Contacts of the strand formed by residues 524 - 527 (chain X) in PDB entry 5VEB
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 SER 524 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A TRP* 3.5 22.9 - - - -
101A GLY* 3.4 33.0 - - - -
49B TYR* 3.4 21.7 + - - -
523X PHE* 1.3 72.3 - - - +
525X PHE* 1.3 59.7 + - - +
541X ASP* 3.5 5.4 - - - -
569X VAL 3.4 1.0 - - - +
570X ILE* 3.3 5.5 - - - -
571X SER* 2.8 35.6 + - - -
573X ASN* 3.8 3.7 + - - -
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Residues in contact with PHE 525 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TYR* 3.5 9.7 - - - -
53B THR* 3.4 16.8 - - - +
509X LEU* 4.0 28.5 - - + -
511X ALA* 3.5 24.2 - - + -
523X PHE 4.1 6.3 - - - -
524X SER* 1.3 75.3 - - - +
526X SER* 1.3 64.8 + - - +
539X ILE* 4.0 8.5 - - + -
541X ASP* 2.8 30.7 + - - +
545X ASN* 3.5 39.0 - - - -
546X THR 3.7 5.8 - - - -
547X ALA* 3.5 21.5 - - + -
568X VAL* 3.9 15.7 - - + -
569X VAL 3.4 3.4 - - - -
570X ILE* 3.5 22.0 - - + -
611X VAL* 4.8 3.4 - - + -
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Residues in contact with SER 526 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 5.5 4.2 - - - -
49B TYR* 3.6 23.1 + - - -
50B ALA* 3.8 12.6 - - - +
53B THR* 3.3 16.4 - - - -
525X PHE* 1.3 78.2 - - - +
527X LEU* 1.3 61.9 + - - +
539X ILE* 4.5 5.9 - - - +
568X VAL* 3.5 8.3 - - - +
569X VAL* 2.8 49.5 + - - +
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Residues in contact with LEU 527 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B SER* 4.7 2.8 + - - -
50B ALA* 4.9 3.7 + - - +
52B SER* 4.4 15.2 + - - +
53B THR* 4.0 4.2 + - - +
526X SER* 1.3 83.2 + - - +
528X ALA* 1.3 66.3 + - - +
529X PRO* 3.8 1.0 - - - +
531X ALA* 3.6 25.6 - - + +
532X ALA* 3.9 24.4 - - - +
535X SER* 4.1 18.8 - - - +
537X PHE* 4.1 10.3 - - + +
538X THR* 5.5 0.2 - - - -
539X ILE* 3.7 33.9 - - + +
566X LEU* 4.3 23.6 - - + -
567X PRO 3.5 12.6 - - - +
568X VAL* 4.4 3.1 - - + -
569X VAL* 4.3 0.4 - - - +
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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
------------------------------------------------------------
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