7 2.5 - + - -
251A VAL* 3.4 24.4 + - + -
252A GLN* 1.3 80.0 - - - +
254A HIS* 1.3 61.0 + - - +
255A PRO* 3.3 5.9 - - - +
298A ARG* 3.8 5.2 - - - +
299A ASP* 5.4 1.0 - - - +
302A SER* 3.0 30.4 + - - +
362A PRO* 4.4 4.3 - - + -
363A THR* 3.5 14.4 - - - +
364A VAL* 3.5 35.9 - - + -
478A GLN* 4.5 12.1 - - - -
481A ALA 3.8 8.1 - - - -
482A ALA* 3.6 19.1 - - + -
483A VAL* 3.5 43.7 - - + -
485A ARG* 4.9 5.2 - - - -
549A ALA* 5.4 6.0 - - + +
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Residues in contact with HIS 254 (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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225A THR* 4.7 3.1 - - + -
252A GLN* 4.0 0.2 - - - +
253A PHE* 1.3 71.0 - - - +
255A PRO* 1.3 75.5 - - + +
256A THR* 3.2 40.7 + - - -
257A GLY 4.2 0.4 + - - +
264A LEU* 3.2 34.8 - - + +
265A ILE 3.8 2.6 + - - -
267A GLU 3.8 14.0 + - - -
270A ARG* 3.6 10.5 + - - -
298A ARG* 3.3 28.6 - - - +
302A SER* 4.0 0.4 - - - -
361A LEU 4.0 0.5 - - - +
362A PRO* 3.2 0.5 - - - +
363A THR* 2.9 33.1 + - - +
365A HIS* 3.3 43.0 + - + +
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Residues in contact with PRO 255 (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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253A PHE 3.3 8.3 - - - +
254A HIS* 1.3 86.7 - - + +
256A THR* 1.3 59.6 + - + +
270A ARG* 3.6 18.6 - - - +
298A ARG* 3.4 35.9 - - + +
301A VAL* 3.5 35.4 - - + -
302A SER* 3.9 8.5 - - - +
305A MET* 3.2 20.5 - - - +
361A LEU 3.2 3.5 - - - -
362A PRO* 3.1 22.5 - - + -
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Residues in contact with THR 256 (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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254A HIS* 3.2 16.0 + - - -
255A PRO* 1.3 80.2 - - + +
257A GLY* 1.3 60.2 + - - +
264A LEU* 4.9 0.2 - - - -
265A ILE* 2.7 49.3 + - - +
266A THR 3.9 5.5 + - - -
270A ARG* 3.7 15.2 + - - +
276A LEU* 3.8 18.6 - - + -
305A MET* 4.7 0.2 - - + -
324A LEU* 3.8 31.2 - - + -
360A VAL* 3.9 19.7 - - + -
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Residues in contact with GLY 257 (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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225A THR* 4.6 2.5 - - - -
254A HIS* 4.2 2.0 + - - -
255A PRO 3.7 0.6 - - - -
256A THR* 1.3 75.8 - - - +
258A ILE* 1.3 64.9 + - - +
262A GLY* 4.3 3.8 - - - -
263A CYS 3.6 8.5 - - - -
264A LEU* 4.5 2.4 - - - +
265A ILE 4.4 0.7 - - - -
360A VAL* 3.3 3.5 - - - -
361A LEU* 2.9 36.0 + - - +
363A THR* 3.4 23.5 + - - -
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Residues in contact with ILE 258 (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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256A THR 4.0 1.2 + - - -
257A GLY* 1.3 72.2 - - - -
259A TYR* 1.3 69.1 + - - +
260A GLY 4.5 2.2 - - - +
261A ALA 4.1 8.3 - - - +
262A GLY* 3.1 26.8 + - - +
263A CYS* 2.8 47.8 + - + +
265A ILE* 3.6 25.9 - - + +
344A THR* 4.1 9.0 - - - +
345A ALA* 3.9 17.5 - - - -
348A PHE* 4.3 8.5 - - + -
349A ALA* 3.8 28.7 - - + -
358A ILE* 4.1 4.7 - - + -
359A PRO* 3.7 13.7 - - + +
360A VAL* 4.7 0.4 - - - -
361A LEU* 5.6 0.3 - - - +
363A THR* 5.2 2.4 - - - +
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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