Contacts of the strand formed by residues 572 - 579 (chain A) in PDB entry 2CG2
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 GLU 572 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539A ASP* 4.9 5.7 - - - +
540A THR* 3.5 8.1 + - - -
567A LEU* 2.8 36.6 + - + +
570A ILE* 3.4 38.7 - - + +
571A GLY* 1.3 82.2 - - - +
573A ASN* 1.3 64.4 + - - +
574A TYR* 3.4 27.5 + - + -
587A ARG* 3.7 37.4 + - - +
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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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565A LEU 3.2 4.7 - - - +
566A ARG* 3.3 47.9 + - - +
567A LEU 4.5 0.5 + - - -
571A GLY 5.0 1.5 - - - -
572A GLU* 1.3 80.0 + - - +
574A TYR* 1.3 64.9 + - - +
587A ARG* 4.3 0.4 - - - +
588A GLY* 2.7 38.5 + - - +
589A VAL 4.3 5.6 - - - +
590A GLN* 3.4 24.6 - - + +
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Residues in contact with TYR 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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539A ASP* 4.1 6.9 + - - -
540A THR* 3.6 26.8 - - + -
541A GLY* 3.3 22.8 + - - -
544A PHE* 5.3 1.3 - + - -
563A ILE 3.7 0.2 - - - +
564A ASN* 3.6 0.2 - - - -
565A LEU* 2.7 44.0 + - + +
567A LEU* 4.1 8.7 - - + -
572A GLU* 3.4 34.5 + - + -
573A ASN* 1.3 79.7 - - - +
575A LEU* 1.3 58.6 + - - +
576A LEU* 3.9 16.4 - - + -
585A ASN* 3.4 29.6 - - + -
586A LEU 3.3 4.7 - - - +
587A ARG* 3.5 43.4 - - + -
589A VAL 3.4 6.3 - - - -
590A GLN* 3.1 4.2 - - - +
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Residues in contact with LEU 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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562A SER* 4.5 4.5 - - - -
563A ILE 3.7 11.4 - - - +
564A ASN* 3.4 21.1 - - - +
574A TYR* 1.3 73.0 - - - +
576A LEU* 1.3 70.6 + - - +
577A GLU* 3.6 36.8 + - + +
584A ASN 3.8 0.7 - - - +
585A ASN* 3.2 4.5 - - - -
586A LEU* 2.9 42.9 + - + +
589A VAL* 3.2 36.8 + - + +
590A GLN* 4.6 0.2 - - - -
591A SER* 3.9 23.3 - - - -
594A ALA* 4.5 1.1 - - + -
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Residues in contact with LEU 576 (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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544A PHE* 3.6 42.2 - - + -
561A LEU* 4.7 1.3 - - + -
562A SER* 3.1 5.4 - - - -
563A ILE* 2.8 62.1 + - + +
565A LEU* 4.5 13.2 - - + -
574A TYR* 4.2 13.0 - - + -
575A LEU* 1.3 74.0 - - - +
577A GLU* 1.3 62.2 + - - +
578A LEU 4.2 0.2 - - - -
583A LEU* 4.5 9.6 - - + -
584A ASN 3.3 5.2 - - - +
585A ASN* 3.6 26.5 - - + -
633A LEU* 5.0 6.5 - - + -
636A LEU* 4.3 17.0 - - + -
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Residues in contact with GLU 577 (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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561A LEU 3.6 3.6 - - - +
562A SER* 3.9 15.6 - - - -
575A LEU* 3.6 31.5 + - + +
576A LEU* 1.3 78.4 - - - +
578A LEU* 1.3 60.6 + - - +
579A LYS* 5.7 2.9 - - + -
582A HIS 3.4 0.2 - - - +
583A LEU* 4.2 2.2 - - - -
584A ASN* 2.8 63.6 + - + +
586A LEU* 5.5 6.1 - - - +
591A SER* 5.9 0.2 - - - -
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Residues in contact with LEU 578 (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 LEU* 3.7 33.2 - - + -
556A ALA* 4.3 7.2 - - + +
559A LYS* 3.9 20.4 - - + +
560A ALA* 3.1 5.7 - - - +
561A LEU* 2.8 54.5 + - + +
576A LEU 4.2 0.4 - - - -
577A GLU* 1.3 72.4 - - - +
579A LYS* 1.3 64.3 + - - +
581A SER* 4.7 0.9 - - - +
582A HIS 3.5 20.6 - - - +
583A LEU* 4.0 13.1 - - + +
636A LEU* 4.4 4.7 - - + -
639A MET* 3.5 35.9 - - + -
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Residues in contact with LYS 579 (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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559A LYS 3.9 7.0 - - - +
560A ALA* 4.3 18.6 - - + -
577A GLU* 3.8 5.4 + - + +
578A LEU* 1.3 77.5 - - - +
580A ASN* 1.3 94.2 + - - +
581A SER 3.2 2.2 - - - +
582A HIS* 3.0 22.8 + - - +
584A ASN* 4.6 7.7 + - - +
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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