Contacts of the strand formed by residues 583 - 588 (chain A) in PDB entry 1GGT
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 LYS 583 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537A ILE 4.1 0.2 - - - -
538A THR* 3.1 5.5 - - - -
539A PHE* 2.7 51.8 + - + +
575A VAL* 4.6 5.2 - - + -
576A THR 3.2 24.7 - - - +
577A LEU* 3.4 30.7 - - + +
578A GLU* 2.7 30.9 + - - -
581A SER* 3.4 6.0 + - - -
582A PHE* 1.3 94.0 + - - +
584A LYS* 1.3 66.0 + - - +
585A GLU* 4.3 12.1 - - - +
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Residues in contact with LYS 584 (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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523A GLU* 4.9 8.1 + - - -
536A SER* 5.0 11.0 - - - -
537A ILE 2.9 7.6 - - - +
538A THR* 3.3 25.1 - - + -
582A PHE* 3.5 19.7 - - + -
583A LYS* 1.3 84.2 - - - +
585A GLU* 1.3 67.9 + - - +
586A ALA* 3.7 3.2 + - + +
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Residues in contact with GLU 585 (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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536A SER* 3.2 1.6 - - - -
537A ILE* 2.7 52.3 + - + +
539A PHE* 3.7 22.2 - - + -
573A PHE* 4.0 29.1 - - + -
575A VAL* 3.3 23.2 - - + +
583A LYS* 4.7 7.6 - - - +
584A LYS* 1.3 77.1 + - - +
586A ALA* 1.3 61.8 + - - +
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Residues in contact with ALA 586 (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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534A LYS* 5.0 13.5 - - + -
535A LEU 3.0 8.1 - - - +
536A SER* 4.3 9.2 - - - +
573A PHE* 5.9 0.9 - - - -
584A LYS 3.7 4.5 + - - +
585A GLU* 1.3 76.8 + - - +
587A VAL* 1.3 63.4 + - - +
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Residues in contact with VAL 587 (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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534A LYS* 2.9 5.6 - - - +
535A LEU* 2.6 60.8 + - + +
537A ILE* 3.7 17.3 - - + -
553A LEU* 3.9 22.2 - - + -
569A LYS* 5.2 4.3 - - + -
571A GLU* 4.8 13.9 - - + +
573A PHE* 4.7 9.2 - - + -
586A ALA* 1.3 77.4 - - - +
588A LEU* 1.3 65.0 + - - +
589A ILE* 4.0 20.2 - - + -
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Residues in contact with LEU 588 (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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532A ASP* 4.4 11.9 - - + -
533A PHE* 3.5 11.0 - - - +
534A LYS* 3.7 26.5 - - + -
569A LYS* 4.1 10.6 - - - -
587A VAL* 1.3 76.5 - - - +
589A ILE* 1.3 71.8 + - - +
590A GLN* 3.1 37.0 + - - +
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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