Contacts of the strand formed by residues 458 - 465 (chain A) in PDB entry 3C7N
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 GLN 458 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442A ALA* 3.8 13.9 - - - +
443A ALA 3.8 9.4 - - - +
444A SER* 4.0 6.9 - - - -
445A TYR* 5.1 0.9 - - - -
456A PRO* 3.4 21.8 + - + +
457A GLU* 1.3 80.9 + - - +
459A ILE* 1.3 60.4 + - - +
460A ALA* 4.0 12.3 - - - +
461A ASN* 3.6 32.0 + - - +
540A PHE* 4.5 8.0 - - - -
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Residues in contact with ILE 459 (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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151A GLU* 3.3 33.8 - - + +
155A TYR* 5.8 0.9 - - - -
402A VAL* 4.0 18.4 - - + -
443A ALA* 3.0 14.2 + - + +
444A SER* 3.7 21.3 - - - +
445A TYR* 3.3 50.3 - - + +
457A GLU 4.0 0.9 - - - +
458A GLN* 1.3 74.5 - - - +
460A ALA* 1.3 67.7 + - + +
490A HIS* 4.3 14.6 - - + +
539A THR* 4.9 2.9 - - - -
540A PHE* 3.8 25.4 - - + -
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Residues in contact with ALA 460 (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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151A GLU* 5.6 0.4 - - - +
155A TYR* 6.4 0.2 - - + -
442A ALA* 3.4 3.1 - - - +
443A ALA 2.9 24.3 + - - +
458A GLN* 3.9 6.5 - - - +
459A ILE* 1.3 88.0 - - + +
461A ASN* 1.3 67.5 + - - +
462A TRP* 3.8 20.4 - - + -
490A HIS 4.5 2.5 - - - +
538A HIS 3.4 16.2 - - - +
539A THR* 3.7 20.6 - - + -
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Residues in contact with ASN 461 (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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441A MET 3.2 13.5 - - - +
442A ALA* 3.8 10.8 - - + -
458A GLN* 3.6 17.3 + - - +
460A ALA* 1.3 78.1 - - - +
462A TRP* 1.3 71.4 + - - +
463A GLU* 4.8 2.4 + - - +
538A HIS* 2.9 66.5 + - - +
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Residues in contact with TRP 462 (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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404A TYR* 3.8 8.7 - + - -
440A SER* 3.7 4.2 - - - -
441A MET 2.8 34.7 + - - +
442A ALA* 3.6 3.4 - - - -
443A ALA* 3.3 47.1 - - + -
460A ALA* 3.6 20.9 - - + -
461A ASN* 1.3 81.4 + - - +
463A GLU* 1.3 68.9 + - - +
464A ILE* 4.4 6.1 - - + -
490A HIS 3.3 22.7 - - - -
491A THR* 4.0 11.0 - - - +
492A ILE* 3.4 44.9 + - + +
535A ILE* 3.9 22.9 - - + -
536A VAL 3.1 8.5 - - - +
537A ALA* 3.6 32.3 - - + +
538A HIS* 4.8 0.2 - - - -
539A THR* 4.8 4.8 - - - +
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Residues in contact with GLU 463 (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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439A PHE 3.8 5.8 - - - +
440A SER* 3.9 14.4 - - - +
461A ASN* 4.8 1.7 + - - +
462A TRP* 1.3 78.8 - - - +
464A ILE* 1.3 63.4 + - - +
465A THR* 4.3 5.6 + - - +
534A THR 3.1 4.5 - - - +
535A ILE* 3.5 1.7 - - - -
536A VAL* 2.8 46.5 + - + +
538A HIS* 2.3 35.1 + - + +
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Residues in contact with ILE 464 (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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438A ASP* 3.5 8.5 - - - +
439A PHE* 2.9 69.1 + - + +
441A MET* 4.3 19.5 - - + -
462A TRP* 4.4 10.5 - - + -
463A GLU* 1.3 80.8 - - - +
465A THR* 1.3 64.6 + - - +
467A VAL* 4.8 0.7 - - + -
480A LEU* 4.5 13.9 - - + -
492A ILE* 5.1 2.9 - - + -
495A ALA* 4.6 3.8 - - + -
533A LEU* 3.5 40.2 - - + -
534A THR 3.2 3.4 - - - +
535A ILE* 4.2 18.4 - - + -
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Residues in contact with THR 465 (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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438A ASP* 3.7 11.4 - - - +
463A GLU* 4.3 8.8 + - - +
464A ILE* 1.3 76.4 - - - +
466A GLY* 1.3 65.4 + - - +
467A VAL 3.4 2.7 - - - -
533A LEU* 3.2 8.2 - - - +
534A THR* 2.8 50.0 + - - +
536A VAL* 5.4 3.3 - - - +
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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