Contacts of the strand formed by residues 517 - 522 (chain A) in PDB entry 4JUA
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 VAL 517 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448A THR 3.1 6.3 + - - -
449A ILE* 3.4 8.7 - - + +
450A PHE* 2.8 28.1 + - - +
492A VAL* 4.0 3.4 - - - -
493A GLN* 3.4 22.7 - - + +
495A LEU* 3.8 30.3 - - + -
510A ALA* 3.9 25.1 - - + +
513A ALA* 3.5 31.6 - - + -
515A GLY 3.6 2.2 - - - +
516A PRO* 1.3 81.4 - - - +
518A LEU* 1.3 69.0 + - - +
519A ILE* 4.3 1.6 - - + -
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Residues in contact with LEU 518 (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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407A LEU* 5.9 1.6 - - + -
435A ILE* 5.6 2.7 - - + -
438A LEU* 4.2 26.5 - - + -
450A PHE* 3.3 15.0 - - + +
452A ILE* 3.8 31.2 - - + -
483A PHE* 3.8 31.9 - - + +
484A ARG* 4.6 3.4 - - - +
487A ALA* 4.0 20.6 - - + -
492A VAL* 3.8 5.6 - - + +
493A GLN 2.8 7.7 + - - +
494A ALA* 3.3 2.7 - - + -
495A LEU* 2.8 27.0 + - - +
517A VAL* 1.3 75.9 - - - +
519A ILE* 1.3 65.6 + - - +
520A GLU* 3.9 14.6 - - + +
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Residues in contact with ILE 519 (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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449A ILE* 4.4 8.3 - - + -
450A PHE 2.8 13.8 + - - +
451A VAL* 3.6 7.2 - - + -
452A ILE 2.8 27.0 + - - -
495A LEU* 3.4 11.0 - - + +
497A ALA* 4.2 10.3 - - + -
503A LEU* 4.8 3.1 - - + -
506A SER* 3.8 40.8 - - - +
507A LEU* 3.7 30.3 - - + -
510A ALA* 3.9 10.5 - - + -
517A VAL* 4.3 10.8 - - + -
518A LEU* 1.3 78.4 - - - +
520A GLU* 1.3 62.0 + - - +
521A VAL* 3.6 19.3 + - + +
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Residues in contact with GLU 520 (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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452A ILE* 3.9 6.7 - - + +
454A ASN* 2.9 34.9 + - + +
481A ILE 4.3 2.9 - - - +
482A ASP* 4.0 4.4 - - - +
483A PHE* 3.0 46.5 + - + +
484A ARG* 3.6 11.2 + - + +
495A LEU 2.9 14.5 + - - +
496A LYS* 3.4 32.5 + - + +
497A ALA 2.8 26.2 + - - +
518A LEU* 3.9 4.2 - - + +
519A ILE* 1.3 71.0 - - - +
521A VAL* 1.3 61.1 + - - +
522A SER* 5.2 1.4 + - - -
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Residues in contact with VAL 521 (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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353A LEU* 3.9 25.6 - - + -
358A VAL* 4.1 8.5 - - + -
451A VAL* 3.7 28.9 - - + -
452A ILE 2.8 13.9 + - - +
453A MET* 4.7 2.2 - - - -
454A ASN* 2.8 32.9 + - - +
497A ALA* 3.4 7.4 - - + +
503A LEU* 3.9 21.8 - - + -
519A ILE* 4.0 11.2 - - + +
520A GLU* 1.3 75.5 - - - +
522A SER* 1.3 61.5 + - - +
523A THR* 3.2 21.0 + - + +
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Residues in contact with SER 522 (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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352A ARG* 3.6 30.7 + - - +
353A LEU* 2.8 28.9 + - - +
454A ASN* 3.7 7.8 - - - +
496A LYS* 4.1 9.7 - - - -
497A ALA 2.9 11.0 + - - -
498A ASP* 2.7 34.4 + - - -
520A GLU* 4.0 2.3 + - - -
521A VAL* 1.3 70.2 - - - +
523A THR* 1.3 58.9 + - - +
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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