Contacts of the strand formed by residues 550 - 554 (chain A) in PDB entry 4YCV
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 THR 550 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A LYS* 5.8 0.7 - - - +
315A ILE* 3.6 28.1 - - + +
348A TYR* 4.9 6.1 - - - -
349A TRP 3.2 13.7 - - - -
350A ALA* 3.5 16.8 - - - -
352A ALA 3.4 4.4 + - - -
480A LYS* 5.0 1.6 - - - +
506A THR* 3.7 3.4 - - - -
507A GLU* 2.9 41.9 + - - +
547A LEU* 4.2 9.1 - - + +
548A PRO* 3.2 23.1 + - + +
549A PRO* 1.3 75.6 - - - +
551A GLY* 1.3 63.0 + - - +
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Residues in contact with GLY 551 (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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347A PHE 4.3 0.5 - - - +
348A TYR* 3.7 2.8 - - - -
349A TRP* 2.9 35.6 + - - +
352A ALA* 2.7 21.8 + - - -
357A LEU* 3.8 19.3 - - - +
505A TYR 3.7 6.5 - - - -
506A THR* 4.0 4.5 - - - -
550A THR* 1.3 73.0 - - - +
552A GLY* 1.3 60.3 + - - -
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Residues in contact with GLY 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A PHE 3.4 8.5 - - - -
348A TYR* 3.5 23.8 - - - -
357A LEU* 3.2 6.4 - - - +
504A ALA* 3.2 6.5 - - - +
505A TYR* 2.8 38.9 + - - -
507A GLU* 4.6 1.4 - - - +
550A THR 3.9 1.4 + - - -
551A GLY* 1.3 74.2 - - - -
553A LEU* 1.3 60.3 + - - -
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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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345A CYS 4.8 0.4 - - - +
346A GLU* 3.2 6.1 - - - +
347A PHE* 2.9 69.6 + - + +
348A TYR* 4.9 3.7 - - - -
357A LEU* 4.1 11.9 - - + +
360A TRP* 3.8 19.7 - - + -
361A SER* 3.8 6.5 - - - +
502A LEU* 3.8 19.7 - - + -
503A ASN 3.6 7.4 - - - -
504A ALA* 3.5 18.4 - - + +
552A GLY* 1.3 73.9 - - - +
554A GLY* 1.3 79.6 + - - +
555A LEU* 3.9 20.2 - - + -
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Residues in contact with GLY 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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345A CYS 3.2 8.7 - - - -
346A GLU* 4.1 12.1 - - - -
501A VAL 4.1 0.3 - - - +
502A LEU* 3.4 6.1 - - - +
503A ASN* 2.9 36.1 + - - -
553A LEU* 1.3 77.8 - - - +
555A LEU* 1.3 64.7 + - - +
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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