Contacts of the strand formed by residues 552 - 556 (chain A) in PDB entry 2J0L
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 552 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506A GLU* 3.8 0.5 - - - -
507A LEU* 2.9 44.7 + - + +
530A LEU* 3.8 31.2 - - + -
547A ILE* 6.2 0.9 - - + -
548A ALA 3.7 15.0 - - - +
549A ALA* 3.1 15.2 + - - +
550A ARG 4.5 1.0 - - - +
551A ASN* 1.3 80.5 - - - +
553A LEU* 1.3 68.7 + - - +
560A VAL* 3.7 28.5 - - + -
561A LYS 3.6 7.9 - - - +
562A LEU* 4.9 8.7 - - + -
611A CYS* 4.3 5.6 - - - -
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Residues in contact with LEU 553 (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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484A VAL* 4.2 14.8 - - + -
502A CYS* 3.7 16.6 - - + -
505A GLY 3.3 6.5 - - - +
506A GLU* 4.0 19.1 - - + -
550A ARG 5.0 2.2 - - - +
551A ASN* 4.7 6.1 - - - +
552A VAL* 1.3 85.5 - - - +
554A VAL* 1.3 64.9 + - - +
555A SER 4.0 0.3 + - - -
560A VAL* 3.2 5.9 - - - +
561A LYS 2.8 36.8 + - - +
563A GLY* 5.2 5.4 - - - +
1689A ANP 3.5 71.3 - - + +
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Residues in contact with VAL 554 (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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502A CYS* 3.3 11.3 - - - +
504A LEU* 3.1 45.2 + - + -
505A GLY 2.7 20.2 + - - +
507A LEU* 4.0 25.8 - - + -
510A PHE* 4.0 37.0 - - + -
526A TYR* 5.6 0.7 - - - +
553A LEU* 1.3 77.0 - - - +
555A SER* 1.3 58.2 + - - +
556A SER 3.2 25.4 - - - +
559A CYS 3.9 4.5 - - - +
560A VAL* 4.3 5.2 - - + +
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Residues in contact with SER 555 (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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500A GLU* 4.7 1.0 + - - -
501A LEU 5.1 1.5 + - - -
502A CYS* 4.0 14.6 - - - +
503A THR* 3.6 20.3 + - - +
504A LEU* 4.3 2.3 - - - +
553A LEU 4.0 1.8 + - - -
554A VAL* 1.3 73.4 - - - +
556A SER* 1.3 64.7 + - - +
559A CYS* 2.9 27.5 + - - -
561A LYS* 2.9 34.8 + - - +
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Residues in contact with SER 556 (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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504A LEU* 3.6 15.5 - - - -
526A TYR* 4.8 0.3 + - - -
554A VAL* 3.2 9.9 - - - +
555A SER* 1.3 81.4 - - - +
557A ASN* 1.3 64.7 + - - +
558A ASP* 2.6 27.9 + - - -
559A CYS* 3.0 25.7 + - - +
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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