Contacts of the strand formed by residues 537 - 541 (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 PHE 537 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496X VAL* 3.9 14.8 - - + -
506X ILE* 4.2 5.4 - - + -
527X LEU* 4.1 8.5 - - + +
535X SER* 3.1 22.9 + - - +
536X ASN* 1.3 84.1 - - + +
538X THR* 1.3 62.1 + - - +
539X ILE* 5.9 0.7 - - + -
549X ILE* 4.0 15.7 - - + -
550X LEU 3.2 16.2 - - - +
551X THR* 4.1 7.6 - - + -
552X ARG* 3.8 9.7 + - - -
556X TYR* 3.6 31.4 - + - -
564X TYR* 3.5 37.2 - + + -
566X LEU* 3.8 36.6 - - + -
586X VAL* 3.8 26.0 - - + -
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Residues in contact with THR 538 (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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52B SER* 4.4 10.3 - - - +
54B LEU* 4.3 18.4 - - + -
527X LEU* 5.5 0.4 - - - -
537X PHE* 1.3 72.0 - - - +
539X ILE* 1.3 75.6 + - - +
548X GLY 3.4 2.9 - - - +
549X ILE* 3.6 3.1 - - - +
550X LEU* 2.7 56.3 + - + +
551X THR 4.5 0.9 + - - -
552X ARG* 3.2 37.8 + - - +
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Residues in contact with ILE 539 (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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52B SER 5.0 2.2 + - - -
53B THR* 3.5 21.4 - - + +
54B LEU 3.0 23.6 + - - -
509X LEU* 4.4 4.3 - - + -
525X PHE* 4.0 27.4 - - + -
526X SER 4.5 5.8 - - - +
527X LEU* 3.7 35.8 - - + +
537X PHE* 4.5 1.1 + - + -
538X THR* 1.3 79.5 - - - +
540X GLN* 1.3 61.4 + - - +
541X ASP 4.0 0.2 - - - -
547X ALA* 4.0 12.6 - - + -
548X GLY 3.4 2.0 - - - +
549X ILE* 3.8 31.0 - - + -
566X LEU* 4.9 3.8 - - + -
568X VAL* 4.2 20.6 - - + -
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Residues in contact with GLN 540 (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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54B LEU* 3.2 32.9 - - + +
55B GLN 3.1 24.4 + - - +
56B SER* 4.3 5.4 - - - +
57B GLY 4.3 3.8 - - - +
58B VAL 3.7 8.1 + - - -
538X THR* 4.0 0.4 + - + -
539X ILE* 1.3 71.7 - - - +
541X ASP* 1.3 62.7 + - - +
542X ASN* 3.4 17.7 + - - +
547X ALA* 3.1 5.4 - - - -
548X GLY* 2.8 40.8 + - - +
550X LEU* 4.3 26.7 - - + +
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Residues in contact with ASP 541 (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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100A TRP* 3.3 29.0 + - - -
53B THR* 4.1 9.8 - - + +
54B LEU 2.9 11.6 + - - +
55B GLN* 4.2 16.3 + - - +
56B SER* 3.0 25.8 + - - -
523X PHE 4.1 1.4 - - - +
524X SER* 3.5 0.2 - - - -
525X PHE* 2.8 45.2 + - + +
539X ILE 4.0 1.4 - - - -
540X GLN* 1.3 69.8 - - - +
542X ASN* 1.4 60.6 + - - +
543X LYS* 3.0 25.4 + - - +
544X ASP 4.7 0.5 + - - -
545X ASN 5.2 0.2 + - - -
546X THR 3.8 1.0 - - - +
547X ALA* 4.1 7.0 - - - -
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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