Contacts of the strand formed by residues 525 - 531 (chain A) in PDB entry 3GEF
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 SER 525 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472A GLN 3.6 2.0 + - - +
473A ASN* 3.5 0.7 - - - -
474A GLY* 2.9 37.9 + - - +
523A GLY 3.4 1.8 - - - -
524A ASN* 1.3 81.7 - - - +
526A LEU* 1.3 65.7 + - - +
527A ARG* 4.1 0.6 - - - +
542A LYS* 3.6 23.1 + - - -
543A LEU 3.5 4.9 - - - -
544A VAL* 4.6 5.3 - - - +
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Residues in contact with LEU 526 (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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445A VAL* 5.4 1.0 - - + +
446A ASP 5.0 0.9 - - - +
447A GLU* 4.7 11.9 - - + +
471A ARG* 3.8 23.8 - - - +
472A GLN 3.7 3.6 - - - -
473A ASN* 3.4 24.5 - - + +
521A GLY 4.2 3.8 - - - +
522A CSD 3.8 11.0 - - - +
523A GLY* 3.7 42.0 - - - +
525A SER* 1.3 82.5 + - - +
527A ARG* 1.3 59.9 + - - +
528A THR* 4.1 2.5 + - - +
541A ARG 4.0 1.4 - - - +
542A LYS* 3.3 4.1 - - - +
543A LEU* 2.9 55.7 + - + +
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Residues in contact with ARG 527 (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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470A LYS 3.4 1.7 - - - +
471A ARG* 3.2 5.5 - - - +
472A GLN* 2.9 55.5 + - + +
525A SER 4.1 0.4 - - - -
526A LEU* 1.3 72.3 - - - +
528A THR* 1.3 63.7 + - - +
529A ALA* 3.5 15.1 - - - +
537A GLU* 2.7 42.0 + - - -
540A MET* 4.1 24.0 - - - +
541A ARG 3.9 2.2 - - - -
542A LYS* 4.0 31.4 - - + +
551B GLU* 4.1 9.9 + - - -
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Residues in contact with THR 528 (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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442A VAL* 4.2 11.1 - - + +
445A VAL* 3.9 12.7 - - - +
452A VAL* 3.9 27.4 - - + -
469A ILE* 3.5 27.8 - - + -
470A LYS 3.5 3.4 - - - -
471A ARG* 3.1 31.4 + - - +
526A LEU 4.7 1.4 + - - -
527A ARG* 1.3 72.5 - - - +
529A ALA* 1.3 58.3 + - - +
540A MET* 3.2 3.8 - - - +
541A ARG 2.9 36.0 + - - -
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Residues in contact with ALA 529 (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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442A VAL* 5.0 1.1 - - - -
469A ILE* 3.2 8.6 - - - -
470A LYS* 2.8 46.0 + - + +
527A ARG* 3.5 16.2 - - - +
528A THR* 1.3 73.8 - - - +
530A LEU* 1.4 61.2 + - - +
531A ILE* 3.9 7.4 + - + -
537A GLU* 3.4 32.5 - - + +
539A ALA 3.4 5.2 - - - -
540A MET* 4.2 1.1 - - + -
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Residues in contact with LEU 530 (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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440A VAL* 3.6 41.7 - - + +
442A VAL* 4.4 9.3 - - + +
454A LEU* 3.9 17.5 - - + -
464A MET* 3.8 19.1 - - + -
467A TRP* 3.8 22.4 - - + -
468A GLN 3.4 15.5 - - - +
469A ILE* 4.1 4.5 - - + +
483A PHE* 4.0 8.5 - - + -
529A ALA* 1.4 72.3 - - - +
531A ILE* 1.3 59.9 + - - +
537A GLU* 3.5 0.5 - - - -
538A VAL* 2.8 41.0 + - + -
539A ALA* 2.8 20.2 + - + +
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Residues in contact with ILE 531 (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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467A TRP* 3.3 9.8 - - - +
468A GLN* 2.8 54.1 + - + +
470A LYS* 3.6 44.0 - - + +
529A ALA* 4.3 9.4 - - + +
530A LEU* 1.3 81.9 - - - +
532A ASN* 1.3 68.1 + - - +
535A GLY* 3.4 35.0 - - - +
536A GLU 3.3 3.6 - - - +
537A GLU* 3.6 25.4 - - + +
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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