Contacts of the strand formed by residues 377 - 382 (chain E) in PDB entry 3FZ7
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 377 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E THR 4.3 6.3 - - - +
215E GLY* 4.1 15.0 - - - -
350E ALA* 3.8 2.9 - - - +
367E CYS* 3.5 7.3 - - - -
369E GLY* 3.0 23.7 + - - -
375E ILE* 2.7 27.8 + - + +
376E PRO* 1.3 74.8 - - - +
378E VAL* 1.3 66.3 + - - +
379E CYS 4.2 0.4 - - - -
422E ARG* 5.0 4.9 - - + -
423E ILE 3.3 10.3 - - - +
424E MET* 4.1 10.1 - - + -
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Residues in contact with VAL 378 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350E ALA* 3.3 33.2 - - + +
353E LEU* 4.2 9.4 - - + -
354E ALA* 3.8 16.2 - - + +
357E ILE* 5.1 3.8 - - + -
365E PHE* 3.8 26.2 - - + -
367E CYS 3.4 10.3 - - - +
377E ALA* 1.3 77.5 - - - +
379E CYS* 1.3 65.1 + - - +
380E PHE* 4.1 12.2 - - + -
421E MET 3.7 1.2 - - - +
422E ARG* 3.2 4.6 - - - +
423E ILE* 2.8 56.0 + - + +
425E CYS* 5.1 0.4 - - - -
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Residues in contact with CYS 379 (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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213E TYR 3.9 20.6 - - - -
214E THR* 3.3 29.2 - - - +
365E PHE* 3.5 1.1 - - - -
366E ILE* 2.8 43.2 + - + -
367E CYS* 2.9 18.9 + - + +
378E VAL* 1.3 76.7 - - - +
380E PHE* 1.3 65.5 + - - +
420E VAL* 4.0 20.0 - - - -
421E MET 3.4 4.7 - - - +
422E ARG* 4.5 5.4 - - + -
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Residues in contact with PHE 380 (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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357E ILE* 3.8 22.2 - - + -
363E TYR* 3.6 36.8 - + + -
364E GLU 3.4 13.5 - - - +
365E PHE* 3.6 26.9 - + + -
366E ILE* 4.4 2.2 - - - +
378E VAL* 4.1 9.0 - - + -
379E CYS* 1.3 77.0 - - - +
381E LYS* 1.3 61.3 + - - +
392E LEU* 3.9 8.2 - - + +
420E VAL* 3.2 7.2 - - - -
421E MET* 2.7 80.8 + - + +
423E ILE* 4.6 5.2 - - + -
441E TYR* 3.3 28.5 - + - -
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Residues in contact with LYS 381 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363E TYR* 3.4 6.0 - - - +
364E GLU* 2.8 66.7 + - + +
366E ILE* 4.8 10.3 - - + -
380E PHE* 1.3 77.8 - - - +
382E LEU* 1.3 79.7 + - - +
384E ASP* 2.9 41.0 + - - +
392E LEU* 4.0 4.5 - - - -
418E ILE* 3.7 40.6 - - + -
419E VAL 3.5 20.0 - - - +
420E VAL* 4.0 3.8 - - + -
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Residues in contact with LEU 382 (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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362E PRO* 3.6 7.2 - - + +
363E TYR* 3.7 28.5 - - + -
381E LYS* 1.3 90.8 + - - +
383E LYS* 1.3 71.5 + - - +
384E ASP* 3.1 1.2 + - - -
386E GLU* 4.3 9.0 - - + +
388E PRO* 3.9 29.6 - - + -
390E TYR* 3.7 24.5 - - + +
391E THR* 4.6 10.3 - - + -
392E LEU* 3.9 23.4 - - + +
419E VAL 4.4 1.2 + - - -
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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