Contacts of the strand formed by residues 571 - 575 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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526F THR* 3.6 19.3 - - - +
527F LEU 4.7 1.2 + - - -
564G ARG* 3.1 44.3 - - + +
565G VAL 3.7 4.5 - - - +
566G GLU* 3.8 19.5 - - + +
567G ASN* 4.4 0.2 - - - +
570G GLY* 1.3 74.6 - - - -
572G VAL* 1.3 68.6 + - - +
573G TRP* 5.2 2.2 - - - -
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Residues in contact with VAL 572 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524F GLN* 3.9 42.4 - - + +
525F LEU* 3.4 12.8 - - - +
526F THR* 3.9 16.8 - - + +
529F GLU* 5.7 0.2 - - - +
564G ARG* 3.4 4.5 - - - +
565G VAL* 2.7 62.3 + - + +
567G ASN* 4.4 16.6 - - + +
569G LYS 6.0 0.2 - - - +
570G GLY 5.5 0.2 - - - -
571G ALA* 1.3 80.8 - - - +
573G TRP* 1.3 62.3 + - - +
574G THR* 4.7 1.1 - - + -
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Residues in contact with TRP 573 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517F ILE* 3.6 12.1 - - + +
524F GLN* 3.2 6.9 - - - -
525F LEU 2.6 39.4 + - - +
527F LEU* 4.1 25.2 - - + +
530F ILE* 4.1 20.6 - - + -
556G LEU* 3.5 64.1 - - + +
557G SER* 4.6 6.1 - - - -
562G PHE 3.8 13.2 - - - -
563G VAL 3.5 5.6 - - - -
564G ARG* 3.7 55.0 - - + +
571G ALA 5.2 1.3 + - - -
572G VAL* 1.3 77.9 - - - +
574G THR* 1.3 62.0 + - - +
604G MG 4.3 1.3 - - - -
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Residues in contact with THR 574 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517F ILE* 4.0 7.5 - - - +
523F ARG 3.9 6.1 - - - +
524F GLN* 3.7 26.0 - - + +
562G PHE* 3.3 8.1 - - - +
563G VAL* 2.8 44.7 + - - +
565G VAL* 3.6 26.5 - - + +
572G VAL* 4.7 0.7 - - + -
573G TRP* 1.3 79.0 - - - +
575G VAL* 1.3 69.3 + - - +
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Residues in contact with VAL 575 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514F ARG* 4.0 20.6 - - + +
517F ILE* 3.6 40.0 - - + +
518F MET* 5.2 4.9 - - + -
523F ARG 5.0 0.6 + - - -
561G CYS 3.3 6.5 - - - +
562G PHE* 4.0 19.3 - - + -
574G THR* 1.3 79.9 - - - +
576G ASP* 1.3 70.3 + - - +
577G GLU* 3.2 23.2 + - + +
580G TYR* 4.3 12.1 - - + -
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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