Contacts of the strand formed by residues 524 - 530 (chain A) in PDB entry 3MTC
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 ASP 524 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A THR* 4.3 10.4 + - + +
272A TYR* 6.0 0.2 - - - -
273A ASN* 4.3 7.8 + - - +
302A GLN* 4.4 2.1 - - - +
446A GLY 3.4 6.0 - - - +
447A ASP* 3.4 27.0 + - - +
498A PHE* 4.6 6.6 - - - -
501A THR* 2.7 28.1 + - - +
522A TRP* 3.3 1.3 - - - -
523A CYS* 1.3 76.3 - - - +
525A ARG* 1.3 67.2 + - - +
538A TYR* 4.3 2.8 + - - -
549A HIS* 2.8 31.9 + - - +
550A LYS 4.0 5.3 - - - +
552A VAL* 3.8 29.6 - - + +
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Residues in contact with ARG 525 (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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271A THR* 4.0 1.8 - - - +
445A LEU* 3.4 1.7 - - - -
446A GLY 3.1 29.6 + - - -
448A LEU* 3.8 26.4 - - + +
450A TYR* 4.6 5.2 + - + +
473A TYR* 3.9 4.2 - - - -
476A ASP* 3.0 38.9 + - - -
478A LEU* 3.8 18.6 - - + +
479A LYS 4.8 0.4 - - - +
493A GLU* 2.7 37.9 + - - +
496A LEU* 3.5 22.2 - - - +
522A TRP* 2.7 39.4 + - - +
523A CYS 3.7 11.2 - - - +
524A ASP* 1.3 83.9 - - - +
526A ILE* 1.3 68.5 + - - +
527A LEU* 4.2 6.5 - - + -
538A TYR* 3.4 7.0 - - - +
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Residues in contact with ILE 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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269A ALA* 3.4 42.4 - - + +
270A GLY 4.6 0.2 - - - +
271A THR* 4.2 7.9 - - + -
443A LEU* 5.7 2.2 - - + -
444A TRP 3.4 9.9 - - - +
445A LEU* 4.0 11.7 - - + -
493A GLU* 3.6 21.0 - - - +
494A GLY 4.8 1.0 + - - -
525A ARG* 1.3 79.4 - - - +
527A LEU* 1.3 67.2 + - - +
528A TRP* 5.0 0.7 - - - -
535A GLN* 5.0 3.5 + - - -
538A TYR* 3.1 19.0 + - + -
552A VAL* 3.9 14.4 - - + +
553A SER* 3.7 8.3 - - - +
554A SER* 3.7 17.7 - - - +
556A PHE* 4.2 24.5 - - + -
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Residues in contact with LEU 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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443A LEU* 3.6 2.1 - - - +
444A TRP 2.7 37.4 + - - +
448A LEU* 3.8 28.9 - - + -
478A LEU* 4.4 12.8 - - + -
482A VAL* 5.1 5.8 - - + -
488A PHE* 4.0 31.2 - - + -
491A PHE* 4.1 22.4 - - + +
492A THR 3.2 12.8 - - - +
493A GLU* 3.9 18.2 - - + +
525A ARG* 4.2 9.4 - - + -
526A ILE* 1.3 84.3 - - - +
528A TRP* 1.3 66.6 + - - +
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Residues in contact with TRP 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 ILE 3.3 11.7 - - - +
443A LEU* 3.8 17.5 - - + -
490A GLY 4.3 0.2 - - - +
491A PHE* 3.4 7.5 - - - -
492A THR* 2.9 76.8 + - + -
493A GLU* 4.2 0.2 - - - -
494A GLY* 3.6 24.9 - - - -
526A ILE 5.0 0.9 - - - -
527A LEU* 1.3 79.1 - - - +
529A LYS* 1.3 65.9 + - - +
530A GLY 4.6 3.4 + - - -
533A ILE* 3.5 44.0 + - + +
535A GLN* 3.7 38.8 - - + -
556A PHE* 3.4 18.8 - + + -
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Residues in contact with LYS 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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437A SER* 5.8 6.0 - - - -
440A ASP 3.9 0.3 - - - +
441A VAL* 3.6 1.9 - - - -
442A ILE* 2.9 51.0 + - + +
489A GLU 3.7 14.6 + - - -
490A GLY* 3.6 28.3 - - - +
491A PHE* 3.9 27.3 - - + -
528A TRP* 1.3 78.0 - - - +
530A GLY* 1.3 62.2 + - - +
533A ILE* 3.8 5.6 - - - +
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Residues in contact with GLY 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 ASP 3.3 16.6 - - - -
528A TRP* 4.6 4.1 + - - -
529A LYS* 1.3 80.8 - - - +
531A LYS* 1.3 66.2 + - - -
533A ILE* 3.6 17.2 + - - +
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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