Contacts of the strand formed by residues 444 - 449 (chain A) in PDB entry 2JED
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 MET 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A LYS* 3.6 19.5 - - + +
432A LEU* 3.6 45.0 + - + +
433A SER* 3.8 7.6 - - - +
435A ALA* 5.1 0.2 - - - +
436A TRP* 5.1 3.6 - - - +
442A THR 3.8 2.0 + - - -
443A HIS* 1.3 73.6 - - - +
445A PHE* 1.3 63.1 + - - +
446A CYS 3.8 26.5 - - - +
447A THR* 3.8 16.6 - - - +
456A PHE* 4.8 2.2 - - + -
457A VAL 3.7 8.3 - - - +
458A MET* 3.7 22.9 - - + -
696A PHE* 3.9 26.1 - - + -
698A ASN* 3.2 21.7 + - - +
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Residues in contact with PHE 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 PHE* 3.5 37.2 - + + -
443A HIS* 4.5 14.8 - - + -
444A MET* 1.3 74.8 - - - +
446A CYS* 1.3 64.8 + - - +
457A VAL* 2.7 18.7 + - + +
458A MET 3.8 2.0 - - - -
459A GLU* 3.3 46.2 - - + -
697A MET* 3.4 10.5 - - + +
698A ASN* 2.9 46.0 + - + +
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Residues in contact with CYS 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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375A LEU* 3.5 34.3 - - + -
444A MET* 3.8 8.2 - - - +
445A PHE* 1.3 84.9 - - - +
447A THR* 1.3 62.8 + - - +
448A PHE* 4.5 4.0 - - - -
455A PHE 4.1 0.2 - - - +
456A PHE* 3.6 2.1 - - - -
457A VAL* 2.7 55.4 + - - +
696A PHE 3.4 13.9 - - - +
697A MET* 3.7 18.6 - - - -
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Residues in contact with THR 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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429A LYS* 4.0 5.7 - - + +
444A MET* 3.8 17.6 - - - +
446A CYS* 1.3 76.6 + - - +
448A PHE* 1.3 66.2 + - - +
455A PHE 3.5 9.8 + - - -
456A PHE* 3.8 16.5 - - - -
694A PHE* 2.3 48.9 - - + +
695A SEP 3.4 8.5 - - - +
696A PHE* 3.0 28.5 + - + +
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Residues in contact with PHE 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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375A LEU* 3.4 43.1 - - + +
376A LYS* 4.0 8.7 - - - -
377A ILE* 3.7 32.3 - - + -
380A PHE* 4.4 5.4 - + - -
446A CYS* 4.5 10.1 - - + -
447A THR* 1.3 78.9 - - - +
449A GLN* 1.3 68.4 + - - +
450A THR* 5.4 2.5 - - - -
455A PHE* 2.9 68.3 + + + +
457A VAL* 3.8 24.9 - - + -
694A PHE* 3.5 5.6 - - - -
695A SEP 4.0 11.7 - - - +
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Residues in contact with GLN 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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413A LYS* 2.8 29.2 + - - +
448A PHE* 1.3 82.4 - - - +
450A THR* 1.3 65.1 + - - +
453A ASN 3.4 12.6 - - - +
454A LEU* 3.8 13.0 - - + -
455A PHE* 5.1 0.7 - - - -
691A PHE* 2.7 28.3 + - - +
692A ARG* 2.8 28.6 + - - +
694A PHE* 3.7 9.7 - - + +
695A SEP 3.3 36.4 + - - +
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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