Contacts of the strand formed by residues 416 - 422 (chain E) in PDB entry 3QS7
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 TYR 416 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369E PHE* 3.6 33.7 - + + -
383E TRP* 4.2 10.8 - + + -
384E THR 3.8 4.3 - - - -
385E PHE* 3.6 39.8 - + + -
406E PHE* 3.8 37.0 - + - -
408E ASN 5.0 0.4 - - - -
409E HIS* 2.6 31.2 + - + -
412E GLN* 3.0 30.4 + - - +
414E GLY 3.6 14.8 - - - -
415E GLU* 1.4 70.3 - - - +
417E ILE* 1.3 61.4 + - - +
429E LYS 3.8 1.6 - - - +
431E PHE* 3.0 38.4 + - + +
433E LEU* 4.5 7.2 - - + -
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Residues in contact with ILE 417 (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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382E THR 3.7 1.7 - - - +
383E TRP* 3.6 3.5 - - - -
384E THR* 2.9 50.4 + - - +
385E PHE* 5.6 0.7 - - - -
386E SER 6.1 0.2 - - - +
415E GLU* 3.5 46.4 - - + +
416E TYR* 1.3 71.2 - - - +
418E PHE* 1.4 65.9 + - - +
419E HIS* 3.9 5.4 + - + +
428E THR* 4.5 14.4 - - - -
429E LYS 3.5 11.2 - - - +
430E MET* 4.2 7.9 - - + +
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Residues in contact with PHE 418 (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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371E VAL* 3.7 32.3 - - + -
373E PHE* 4.4 13.9 - + - -
379E ILE* 4.8 0.2 - - + -
381E CYS* 3.7 20.6 - - + -
382E THR 3.6 4.3 - - - -
383E TRP* 3.4 44.4 - + + -
392E CYS* 4.0 0.7 - - - -
404E SER* 3.5 26.0 - - - -
416E TYR 4.0 0.6 + - - -
417E ILE* 1.4 70.3 - - - +
419E HIS* 1.3 59.8 + - - +
420E ALA* 3.8 25.1 - - + -
427E PHE* 4.0 17.7 - + - -
428E THR* 3.1 4.3 + - - -
429E LYS* 2.9 40.7 + - + +
431E PHE* 4.8 0.9 - - + -
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Residues in contact with HIS 419 (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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380E ARG 4.0 1.4 - - - +
381E CYS* 3.6 0.9 - - - -
382E THR* 2.9 44.8 + - - +
384E THR* 6.5 0.9 - - - -
417E ILE* 3.9 6.2 + - + +
418E PHE* 1.3 71.2 - - - +
420E ALA* 1.3 60.3 + - - +
427E PHE 3.3 10.5 - - - +
428E THR* 4.2 8.3 - - - +
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Residues in contact with ALA 420 (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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350E ILE* 3.6 6.6 - - + +
373E PHE* 6.3 0.4 - - + -
379E ILE* 3.7 28.9 - - + -
380E ARG 3.4 4.5 - - - -
381E CYS* 4.0 2.2 - - + -
418E PHE* 3.8 25.2 + - + -
419E HIS* 1.3 74.6 - - - +
421E GLU* 1.3 61.1 + - - +
427E PHE* 2.9 42.7 + - + +
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Residues in contact with GLU 421 (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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350E ILE* 3.8 3.4 - - - -
379E ILE* 3.8 5.7 - - - +
380E ARG* 2.9 37.2 + - + +
420E ALA* 1.3 76.7 - - - +
422E ASN* 1.3 62.3 + - - +
425E ALA 3.4 13.2 - - - +
426E GLN* 3.8 11.7 - - + -
427E PHE 4.8 0.2 - - - +
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Residues in contact with ASN 422 (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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348E GLY* 3.7 4.7 - - - -
349E PHE 3.3 25.1 + - - -
350E ILE* 3.4 17.8 - - - +
376E TYR 3.5 5.9 + - - -
377E PRO* 3.4 38.4 + - + +
378E GLN 4.4 3.6 - - - +
379E ILE* 3.7 7.6 - - + +
421E GLU* 1.3 77.3 - - - +
423E ASP* 1.4 63.0 + - - +
424E ASP 3.0 26.9 + - - -
425E ALA* 2.8 29.4 + - - +
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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