Contacts of the helix formed by residues 487 - 494 (chain I) in PDB entry 4XLN
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 THR 487 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329I GLY* 5.7 1.7 - - - -
437I ARG* 3.7 2.0 - - - -
462I ASP* 4.4 1.6 - - - +
466I PHE* 4.2 32.3 - - + -
467I ILE 3.6 12.8 - - - +
468I ARG* 3.9 28.7 - - + +
485I TYR 5.4 0.2 - - - +
486I MET* 1.3 75.1 - - - +
488I ALA* 1.3 59.5 + - - +
489I SER* 3.8 5.4 + - - -
490I GLU* 3.2 29.2 + - + +
491I GLU* 2.8 27.2 + - - +
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Residues in contact with ALA 488 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327I HIS* 3.4 11.0 - - + -
328I LEU* 3.7 16.1 + - + +
329I GLY* 3.2 31.7 - - - +
433I THR* 4.4 1.8 - - - -
437I ARG* 3.7 23.1 + - - +
467I ILE 4.0 3.2 + - - +
487I THR* 1.3 77.0 - - - +
489I SER* 1.3 58.3 + - - +
491I GLU* 3.4 2.6 + - - +
492I ASP* 2.9 34.9 + - - +
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Residues in contact with SER 489 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327I HIS* 4.3 5.0 - - - -
329I GLY* 4.1 17.1 - - - -
330I ASN* 6.2 0.2 - - - -
487I THR* 3.8 5.6 + - - -
488I ALA* 1.3 73.5 - - - +
490I GLU* 1.3 67.4 + - - +
492I ASP* 2.9 21.6 + - - +
493I ARG* 3.0 13.5 + - - +
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Residues in contact with GLU 490 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485I TYR 5.6 1.0 - - - +
486I MET* 3.7 11.8 - - + -
487I THR* 3.2 39.0 + - + +
489I SER* 1.3 79.9 - - - +
491I GLU* 1.3 61.1 + - - +
493I ARG* 3.2 12.5 + - - +
494I TYR* 3.0 40.7 + - + -
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Residues in contact with GLU 491 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433I THR* 5.8 1.5 - - - -
435I TYR* 4.6 2.4 - - - +
437I ARG* 2.5 35.0 + - - +
471I TYR* 2.7 23.7 + - + -
486I MET* 3.7 19.2 - - + +
487I THR 2.8 20.0 + - - +
488I ALA 3.6 3.4 - - - +
490I GLU* 1.3 73.7 - - - +
492I ASP* 1.3 68.3 + - - +
493I ARG 3.2 0.9 + - - -
494I TYR* 3.2 20.6 + - - +
496I ILE* 3.5 16.2 - - + +
516I ARG* 2.5 34.7 + - - -
518I ARG* 5.2 2.4 + - - +
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Residues in contact with ASP 492 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327I HIS* 2.5 38.0 + - - -
433I THR* 3.4 15.9 - - - +
488I ALA 2.9 18.7 + - - +
489I SER* 2.9 12.4 + - - +
491I GLU* 1.3 81.1 - - - +
493I ARG* 1.3 63.8 + - - +
494I TYR 3.7 4.0 - - - +
517I ARG* 5.1 2.8 - - - +
518I ARG* 3.5 51.5 + - - +
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Residues in contact with ARG 493 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489I SER 3.0 10.1 + - - +
490I GLU* 3.3 15.4 + - - +
491I GLU 3.1 0.2 - - - -
492I ASP* 1.3 80.5 - - - +
494I TYR* 1.3 96.8 + - + +
495I THR* 5.0 1.7 - - - +
517I ARG* 5.5 2.4 - - - +
530I GLU* 4.8 1.8 - - - +
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Residues in contact with TYR 494 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486I MET* 3.5 34.3 - - + -
490I GLU* 3.0 42.6 + - - -
491I GLU 3.2 14.0 + - - +
492I ASP 3.7 4.0 - - - +
493I ARG* 1.3 104.6 + - - +
495I THR* 1.3 63.9 + - - +
496I ILE* 4.1 2.1 + - + +
516I ARG 4.2 3.8 - - - +
517I ARG* 4.4 6.8 - - - +
530I GLU* 3.5 22.9 - - + -
531I PHE* 3.5 33.2 - + + -
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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