Contacts of the strand formed by residues 571 - 575 (chain A) in PDB entry 3RGZ
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 LEU 571 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546A ASN 5.5 0.2 - - - +
547A SER* 4.2 28.5 - - - +
548A PHE 2.7 18.1 + - - +
549A SER* 3.7 17.9 - - - -
550A GLY 4.1 1.0 + - - -
570A ASN* 1.3 83.5 - - - +
572A PHE* 1.3 68.3 + - - +
573A ASN* 3.4 4.2 + - - +
664A ASN* 3.8 1.6 - - - +
665A MET* 3.6 32.1 - - + +
1E NAG 5.5 0.3 - - - +
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Residues in contact with PHE 572 (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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528A ILE* 3.5 39.0 - - + -
548A PHE* 3.3 28.7 + + + -
549A SER* 3.7 13.9 - - - +
550A GLY 3.3 13.5 - - - +
551A ASN 4.4 3.4 - - - -
552A ILE* 3.7 27.1 - - + -
567A LEU* 3.9 21.1 - - + -
570A ASN* 3.6 23.8 - - + -
571A LEU* 1.3 78.8 - - - +
573A ASN* 1.3 59.6 + - - +
661A MET* 6.5 0.2 - - + -
664A ASN* 3.1 34.3 + - + +
665A MET* 2.8 31.9 + - - -
666A LEU* 3.6 5.3 + - + -
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Residues in contact with ASN 573 (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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550A GLY* 2.9 23.4 + - - -
551A ASN* 3.3 24.0 - - - +
552A ILE 4.1 1.2 + - - -
571A LEU 4.3 6.4 + - - +
572A PHE* 1.3 76.1 - - - +
574A GLY* 1.3 69.3 - - - +
575A THR 5.0 0.3 - - - +
665A MET* 3.7 27.9 - - + +
666A LEU* 3.7 8.2 - - - +
1E NAG 1.5 67.0 + - + +
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Residues in contact with GLY 574 (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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551A ASN* 3.8 14.4 - - - -
573A ASN* 1.3 86.3 - - - +
575A THR* 1.3 65.2 + - - -
665A MET 4.3 2.0 + - - -
666A LEU* 3.4 5.0 - - - +
667A SER* 2.9 30.3 + - - -
1E NAG 4.3 14.5 - - - +
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Residues in contact with THR 575 (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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551A ASN* 5.4 4.8 - - - +
552A ILE* 5.0 5.5 + - - +
573A ASN 5.0 1.2 - - - +
574A GLY* 1.3 77.6 - - - -
576A ILE* 1.3 70.1 + - - +
577A PRO* 3.2 12.1 - - - +
666A LEU* 5.1 2.9 - - - -
667A SER* 3.4 20.6 - - - +
668A GLY* 3.9 15.7 - - - +
669A TYR 5.0 4.7 - - - +
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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