Contacts of the strand formed by residues 512 - 516 (chain A) in PDB entry 1RS0
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 ILE 512 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474A ILE* 4.2 9.2 - - + -
475A SER 3.4 9.0 - - - +
476A VAL* 4.4 12.8 - - + -
503A PHE* 3.8 36.6 - - + -
507A ASP* 4.3 13.9 - - + +
508A LYS 3.7 15.7 - - - +
509A GLU* 3.1 15.4 + - - +
510A HIS 3.1 0.2 - - - -
511A SER* 1.3 85.1 - - - +
513A LYS* 1.3 75.5 + - - +
523A LEU 4.3 2.1 - - - +
525A ILE* 3.6 29.7 + - + +
528A VAL* 3.9 20.0 - - + -
555A ILE* 4.9 3.6 - - + -
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Residues in contact with LYS 513 (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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473A LYS 4.0 0.3 - - - +
474A ILE* 3.5 4.7 - - - +
475A SER* 2.9 44.7 + - - +
477A ILE* 6.3 1.3 - - + -
510A HIS* 3.3 32.5 + - - +
511A SER 5.1 2.7 - - - +
512A ILE* 1.3 81.4 + - - +
514A VAL* 1.3 66.5 + - - +
522A ASP* 4.1 26.0 - - + +
523A LEU 3.5 13.2 - - - +
524A GLU* 3.1 32.9 - - + +
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Residues in contact with VAL 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ALA* 4.3 9.6 - - + -
473A LYS 3.5 7.4 - - - +
474A ILE* 4.4 9.2 - - + -
496A VAL* 4.6 6.7 - - + -
512A ILE* 5.1 0.7 - - + -
513A LYS* 1.3 79.7 - - - +
515A SER* 1.3 64.5 + - - +
516A VAL* 4.0 21.5 - - + -
522A ASP* 3.5 2.7 - - - -
523A LEU* 2.6 46.8 + - + +
525A ILE* 3.9 22.4 - - + -
555A ILE* 4.3 20.2 - - + -
557A LEU* 4.2 22.2 - - + -
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Residues in contact with SER 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A GLN 4.3 0.3 - - - +
472A ALA* 3.4 0.7 - - - -
473A LYS* 2.8 54.8 + - - +
514A VAL* 1.3 74.4 - - - +
516A VAL* 1.3 66.6 + - - +
518A GLY* 5.6 1.0 + - - -
519A GLU 4.3 13.0 + - - -
521A ARG 4.8 6.5 - - - -
522A ASP* 4.1 15.3 - - - -
523A LEU* 5.2 0.4 - - - -
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Residues in contact with VAL 516 (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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469A PRO 5.7 0.7 - - - +
471A GLN 4.2 9.0 - - - +
472A ALA* 3.6 23.8 - - + -
490A VAL* 4.4 12.1 - - + -
496A VAL* 5.2 1.6 - - + -
514A VAL* 4.0 11.6 - - + -
515A SER* 1.3 80.0 + - - +
517A GLY* 1.3 62.0 + - - +
518A GLY 3.1 8.8 + - - -
519A GLU* 3.3 26.5 + - - +
521A ARG 5.5 0.8 + - - -
523A LEU* 3.9 22.0 - - + +
561A LEU* 4.0 13.0 - - + -
567A ILE* 3.9 26.9 - - + -
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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