Contacts of the strand formed by residues 520 - 523 (chain B) in PDB entry 5U03
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 520 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B ILE* 3.8 26.5 - - + -
389B ARG* 3.7 30.3 - - + -
395B PHE* 3.4 47.6 - + + -
405B ALA* 4.0 14.8 - - + -
408B GLU* 5.0 1.1 - - - -
409B PHE* 6.5 0.9 - + + -
497B LEU* 5.1 9.6 - - + -
512B VAL* 5.8 4.4 - - + +
514B LEU* 3.0 50.9 + - + +
517B HIS* 3.5 34.9 + + + +
519B PHE* 1.3 74.7 - - - +
521B VAL* 1.3 65.6 + - - +
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Residues in contact with VAL 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 2.9 16.6 + - - +
396B LEU* 3.6 22.0 - - + -
397B GLY 3.0 21.1 + - - -
463B VAL* 6.0 3.1 - - + -
464B MET* 4.8 18.4 - - + -
511B ILE* 5.7 0.7 - - + -
512B VAL* 3.3 9.2 - - - +
513B GLU* 3.8 27.6 - - + -
519B PHE* 3.7 28.3 - - + -
520B PHE* 1.3 88.1 - - - +
522B GLY* 1.3 60.8 + - - +
523B VAL* 5.4 3.4 - - + -
539B PRO* 5.5 0.2 - - + -
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Residues in contact with GLY 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 5.1 1.1 - - - -
397B GLY* 3.2 11.7 - - - -
402B MET* 3.3 18.1 - - - +
511B ILE* 3.5 0.9 - - - +
512B VAL* 3.0 44.6 + - - +
521B VAL* 1.3 74.8 - - - +
523B VAL* 1.4 67.9 + - - +
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Residues in contact with VAL 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B LEU* 4.8 12.5 - - + +
397B GLY 3.0 9.2 + - - +
398B VAL* 3.2 14.2 - - + -
399B CYS 2.7 29.8 + - - -
402B MET* 3.5 6.1 - - - +
464B MET* 5.3 3.4 - - + -
510B GLU 3.2 6.5 - - - +
511B ILE* 4.3 9.6 - - + -
521B VAL* 5.4 3.4 - - + -
522B GLY* 1.4 80.1 - - - +
524B GLN* 1.3 52.0 + - - +
525B TYR* 3.5 55.6 - - + +
527B PRO* 4.5 7.6 - - + -
539B PRO* 5.2 7.9 - - + -
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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
------------------------------------------------------------
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