Contacts of the strand formed by residues 578 - 582 (chain N) in PDB entry 3HOU
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 578 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576N ASP 3.0 11.6 + - - -
577N ALA* 1.3 67.7 - - - +
579N ARG* 1.3 60.9 + - - +
580N VAL* 3.2 7.3 + - + +
589N VAL* 3.1 11.5 - - - +
590N HIS* 3.5 18.9 + - - +
593N PRO* 3.5 36.6 - - + +
617N ARG* 5.4 4.9 + - + -
622N LYS* 3.5 17.1 - - - +
623N GLU 3.6 33.4 - - - +
624N LEU* 4.0 9.4 - - + +
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Residues in contact with ARG 579 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303N TYR* 4.1 18.4 - - - -
380N TYR* 3.7 23.8 - - - -
383N ASN* 5.1 8.5 - - - +
384N ARG* 6.2 0.6 - - - +
569N TYR* 6.0 0.9 - - - +
577N ALA 2.8 14.9 + - - +
578N THR* 1.3 68.1 - - - +
580N VAL* 1.3 60.6 + - - +
581N PHE* 3.9 7.2 + - + -
586N TRP* 2.9 47.6 - - + +
588N GLY 4.1 0.2 - - - +
589N VAL* 3.4 12.6 - - + -
621N GLU* 3.3 18.0 + - - +
622N LYS* 2.4 34.6 + - - +
623N GLU* 3.2 32.9 + - + +
624N LEU 3.1 19.9 + - - -
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Residues in contact with VAL 580 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558N LEU* 3.7 26.2 - - + -
563N MET* 3.5 26.0 - - + -
578N THR* 3.2 10.0 + - + +
579N ARG* 1.3 72.0 - - - +
581N PHE* 1.3 73.6 + - - +
582N VAL* 5.3 1.8 - - + -
586N TRP* 3.1 21.0 - - - -
587N HIS* 3.2 16.1 + - + -
588N GLY 3.0 7.1 + - - +
589N VAL* 4.1 0.2 - - - +
590N HIS* 4.5 6.7 - - + -
596N LEU* 4.4 13.2 - - + -
624N LEU* 3.5 33.7 - - + +
626N ILE* 5.6 0.2 - - + -
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Residues in contact with PHE 581 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377N PHE* 3.6 24.9 - + - -
380N TYR* 3.5 37.7 - + - -
579N ARG* 4.1 17.3 - - + -
580N VAL* 1.3 76.3 - - - +
582N VAL* 1.3 64.8 + - - +
583N ASN 4.3 0.2 - - - -
584N GLY 4.7 3.1 - - - +
585N VAL 3.1 22.9 - - - +
586N TRP* 3.8 22.9 - + + -
623N GLU* 2.9 31.9 - - + -
624N LEU 2.5 23.8 + - - +
625N LYS* 3.9 29.2 - - + +
626N ILE* 2.9 18.6 + - - +
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Residues in contact with VAL 582 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551N PRO* 4.8 11.4 - - + +
554N ILE* 4.4 12.3 - - + -
555N ILE* 4.3 12.3 - - + -
558N LEU* 5.1 7.4 - - + -
580N VAL* 5.3 0.4 - - + -
581N PHE* 1.3 73.8 - - - +
583N ASN* 1.3 78.3 + - + +
585N VAL* 3.1 23.0 + - - +
587N HIS* 3.2 30.0 - - + +
626N ILE* 3.1 43.3 - - + +
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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
------------------------------------------------------------
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