Contacts of the helix formed by residues 511 - 521 (chain B) in PDB entry 1XR2
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 511 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465B ARG* 3.6 28.7 - - - +
471B PHE* 3.9 5.4 - - + -
472B PHE* 3.7 24.9 - - + -
510B MET* 1.3 78.6 - - + +
512B LEU* 1.3 64.2 + - - +
513B LYS 3.5 2.0 - - - -
514B GLU* 3.4 16.0 - - - +
515B ILE* 3.1 33.1 + - - +
529B MET 5.1 1.1 + - - -
530B LEU* 4.1 13.0 - - + +
562B GLU* 2.7 25.6 + - - +
566B LEU* 4.2 7.8 - - - +
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Residues in contact with LEU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B PRO* 4.0 28.4 - - + +
510B MET 3.9 1.6 - - - +
511B THR* 1.3 77.9 + - - +
513B LYS* 1.3 54.1 + - - +
515B ILE* 3.2 1.9 + - - -
516B THR* 2.7 50.9 + - + +
562B GLU* 3.7 3.1 + - - +
565B ASP* 3.8 29.6 - - + +
566B LEU* 3.7 22.2 - - + -
569B ALA* 3.7 29.6 - - + -
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Residues in contact with LYS 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B LYS* 4.9 7.2 - - - +
436B GLU* 3.0 39.9 + - + +
439B ILE* 6.3 0.4 - - - +
475B LYS* 5.0 11.3 - - - +
510B MET 5.7 0.4 - - - -
512B LEU* 1.3 77.3 - - - +
514B GLU* 1.3 96.4 + - - +
516B THR* 3.2 5.9 + - - -
517B TYR* 3.1 30.1 + - - +
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Residues in contact with GLU 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B ILE* 4.9 6.0 - - + +
443B ILE* 3.9 26.6 - - + +
460B HIS* 4.1 11.4 - - + +
464B GLU* 3.8 35.5 - - - +
471B PHE* 5.1 4.0 - - + -
475B LYS* 4.7 1.5 + - - -
510B MET 3.8 6.0 - - - +
511B THR* 3.4 32.1 - - - +
513B LYS* 1.3 114.8 + - - +
515B ILE* 1.3 64.3 - - + +
517B TYR* 3.5 3.9 + - - +
518B ALA* 3.1 23.0 + - - +
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Residues in contact with ILE 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B HIS* 3.5 37.7 - - + +
465B ARG* 4.6 4.5 - - - +
511B THR* 3.1 30.8 + - - +
512B LEU 4.0 1.3 - - - +
514B GLU* 1.3 73.4 - - + +
516B THR* 1.3 67.3 + - - +
518B ALA* 3.2 6.9 + - - +
519B GLN* 3.0 21.5 + - - +
526B VAL* 4.6 6.6 - - + +
527B LYS 3.9 22.7 - - - +
528B GLY* 4.1 6.5 - - - -
529B MET 4.2 9.6 - - - +
566B LEU* 4.2 10.1 - - + -
571B ILE* 3.6 28.5 - - + -
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Residues in contact with THR 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512B LEU* 2.7 55.2 + - + +
513B LYS* 3.2 7.4 + - - -
515B ILE* 1.3 72.5 - - - +
517B TYR* 1.3 64.9 + - - +
519B GLN* 3.3 7.8 + - - +
520B SER* 3.1 23.4 + - - -
569B ALA* 3.7 20.4 - - + +
571B ILE* 4.3 6.1 - - + -
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Residues in contact with TYR 517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B LYS* 3.3 49.5 + - + +
443B ILE* 3.9 16.6 - - + -
444B LYS* 4.2 5.7 - - - +
513B LYS 3.1 17.8 + - - +
514B GLU* 3.7 4.0 - - - +
515B ILE 3.2 0.2 - - - -
516B THR* 1.3 83.3 + - - +
518B ALA* 1.3 61.0 + - - +
520B SER* 2.5 26.5 + - - -
521B LEU* 3.4 43.1 - - + +
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Residues in contact with ALA 518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B ILE* 3.6 25.4 - - + -
447B ILE* 4.1 10.2 - - + +
460B HIS* 3.9 14.8 - - + -
514B GLU 3.1 17.0 + - - +
515B ILE 3.2 4.7 + - - +
517B TYR* 1.3 74.8 - - - +
519B GLN* 1.3 66.4 + - - +
521B LEU* 3.1 19.0 + - - +
522B THR* 3.7 11.4 - - - +
526B VAL* 3.8 15.2 - - + +
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Residues in contact with GLN 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515B ILE 3.0 15.5 + - - +
516B THR* 3.3 8.5 + - - +
518B ALA* 1.3 77.7 - - - +
520B SER* 1.3 57.1 + - - +
522B THR 2.8 32.8 + - - +
523B GLU* 4.6 2.4 + - - +
524B LYS 2.8 25.5 + - - -
525B PRO* 3.7 4.5 - - - +
526B VAL* 2.9 36.1 + - + +
570B GLY 5.0 14.0 - - - +
571B ILE* 5.0 12.4 - - + -
572B LYS* 5.1 2.3 + - - +
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Residues in contact with SER 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516B THR 3.1 11.9 + - - -
517B TYR* 2.5 30.9 + - - -
519B GLN* 1.3 79.2 - - - +
521B LEU* 1.3 68.3 + - - +
522B THR 3.2 2.6 + - - +
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Residues in contact with LEU 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B ILE* 4.6 1.1 - - + -
444B LYS* 3.5 39.7 - - + +
447B ILE* 4.1 18.6 - - + +
448B GLU* 6.5 0.2 - - + -
451B GLU* 3.8 6.9 - - - +
517B TYR* 3.4 42.8 - - + +
518B ALA 3.1 7.9 + - - +
520B SER* 1.3 85.3 - - - +
522B THR* 1.3 61.0 + - - +
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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