Contacts of the strand formed by residues 626 - 631 (chain A) in PDB entry 5JAJ
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 VAL 626 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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622A ILE* 3.4 5.9 - - - +
623A TYR* 2.8 40.4 + - + +
624A ARG 3.4 0.2 - - - -
625A ASN* 1.3 85.5 - - + +
627A THR* 1.3 62.8 + - - +
628A LEU* 4.0 24.9 - - + -
660A PHE* 4.8 0.2 - - + -
662A TYR* 3.8 22.7 - - + +
665A TYR* 3.9 30.7 - - + -
666A CYS* 4.1 10.3 - - - -
669A THR* 5.7 1.8 - - - +
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Residues in contact with THR 627 (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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586A TYR* 6.1 0.9 - - - +
620A GLU* 3.6 39.7 - - + +
621A MET 3.3 8.7 - - - +
622A ILE* 3.8 20.9 - - + +
626A VAL* 1.3 77.5 + - - +
628A LEU* 1.3 71.3 + - - +
629A PRO* 4.6 1.6 - - - +
665A TYR* 4.6 3.6 + - - -
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Residues in contact with LEU 628 (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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576A VAL* 4.1 25.8 - - + -
577A ASN 4.4 12.1 - - - +
578A ILE* 4.8 2.5 - - + -
620A GLU* 3.5 3.2 - - - -
621A MET* 2.7 44.6 + - + +
623A TYR* 4.8 7.9 - - + -
626A VAL* 4.0 13.0 - - + -
627A THR* 1.3 80.7 - - - +
629A PRO* 1.3 67.6 - - + +
660A PHE* 3.5 38.1 - - + -
665A TYR* 3.4 40.6 - - + +
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Residues in contact with PRO 629 (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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575A HIS 3.9 0.2 - - - +
576A VAL* 3.1 3.7 - - - -
577A ASN* 3.1 46.9 + - + +
582A PHE* 3.7 26.2 - - + -
586A TYR* 3.9 26.0 - - + +
608A ILE* 3.6 24.7 - - + -
619A MET 3.9 4.0 - - - +
620A GLU* 4.4 4.0 - - + -
627A THR 4.6 1.8 - - - +
628A LEU* 1.3 85.7 - - + +
630A ILE* 1.3 62.5 + - - +
631A LEU* 4.0 1.1 + - - +
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Residues in contact with ILE 630 (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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574A HIS* 3.5 13.9 - - + -
575A HIS 3.4 21.3 - - - +
576A VAL* 3.3 26.7 - - + -
602A TRP* 5.8 0.4 - - + -
608A ILE* 4.2 1.0 - - - +
618A GLY* 3.2 7.6 - - - -
619A MET* 2.8 55.1 + - + +
620A GLU 4.5 0.4 - - - -
621A MET* 3.3 43.7 - - + +
629A PRO* 1.3 71.5 - - - +
631A LEU* 1.3 69.4 + - - +
2X G 3.9 21.4 - - - +
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Residues in contact with LEU 631 (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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552A PHE* 5.3 3.8 - - + -
562A CYS* 4.3 10.5 - - - -
567A ILE* 3.9 26.5 - - + -
575A HIS* 2.8 22.2 + - - +
577A ASN* 4.4 3.4 - - + -
582A PHE* 4.0 32.8 - - + -
608A ILE* 4.2 13.5 - - + -
617A TRP* 3.8 5.4 - - + +
629A PRO 4.6 5.6 - - - +
630A ILE* 1.3 83.2 - - - +
632A SER* 1.3 59.5 + - - +
636A PHE* 4.0 32.8 - - + -
650A TRP* 3.2 29.6 + - + -
2X G 4.0 6.4 - - - +
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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