Contacts of the strand formed by residues 440 - 446 (chain A) in PDB entry 5GJE
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 440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A ASP* 2.7 38.5 + - + +
438A VAL* 3.3 30.7 - - + -
439A GLY* 1.3 80.5 - - - +
441A MET* 1.3 57.2 + - - +
442A TYR* 3.7 31.1 - - + +
454A ARG* 3.5 46.8 + - - -
455A ALA* 3.2 22.2 - - - +
456A ALA* 4.3 2.9 - - + -
457A LEU* 3.5 7.2 - - - +
461A ASP* 5.5 6.3 - - + -
500A THR* 5.7 0.7 - - - -
588A PRO* 4.1 24.8 - - + +
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Residues in contact with MET 441 (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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399A TYR* 4.6 11.0 - - - -
408A ILE* 4.6 13.9 - - + -
421A LEU* 3.8 25.6 - - + -
422A ILE* 5.1 2.7 - - + -
432A ILE* 4.7 5.4 - - + -
433A VAL 3.5 4.7 - - - +
434A LEU* 3.7 14.6 - - + -
440A TYR* 1.3 73.1 - - - +
442A TYR* 1.3 61.6 + - - +
443A TRP* 3.3 24.9 - - + -
455A ALA* 2.6 32.5 + - + +
456A ALA 3.1 16.2 - - - +
457A LEU* 3.5 16.8 - - + -
458A ASP 4.1 1.6 - - - +
459A GLY* 3.2 38.4 - - - +
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Residues in contact with TYR 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A ILE* 3.5 2.5 - - - +
433A VAL* 2.8 48.1 + - + +
435A ASP* 4.1 14.0 + - + -
438A VAL* 5.1 0.9 - - - +
440A TYR* 3.7 33.2 - - + +
441A MET* 1.3 76.1 - - - +
443A TRP* 1.3 63.2 + - - +
452A ILE* 5.5 2.5 - - + -
453A GLU 3.8 7.4 - - - +
454A ARG* 3.4 31.8 + - + +
465A LEU* 3.5 24.9 - - + -
476A LEU* 4.0 6.3 - - + -
478A LEU* 4.0 35.6 - - + +
485A ILE* 4.6 11.7 - - + -
500A THR* 3.3 29.7 + - - -
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Residues in contact with TRP 443 (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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401A THR* 5.1 1.8 - - + -
408A ILE* 3.6 23.7 - - + +
422A ILE* 3.2 35.4 - - + +
424A GLU* 4.8 1.0 + - - -
429A PRO* 4.4 8.1 - - + +
431A ALA 3.0 15.9 - - - +
432A ILE* 4.0 12.1 - - + -
441A MET* 3.3 39.5 - - - -
442A TYR* 1.3 77.2 - - - +
444A THR* 1.3 70.4 + - - +
445A ASP* 2.9 26.9 + - + +
452A ILE* 3.8 2.7 - - - -
453A GLU* 3.1 61.9 + - + +
454A ARG* 3.7 19.1 - - - -
455A ALA* 3.8 9.0 - - + -
462A ARG* 4.2 1.6 - - - -
476A LEU* 3.6 6.7 - - - +
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Residues in contact with THR 444 (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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430A ARG* 3.0 22.0 + - - +
431A ALA* 2.8 19.6 + - + +
443A TRP* 1.3 79.2 - - - +
445A ASP* 1.3 60.8 + - - +
451A LYS 4.0 5.2 - - - -
452A ILE* 4.4 8.7 - - + -
473A PRO* 3.3 36.6 + - + -
474A ASN 3.7 12.3 - - - +
475A GLY 4.1 2.7 - - - +
476A LEU* 3.4 37.0 - - + -
487A TRP* 5.3 0.2 - - + -
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Residues in contact with ASP 445 (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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424A GLU* 4.6 1.9 - - - +
427A GLU* 3.6 19.2 - - - +
428A GLU 3.1 21.1 - - - +
429A PRO* 3.4 13.2 - - + +
430A ARG* 3.7 4.0 - - - -
443A TRP* 2.9 22.1 + - + -
444A THR* 1.3 75.5 - - - +
446A TRP* 1.3 67.6 + - - +
450A PRO* 3.8 1.2 - - - +
451A LYS* 3.1 37.7 + - - +
453A GLU* 3.0 19.5 - - - +
473A PRO* 4.0 3.9 - - - +
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Residues in contact with TRP 446 (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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427A GLU* 2.9 14.3 - - - +
428A GLU* 3.1 34.1 + - - +
430A ARG* 3.3 52.7 - - + +
445A ASP* 1.3 77.9 - - - +
447A GLY* 1.3 59.9 + - - +
450A PRO* 4.3 7.6 - - - -
472A TRP* 3.3 49.6 - + + -
473A PRO* 2.7 42.0 + - + -
474A ASN* 3.7 19.5 - - - -
490A ALA* 5.1 0.7 - - + -
515A HIS* 3.7 33.0 - + + -
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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