Contacts of the strand formed by residues 571 - 575 (chain H) in PDB entry 2A07
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 ALA 571 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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564H ARG* 3.4 39.0 - - + +
565H VAL 3.8 4.7 - - - +
566H GLU* 3.8 20.2 - - + +
570H GLY* 1.3 74.7 - - - -
572H VAL* 1.3 68.5 + - - +
573H TRP* 5.1 2.0 - - - +
526I THR* 3.7 18.5 - - - +
527I LEU 4.7 1.9 + - - -
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Residues in contact with VAL 572 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564H ARG* 3.4 5.4 - - - +
565H VAL* 2.7 62.6 + - + +
567H ASN* 4.3 20.9 - - - +
569H LYS 6.0 0.2 - - - +
570H GLY 5.5 0.4 - - - -
571H ALA* 1.3 79.9 - - - +
573H TRP* 1.3 62.1 + - - +
574H THR* 4.6 1.1 - - + -
524I GLN* 4.0 35.2 - - + +
525I LEU* 3.4 13.0 - - - +
526I THR* 3.9 18.4 - - + +
529I GLU* 5.2 0.9 - - - +
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Residues in contact with TRP 573 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556H LEU* 3.6 63.0 - - + +
557H SER* 4.6 5.4 - - - -
562H PHE* 3.7 15.9 - - + -
563H VAL 3.6 5.6 - - - -
564H ARG* 3.7 52.2 - - + +
571H ALA* 5.1 2.1 + - - +
572H VAL* 1.3 75.7 - - - +
574H THR* 1.3 64.3 + - - +
602H MG 4.4 0.9 - - - -
517I ILE* 3.5 13.0 - - + +
524I GLN* 3.4 6.2 - - - -
525I LEU 2.6 38.1 + - - +
527I LEU* 4.1 25.5 - - - +
530I ILE* 4.0 20.2 - - + -
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Residues in contact with THR 574 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562H PHE* 3.4 7.4 - - - +
563H VAL* 2.8 47.5 + - - +
565H VAL* 3.6 27.6 - - + +
572H VAL* 4.6 0.7 - - + -
573H TRP* 1.3 80.7 - - - +
575H VAL* 1.3 70.2 + - - +
517I ILE* 4.1 7.0 - - - +
523I ARG 4.1 4.5 - - - +
524I GLN* 3.8 31.9 - - + +
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Residues in contact with VAL 575 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561H CYS 3.3 7.9 - - - +
562H PHE* 4.0 11.0 - - + -
563H VAL* 5.7 0.4 - - - -
574H THR* 1.3 84.4 + - - +
576H ASP* 1.3 71.0 + - - +
577H GLU* 3.4 22.5 + - + +
580H TYR* 4.3 11.9 - - + -
514I ARG* 4.0 26.5 - - + -
517I ILE* 3.7 33.8 - - + +
518I MET* 3.9 16.8 - - + +
523I ARG 4.9 0.2 + - - -
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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