Contacts of the strand formed by residues 352 - 358 (chain A) in PDB entry 4X8G
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 MET 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A TYR* 5.4 11.9 - - + -
349A GLN* 3.0 27.1 - - + +
350A ASP 3.3 2.1 + - - -
351A GLU* 1.3 82.6 - - + +
353A GLU* 1.3 67.4 + - - +
354A ILE* 4.5 15.0 - - + -
367A VAL* 3.7 22.9 - - + -
368A PHE 3.5 10.5 - - - +
369A ASP* 3.9 13.7 - - - +
384A VAL* 5.3 13.2 - - + -
389A PHE* 6.5 0.9 - - + -
407A PHE* 4.0 6.8 - - - +
648A ASN* 3.4 33.9 + - + +
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Residues in contact with GLU 353 (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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296A TRP* 3.7 18.0 - - + -
298A MET* 3.4 34.4 - - + +
299A THR 5.2 3.8 - - - +
352A MET* 1.3 78.3 - - - +
354A ILE* 1.3 69.9 + - - +
355A GLY 3.5 1.2 + - - -
367A VAL* 3.5 1.5 - - - -
368A PHE* 2.8 36.9 + - - +
407A PHE* 3.3 26.5 - - + +
410A LEU* 3.4 3.6 - - + +
411A GLU* 4.5 4.5 - - - +
648A ASN* 5.2 1.6 - - - +
701A CA 2.9 26.6 - - - -
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Residues in contact with ILE 354 (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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296A TRP* 4.5 1.1 - - - -
298A MET* 5.2 0.3 - - - -
299A THR* 3.9 17.8 + - - -
309A TYR* 4.3 18.2 - - + -
352A MET* 4.5 21.1 - - + -
353A GLU* 1.3 77.8 - - - +
355A GLY* 1.3 68.6 + - - +
365A PRO* 4.6 6.5 - - + -
366A VAL 3.9 5.8 - - - +
367A VAL* 4.3 9.2 - - + +
389A PHE* 4.9 12.1 - - + -
648A ASN* 4.3 12.6 + - - +
649A VAL 3.4 30.7 + - - +
650A ARG* 4.1 31.9 - - + -
651A ARG 5.6 1.3 + - - +
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Residues in contact with GLY 355 (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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296A TRP* 3.3 16.0 - - - +
297A ILE 3.3 12.8 - - - -
298A MET* 4.7 2.5 - - - -
299A THR* 5.4 0.4 - - - -
353A GLU 3.5 3.6 + - - -
354A ILE* 1.3 77.4 - - - +
356A TYR* 1.3 62.9 + - - +
365A PRO* 3.3 8.3 - - - +
366A VAL 2.7 37.3 + - - -
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Residues in contact with TYR 356 (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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295A PRO 3.8 1.0 - - - +
296A TRP* 3.8 4.3 - - - +
297A ILE* 3.1 67.3 + - + +
298A MET 4.2 0.2 - - - -
299A THR* 3.7 25.6 - - + -
355A GLY* 1.3 76.8 - - - +
357A ILE* 1.3 78.1 + - - +
358A GLN* 3.9 29.2 + - + -
363A THR* 4.4 1.8 - - + -
364A LEU 3.4 16.2 - - - +
365A PRO* 3.9 4.3 - - + -
366A VAL* 3.7 5.6 - - - +
425A LEU* 4.6 3.5 - - - +
653A PRO* 3.5 38.1 - - + -
654A PHE* 3.4 30.0 + + - +
658A TRP* 6.0 0.3 - - - +
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Residues in contact with ILE 357 (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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151A LEU* 3.9 24.6 - - + +
152A VAL 3.5 31.2 - - - +
154A CYS* 4.1 4.7 - - - -
256A PHE* 3.6 26.9 - - + -
294A ALA* 4.2 5.2 - - + +
295A PRO 3.4 23.8 - - - +
296A TRP* 4.3 1.6 - - - -
297A ILE* 4.9 0.7 - - - -
356A TYR* 1.3 78.3 - - - +
358A GLN* 1.3 62.1 + - - +
363A THR* 3.7 1.9 - - - +
364A LEU* 3.1 51.0 + - + +
366A VAL* 3.8 11.6 - - + +
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Residues in contact with GLN 358 (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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149A ILE* 4.1 0.5 - - - +
151A LEU* 3.7 8.0 - - - +
294A ALA* 3.9 2.9 - - - +
297A ILE* 5.1 1.2 - - + +
356A TYR* 3.9 20.5 + - + -
357A ILE* 1.3 76.2 - - - +
359A ALA* 1.3 63.6 + - - +
362A LYS 3.7 4.0 - - - -
363A THR* 3.2 27.0 + - + +
653A PRO* 5.3 1.0 - - - +
654A PHE 4.1 10.4 + - - +
656A PHE 3.5 8.1 + - - -
657A LYS* 3.4 30.2 - - - +
658A TRP* 2.8 72.1 + - + +
659A TRP* 3.5 3.0 - - - -
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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