Contacts of the strand formed by residues 443 - 447 (chain A) in PDB entry 2JGN
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 THR 443 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A LEU* 3.8 17.2 - - + +
439A LYS* 3.8 25.8 + - - +
441A SER 4.1 1.0 + - - -
442A LEU* 1.3 76.4 - - - +
444A LEU* 1.3 59.8 + - - +
445A VAL* 4.0 9.4 + - + -
486A PHE* 3.4 3.0 - - - -
492A PRO 3.0 9.8 + - - -
493A ILE* 3.5 11.3 - - + +
494A LEU 3.1 24.6 + - - +
511A HIS* 3.4 16.9 + - + +
513A ILE* 3.6 31.4 - - + -
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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
----------------------------------------------------------
442A LEU 3.9 1.0 - - - -
443A THR* 1.3 73.8 - - - +
445A VAL* 1.3 55.1 + - - +
446A PHE* 3.6 34.5 + - + -
486A PHE* 4.2 8.5 - - + -
494A LEU* 3.5 44.0 - - + +
496A ALA* 4.2 13.2 - - + -
506A ILE* 4.0 18.8 - - + -
509A VAL* 4.3 9.6 - - + -
511A HIS 2.8 13.5 + - - +
512A VAL* 3.4 6.6 - - + +
513A ILE* 2.7 32.7 + - - +
530A ARG* 3.9 23.6 - - + -
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Residues in contact with VAL 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 4.5 12.1 - - + -
434A LEU* 5.3 0.7 - - + -
443A THR* 4.0 14.8 - - + -
444A LEU* 1.3 76.4 - - - +
446A PHE* 1.3 61.8 + - - +
447A VAL* 3.8 1.2 + - + -
456A LEU* 3.9 21.1 - - + -
493A ILE* 3.8 24.7 - - + -
494A LEU 2.9 10.2 + - - +
495A VAL* 3.4 9.3 - - + +
496A ALA 2.9 26.7 + - - +
513A ILE* 3.3 20.0 - - + +
515A PHE* 3.7 28.0 - - + -
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Residues in contact with PHE 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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444A LEU* 3.6 31.6 - - + -
445A VAL* 1.3 71.0 - - - +
447A VAL* 1.3 61.0 + - - +
496A ALA* 3.3 22.7 - - + -
497A THR 4.1 19.1 - - - -
498A ALA* 4.5 7.4 - - - -
512A VAL* 3.9 12.3 - - + -
513A ILE 2.8 9.6 + - - +
514A ASN* 3.7 17.5 - - - +
515A PHE* 3.0 26.7 + - - +
516A ASP 3.2 6.0 + - - +
523A GLU* 5.9 0.2 - - - -
527A ARG* 3.5 60.6 - - + +
530A ARG* 3.9 18.6 - - - -
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Residues in contact with VAL 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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445A VAL* 4.5 0.9 - - + -
446A PHE* 1.3 79.0 - - - +
448A GLU* 1.3 62.1 + - - +
449A THR 3.6 10.1 - - - +
452A GLY* 4.6 7.0 - - - +
453A ALA* 3.6 35.2 - - + +
456A LEU* 3.8 29.8 - - + -
495A VAL* 4.1 8.7 - - + -
496A ALA 2.9 11.7 + - - +
497A THR* 3.6 16.5 - - + -
498A ALA* 4.1 4.5 + - - +
515A PHE* 3.9 14.6 - - + -
516A ASP* 3.4 11.2 - - - +
527A ARG* 4.6 7.2 + - - -
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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