Contacts of the strand formed by residues 345 - 350 (chain E) in PDB entry 3HYW
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 345 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199E ILE* 6.5 0.7 - - + -
313E THR* 3.3 24.0 - - + +
315E MET* 3.8 6.5 - - - -
344E SER* 1.3 73.4 + - - +
346E ILE* 1.3 59.2 + - - +
347E CSS 3.9 14.3 - - - -
358E PHE 3.7 0.5 - - - +
359E PHE* 3.2 11.2 - - - -
360E ALA* 2.8 39.2 + - + +
363E VAL* 3.2 26.2 - - + -
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Residues in contact with ILE 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E THR* 5.2 0.3 + - - -
315E MET* 3.6 31.4 - - + +
345E ALA* 1.3 71.7 - - - +
347E CSS 1.3 65.1 + - - +
348E ILE* 4.3 3.6 - - + -
357E PHE* 3.5 35.9 - - + -
358E PHE 3.4 4.3 - - - +
359E PHE* 3.5 20.9 - - + -
407E LEU* 4.5 2.9 - - + -
411E LEU* 3.7 28.7 - - + -
413E VAL* 6.0 0.2 - - + -
441E FAD 4.5 1.2 - - - +
500E DCQ 3.3 59.8 - - + +
600E LMT 5.2 4.0 - - + -
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Residues in contact with CSS 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E ILE* 5.6 4.7 - - + -
313E THR* 3.5 35.9 - - - -
345E ALA* 4.0 10.3 - - - -
346E ILE* 1.3 79.2 - - - +
348E ILE* 1.3 61.5 + - - +
349E ALA 4.1 0.4 - - - -
356E GLY 3.9 0.7 - - - +
357E PHE* 3.7 0.3 - - - -
358E PHE* 2.6 52.0 + - + +
441E FAD 4.5 2.7 - - - -
500E DCQ 5.2 0.4 - - - -
800E PS9 3.7 39.7 - - - -
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Residues in contact with ILE 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E GLU* 3.4 3.6 - - - +
346E ILE* 4.3 2.0 - - + -
347E CSS 1.3 77.7 - - - +
349E ALA* 1.3 61.2 + - - +
355E ALA* 3.8 13.0 - - + -
356E GLY 3.3 10.8 - - - +
357E PHE* 3.8 26.2 - - + -
378E ALA* 3.4 28.5 - - + +
381E PHE* 3.4 35.0 - - + -
382E LYS* 2.9 48.3 + - + +
441E FAD 4.1 3.9 + - - -
500E DCQ 3.8 21.3 + - - +
800E PS9 4.6 6.3 - - - -
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Residues in contact with ALA 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E GLY 4.9 2.7 - - - +
161E TYR* 5.5 3.6 - - + -
162E GLU* 3.6 18.2 - - + +
194E PHE* 6.4 0.4 - - + -
347E CSS 4.1 0.8 - - - -
348E ILE* 1.3 68.8 - - - +
350E ASP* 1.3 63.6 + - - +
351E PHE* 3.3 25.0 - - + -
355E ALA* 3.2 4.8 - - - +
356E GLY 2.8 38.2 + - - +
358E PHE* 4.5 10.7 - - + -
800E PS9 4.4 14.7 - - - -
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Residues in contact with ASP 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E HIS* 2.7 24.9 + - - +
52E TRP* 5.8 0.8 - - - -
53E ARG* 5.2 0.3 + - - -
162E GLU* 2.7 31.4 + - - +
166E MET* 3.5 24.5 - - + +
348E ILE 3.5 2.0 + - - -
349E ALA* 1.3 72.8 - - - +
351E PHE* 1.3 72.6 + - - +
352E GLY* 3.4 7.2 + - - -
354E ASP 3.7 1.9 - - - +
355E ALA* 3.8 5.6 - - - -
379E HIS* 2.9 41.1 + - - +
382E LYS* 3.5 19.0 - - + +
383E THR* 4.9 2.6 + - - -
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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