Contacts of the strand formed by residues 579 - 585 (chain C) in PDB entry 3DXD
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 579 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546C TYR* 3.4 1.1 - - - -
547C TYR* 2.8 47.6 + - + -
577C GLN 3.4 7.4 + - - -
578C TRP* 1.3 68.8 - - - +
580C PRO* 1.3 70.1 - - - +
581C SER* 3.3 2.3 + - - -
594C HIS* 3.6 34.8 - - + +
601C LEU* 3.8 22.0 - - + -
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Residues in contact with PRO 580 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544C GLN* 3.6 14.8 - - - +
545C VAL 3.7 6.1 - - - +
546C TYR* 3.7 15.7 - - + -
578C TRP 3.2 12.3 - - - +
579C THR* 1.3 86.7 - - + +
581C SER* 1.3 61.5 + - - +
594C HIS* 3.7 18.0 + - + +
595C GLN* 3.0 46.9 + - + +
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Residues in contact with SER 581 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544C GLN* 3.5 8.6 + - - +
545C VAL* 3.0 31.0 + - - +
546C TYR 4.3 0.3 - - - -
547C TYR* 3.5 21.3 + - - +
579C THR 3.3 11.6 + - - -
580C PRO* 1.3 76.0 - - - +
582C HIS* 1.3 65.1 + - - +
583C VAL* 5.9 0.2 - - - +
592C ILE* 4.1 5.8 - - - +
593C LEU 2.8 27.8 - - - -
595C GLN* 3.7 7.6 - - - +
601C LEU* 4.1 8.3 - - - -
637C PHE* 5.2 0.9 - - - -
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Residues in contact with HIS 582 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543C PHE* 6.2 4.3 - - + -
545C VAL* 4.7 7.0 - - + -
581C SER* 1.3 80.4 - - - +
583C VAL* 1.3 73.6 + - - +
584C SER* 5.2 2.1 - - - -
591C THR 3.6 1.0 - - - +
592C ILE* 3.8 1.2 - - - -
593C LEU* 3.0 55.9 + - + +
594C HIS 4.4 0.4 - - - -
595C GLN* 4.2 13.7 - - - -
598C GLU* 3.0 34.7 + - - -
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Residues in contact with VAL 583 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545C VAL* 4.8 4.6 - - + +
581C SER* 5.9 0.2 - - - +
582C HIS* 1.3 83.5 + - - +
584C SER* 1.3 63.0 + - - +
585C VAL* 3.6 24.3 + - + +
590C LEU* 4.1 23.1 - - + -
591C THR 3.4 9.6 - - - +
592C ILE* 4.7 8.5 - - + +
623C PHE* 6.0 1.6 - - + -
637C PHE* 3.8 33.2 - - + -
646C LEU* 4.0 30.1 - - + +
650C VAL* 5.2 2.2 - - + -
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Residues in contact with SER 584 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582C HIS* 4.0 3.9 + - - -
583C VAL* 1.3 70.9 - - - +
585C VAL* 1.3 59.7 + - - +
586C ALA* 3.8 0.8 + - - +
589C THR 3.8 2.1 - - - +
590C LEU* 3.3 4.0 - - - -
591C THR* 2.7 50.0 + - - -
593C LEU* 3.9 19.7 - - - +
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Residues in contact with VAL 585 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583C VAL* 3.6 26.1 + - + +
584C SER* 1.3 73.9 + - - +
586C ALA* 1.3 60.8 + - - +
587C PRO* 4.8 1.3 - - + +
590C LEU* 3.7 14.1 - - + -
646C LEU* 4.4 5.4 - - + -
649C ALA* 3.5 44.0 - - + +
650C VAL* 4.3 7.0 - - + -
653C ALA* 3.7 17.7 - - + -
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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