Contacts of the strand formed by residues 575 - 579 (chain B) in PDB entry 1D0N
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 ALA 575 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568B VAL* 5.7 0.2 - - + -
569B LEU 3.2 8.3 - - - +
570B LYS* 4.5 9.2 - - + +
574B ALA* 1.3 76.2 - - - +
576B TYR* 1.3 62.5 + - - +
595B LEU* 4.5 13.9 - - + -
600B ALA* 4.0 27.4 - - + -
601B GLN 4.1 12.4 + - - +
602B PRO* 3.7 1.4 - - + +
603B VAL* 3.0 31.0 + - - +
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Residues in contact with TYR 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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568B VAL* 3.3 9.4 - - - +
569B LEU* 2.8 61.6 + - + +
571B THR* 4.4 18.6 - - + -
574B ALA* 4.7 13.8 - - + +
575B ALA* 1.3 75.4 - - - +
577B LEU* 1.3 60.1 + - - +
578B TRP 3.8 0.4 - - - -
595B LEU* 5.0 1.2 - - - +
602B PRO* 5.5 1.1 - - - -
603B VAL* 3.5 21.8 - - + +
605B VAL* 4.0 21.1 - - + -
611B PRO* 5.1 8.5 - - + -
613B SER* 2.8 33.7 + - - -
614B PHE* 3.8 42.4 - + + -
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Residues in contact with LEU 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566B ALA* 4.7 4.0 - - + -
567B PHE 3.6 10.3 - - - +
568B VAL* 4.0 4.5 - - + +
576B TYR* 1.3 71.2 - - - +
578B TRP* 1.3 64.2 + - - +
579B VAL* 3.5 5.2 + - + +
588B LYS* 4.8 10.5 - - + +
591B ALA* 3.3 32.3 - - + -
592B GLN* 4.6 16.6 - - + +
595B LEU* 4.0 22.9 - - + -
602B PRO* 4.4 11.2 - - + -
603B VAL 3.1 8.9 + - - +
604B GLN* 3.6 31.0 - - + +
605B VAL* 3.0 26.2 + - - +
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Residues in contact with TRP 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561B LEU* 4.3 15.1 - - + +
562B ASN 3.2 32.1 - - - -
566B ALA* 3.4 1.9 - - - +
567B PHE* 2.7 70.6 + + + +
569B LEU 6.2 0.2 - - - +
576B TYR 3.8 1.8 - - - -
577B LEU* 1.3 72.6 - - - +
579B VAL* 1.3 59.2 + - - +
580B GLY* 3.7 18.4 - - - -
605B VAL* 3.4 24.2 - - + +
607B GLU* 3.6 35.1 - - + +
610B GLU* 3.4 22.8 + - + +
614B PHE* 3.6 32.3 - + + -
624B TYR* 3.0 27.1 + + - -
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Residues in contact with VAL 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566B ALA* 4.4 7.0 - - + -
577B LEU* 3.5 5.1 + - + +
578B TRP* 1.3 73.3 - - - +
580B GLY* 1.3 74.2 + - - +
581B ALA* 4.6 0.2 - - - -
583B ALA* 3.6 12.3 - - + -
588B LYS* 3.3 40.2 - - + +
604B GLN* 4.3 22.2 - - + +
605B VAL 3.1 18.9 + - - +
606B ALA* 3.9 10.9 - - + +
607B GLU 3.3 15.8 + - - -
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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