Contacts of the strand formed by residues 509 - 513 (chain B) in PDB entry 2PDA
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 509 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485B ASP 3.2 16.9 + - - +
486B TYR* 3.2 26.2 - - + -
487B VAL 3.5 8.0 + - - -
504B ILE* 3.5 7.1 - - - +
507B GLY 3.5 3.7 + - - +
508B GLY* 1.3 77.3 - - - +
510B PHE* 1.3 62.3 + - - +
540B LYS* 3.4 24.9 - - + +
542B TYR* 3.9 18.7 - - - +
570B LEU* 3.5 24.7 - - + +
571B ALA 5.6 1.1 - - - +
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Residues in contact with PHE 510 (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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487B VAL 3.2 15.3 - - - +
489B CYS* 4.2 16.2 - - + -
495B VAL* 6.2 2.2 - - + -
500B ILE* 4.3 11.9 - - + -
501B LEU* 3.5 47.1 - - + -
504B ILE* 4.3 4.3 - - + -
509B THR* 1.3 79.3 + - - +
511B VAL* 1.3 81.5 + - - +
512B LEU* 4.4 10.5 - - + -
526B LEU* 6.1 0.2 - - + -
530B ILE* 4.7 7.0 - - + -
534B ILE* 4.2 9.9 - - + -
539B LEU* 3.9 20.6 - - + -
540B LYS 3.0 7.7 + - - +
541B PHE* 3.4 30.1 - + + -
542B TYR* 2.8 25.6 + - - -
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Residues in contact with VAL 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B TYR* 3.2 44.0 - - + +
487B VAL 3.2 2.2 + - - -
488B ALA* 3.5 4.3 - - + -
489B CYS 3.0 22.7 + - - +
509B THR* 4.5 1.1 - - - +
510B PHE* 1.3 86.4 - - - +
512B LEU* 1.3 63.3 + - - +
542B TYR* 3.1 15.9 - - + +
544B ILE* 4.1 12.6 - - + -
563B MET* 3.3 33.4 - - + -
566B ALA* 4.3 4.3 - - + -
570B LEU* 4.0 14.4 - - + -
613B LEU* 5.4 0.4 - - + -
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Residues in contact with LEU 512 (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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489B CYS* 3.8 18.6 - - + +
492B PRO* 4.2 12.3 - - + +
495B VAL* 5.0 7.4 - - + -
510B PHE* 4.4 11.0 - - + -
511B VAL* 1.3 81.0 - - - +
513B ASN* 1.3 87.1 + - - +
514B SER* 3.5 12.5 + - - -
516B TRP* 4.0 10.1 - - + -
522B MET* 4.2 4.9 - - + -
526B LEU* 3.7 29.4 - - + -
541B PHE* 3.8 26.7 - - + -
542B TYR 3.1 5.0 + - - +
543B ASN* 3.7 3.5 - - - +
544B ILE* 2.8 28.4 + - - +
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Residues in contact with ASN 513 (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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489B CYS 2.9 17.8 + - - +
490B HIS* 3.3 25.6 - - - +
492B PRO* 3.2 25.1 - - - +
511B VAL* 4.8 0.8 - - - +
512B LEU* 1.3 85.6 - - - +
514B SER* 1.3 63.2 + - - +
544B ILE* 3.0 13.8 + - - -
545B ASP* 4.0 1.4 - - - +
546B ALA* 3.3 25.5 - - - +
547B VAL* 4.0 16.0 - - - +
559B ILE* 3.7 15.3 - - - +
563B MET* 4.0 12.3 - - - +
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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
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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