Contacts of the strand formed by residues 443 - 450 (chain A) in PDB entry 5JPM
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 GLU 443 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378A LEU* 4.6 3.8 - - - -
409A VAL* 4.3 1.9 - - - +
410A SER* 3.1 43.7 + - - +
441A ILE* 3.9 3.3 - - - +
442A SER* 1.3 83.8 - - - +
444A LEU* 1.3 61.3 + - - +
445A GLN* 4.1 17.7 + - + -
461A THR* 3.6 21.1 - - + +
462A VAL 3.3 12.1 - - - +
463A ALA* 4.2 7.6 - - + -
464A ALA* 4.3 3.1 - - - +
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Residues in contact with LEU 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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378A LEU* 3.8 35.4 - - + +
384A PHE* 4.1 20.9 - - + -
407A ALA* 4.3 5.2 - - + -
408A THR 3.5 17.7 - - - +
409A VAL* 3.9 23.8 - - + -
435A ILE* 4.7 3.4 - - + -
437A ILE* 4.2 16.4 - - + -
443A GLU* 1.3 74.8 - - - +
445A GLN* 1.3 61.5 + - - +
446A LEU* 3.7 32.4 + - + +
460A LEU 4.0 0.5 - - - +
461A THR* 3.4 2.1 - - - +
462A VAL* 2.6 43.8 + - + +
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Residues in contact with GLN 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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406A SER 3.7 2.3 - - - +
407A ALA* 3.8 0.9 - - - -
408A THR* 2.9 54.1 + - - +
410A SER* 4.4 9.5 + - - +
443A GLU* 4.1 20.1 + - + +
444A LEU* 1.3 75.8 - - - +
446A LEU* 1.3 61.8 + - - +
447A SER* 5.3 1.0 + - - -
460A LEU 3.5 4.3 - - - +
461A THR* 3.4 28.8 + - + +
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Residues in contact with LEU 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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371A LEU* 6.2 0.2 - - + -
384A PHE* 3.8 30.1 - - + -
386A LEU* 4.0 20.4 - - + -
405A VAL* 4.3 7.2 - - + -
406A SER 3.7 0.9 - - - -
407A ALA* 3.6 30.3 - - + -
435A ILE* 3.7 13.9 - - + -
444A LEU* 3.7 22.7 - - + +
445A GLN* 1.3 75.0 - - - +
447A SER* 1.3 63.9 + - - +
448A VAL* 4.1 6.1 - - + -
458A ALA 4.7 0.2 - - - -
459A ARG* 3.3 5.9 - - - +
460A LEU* 2.6 57.0 + - + +
462A VAL* 5.3 2.7 - - + -
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Residues in contact with SER 447 (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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404A LYS 3.9 0.9 - - - +
405A VAL* 3.4 1.3 - - - +
406A SER* 2.7 50.7 + - - -
445A GLN 5.3 0.5 + - - -
446A LEU* 1.3 74.6 + - - +
448A VAL* 1.3 61.2 + - - +
449A SER* 4.1 1.1 + - - -
458A ALA 3.9 3.1 - - - -
459A ARG* 3.3 37.1 + - - +
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Residues in contact with VAL 448 (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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369A LEU* 3.7 20.4 - - + -
371A LEU* 4.4 14.6 - - + -
386A LEU* 4.2 28.0 - - + -
388A ALA* 5.1 0.7 - - + -
403A VAL* 3.7 26.7 - - + -
404A LYS 3.5 5.4 - - - +
405A VAL* 4.1 17.0 - - + +
446A LEU* 4.8 4.5 - - + -
447A SER* 1.3 77.7 - - - +
449A SER* 1.3 63.3 + - - +
450A ALA 4.3 0.4 - - - -
456A ALA 3.7 0.3 - - - +
457A ILE* 3.3 8.0 - - - +
458A ALA* 2.9 41.6 + - + +
460A LEU* 6.2 0.4 - - + +
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Residues in contact with SER 449 (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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402A PRO 4.1 0.9 - - - +
403A VAL* 3.4 1.4 - - - -
404A LYS* 2.7 50.3 + - - +
447A SER 4.1 1.1 + - - -
448A VAL* 1.3 73.8 - - - +
450A ALA* 1.3 58.4 + - - +
451A GLY 5.0 0.4 + - - -
455A PRO* 3.2 27.9 - - - +
456A ALA 3.5 4.3 - - - -
457A ILE* 4.5 7.4 - - - +
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Residues in contact with ALA 450 (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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367A PHE* 4.6 3.2 - - - +
369A LEU* 3.7 31.2 - - + +
390A VAL* 4.0 13.9 - - + -
401A ILE* 4.4 1.6 - - + -
402A PRO 3.6 4.5 - - - +
403A VAL* 3.7 20.4 - - + -
449A SER* 1.3 74.3 + - - +
451A GLY* 1.3 61.8 + - - +
455A PRO* 3.2 0.6 - - - +
456A ALA* 2.7 40.3 + - + +
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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