Contacts of the strand formed by residues 569 - 573 (chain A) in PDB entry 5FZ9
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 TYR 569 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PRO* 4.1 3.4 - - - -
30A PRO* 3.3 31.0 - - + +
31A GLU 3.9 12.8 - - - -
32A CYS* 3.9 17.3 - - + -
58A GLN 4.1 8.2 + - - -
59A THR* 3.7 51.5 - - + +
61A ILE* 4.8 2.5 - - + -
520A TYR* 3.3 4.9 - - - -
521A GLY 2.9 37.1 + - - +
523A PRO* 4.5 2.7 - - + -
525A TYR* 5.7 0.5 + - - -
567A PRO* 4.4 21.5 - - + +
568A VAL* 1.3 83.2 - - - +
570A ARG* 1.3 61.6 + - - +
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Residues in contact with ARG 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A PRO* 3.9 15.0 - - - -
29A PRO* 3.2 29.8 - - + +
30A PRO 2.9 8.5 + - - +
31A GLU* 3.0 35.4 + - - +
32A CYS* 2.8 25.7 + - - +
61A ILE* 4.8 1.6 - - - -
403A THR 5.9 1.0 + - - -
404A GLU* 6.4 0.6 - - - +
407A GLU* 3.0 40.8 + - - +
518A THR* 3.6 10.5 + - - +
519A TRP 3.2 12.8 - - - +
520A TYR* 3.8 12.8 - - + -
569A TYR* 1.3 75.2 - - - +
571A THR* 1.3 67.9 + - - +
572A ASN* 3.1 41.6 + - - +
592A GLN* 5.7 0.4 - - - +
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Residues in contact with THR 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 3.8 12.3 + - - -
32A CYS* 3.6 21.2 + - - -
34A VAL* 5.0 2.3 - - - +
61A ILE* 4.7 2.5 - - + -
63A LYS* 3.2 33.6 + - + -
517A LYS 3.9 0.2 - - - +
518A THR* 3.5 4.0 - - - +
519A TRP* 2.8 56.5 + - + +
570A ARG* 1.3 82.6 - - - +
572A ASN* 1.3 66.9 + - - +
573A GLN 4.3 0.4 - - - +
579A VAL* 4.4 8.5 - - + -
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Residues in contact with ASN 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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31A GLU* 4.6 1.8 + - - -
63A LYS* 2.7 30.3 + - - +
403A THR* 3.8 26.6 + - + +
404A GLU* 6.0 1.4 - - - +
516A PRO* 4.5 14.1 - - + -
517A LYS 3.7 3.1 - - - -
518A THR* 2.8 27.0 + - - -
570A ARG* 3.1 30.0 + - - +
571A THR* 1.3 73.1 + - - +
573A GLN* 1.3 59.1 + - - +
574A CYS* 3.7 10.2 + - - -
577A GLU* 3.9 0.2 - - - +
592A GLN* 4.3 4.0 + - - +
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Residues in contact with GLN 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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63A LYS* 4.2 3.6 - - + -
509A ASN* 3.2 37.4 + - - +
511A LEU* 3.4 17.1 - - + +
516A PRO* 3.2 5.1 - - - +
517A LYS* 2.8 51.8 + - - +
519A TRP* 3.0 19.1 + - + +
571A THR 4.0 1.2 - - - -
572A ASN* 1.3 71.6 - - - +
574A CYS* 1.3 64.9 + - - +
577A GLU* 3.0 35.6 + - + +
579A VAL* 3.7 30.5 - - + +
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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