Contacts of the helix formed by residues 448 - 457 (chain A) in PDB entry 2I91
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 ALA 448 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLN* 4.6 0.6 + - - +
446A ASP* 2.9 9.6 + - - +
447A CYS* 1.3 77.3 - - - +
449A LEU* 1.3 65.3 + - - +
450A PRO* 3.2 4.1 - - - -
451A MET* 3.4 8.0 + - - +
452A LEU* 3.1 25.2 + - + +
476A ASP* 3.9 8.1 - - - +
477A VAL* 3.4 26.0 - - + +
479A PRO* 3.7 21.3 - - + -
482A ALA* 3.8 8.7 - - + -
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Residues in contact with LEU 449 (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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415A PHE* 4.2 4.7 - - + -
416A SER 3.6 5.6 - - - +
417A ASP 3.4 9.6 - - - +
418A GLU* 3.1 46.2 - - - +
419A MET* 3.7 19.0 - - + +
446A ASP* 3.1 37.5 - - + +
448A ALA* 1.3 78.1 - - - +
450A PRO* 1.3 58.5 - - + +
452A LEU* 3.5 10.0 - - + +
453A TRP* 2.5 39.2 + - - +
476A ASP* 4.4 4.5 - - - +
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Residues in contact with PRO 450 (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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372A LEU* 4.4 12.6 - - + +
374A ALA* 3.5 32.5 - - + -
413A VAL* 5.3 0.4 - - + -
415A PHE* 3.7 20.0 - - + -
419A MET* 4.2 7.4 - - + -
446A ASP 4.3 0.4 - - - +
447A CYS 3.9 11.4 - - - +
448A ALA 3.3 4.7 - - - -
449A LEU* 1.3 95.2 - - + +
451A MET* 1.3 72.8 + - - +
453A TRP* 3.1 7.5 + - + +
454A ALA* 2.8 25.1 + - - +
464A PHE* 4.8 2.2 - - + -
466A VAL* 4.5 9.6 - - + -
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Residues in contact with MET 451 (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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447A CYS 3.6 24.0 - - - +
448A ALA* 3.4 3.3 + - - +
450A PRO* 1.3 85.7 - - + +
452A LEU* 1.3 64.7 + - - +
454A ALA* 3.0 5.2 + - - +
455A GLN* 3.0 20.9 + - - +
464A PHE* 3.3 41.7 - - + -
466A VAL* 4.7 5.4 - - + -
479A PRO* 3.6 27.4 - - + +
482A ALA* 3.7 22.9 - - + +
483A LEU* 3.7 20.4 - - + -
486A TYR* 3.8 6.9 - - + -
496A LEU* 4.3 23.8 - - + -
508A ILE* 5.3 0.7 - - + -
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Residues in contact with LEU 452 (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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448A ALA* 3.1 22.8 + - + +
449A LEU* 3.5 13.0 - - + +
451A MET* 1.3 79.1 - - - +
453A TRP* 1.3 62.5 + - - +
455A GLN* 3.3 10.9 + - + +
456A LYS* 3.2 27.1 + - + +
476A ASP* 3.1 32.3 - - - +
477A VAL* 4.3 8.3 - - + -
482A ALA* 4.1 17.3 - - + +
485A GLN* 4.2 19.3 - - - +
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Residues in contact with TRP 453 (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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372A LEU* 3.8 28.3 - - + -
411A HIS* 4.1 27.8 - + - -
413A VAL* 4.3 6.7 - - + -
419A MET* 3.3 47.3 - - + +
449A LEU 2.5 22.2 + - - +
450A PRO 3.5 3.1 - - - +
452A LEU* 1.3 71.5 - - - +
454A ALA* 1.3 75.3 + - + +
456A LYS* 3.2 9.4 + - + +
457A THR* 2.4 60.3 + - + +
459A THR* 3.6 28.5 - - + -
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Residues in contact with ALA 454 (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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372A LEU* 5.1 3.8 - - + -
450A PRO 2.8 12.4 + - - +
451A MET 3.2 10.1 - - - +
453A TRP* 1.3 93.3 - - + +
455A GLN* 1.3 60.0 + - - +
457A THR* 3.6 1.1 + - - -
458A ASN 3.3 1.9 + - - -
459A THR* 2.8 41.4 + - + +
464A PHE* 3.7 17.5 - - + -
486A TYR* 3.6 18.4 - - + -
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Residues in contact with GLN 455 (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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451A MET 3.0 11.9 + - - +
452A LEU* 3.9 12.7 - - - +
453A TRP 3.3 0.2 - - - -
454A ALA* 1.3 74.0 - - - +
456A LYS* 1.3 65.0 + - - +
458A ASN* 2.9 21.0 + - - +
485A GLN* 3.7 29.6 + - - +
486A TYR* 3.7 18.2 + - + -
489A LYS* 3.4 51.3 - - + +
490A MET* 4.3 7.4 - - - +
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Residues in contact with LYS 456 (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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452A LEU 3.2 12.2 + - - +
453A TRP* 3.2 12.7 + - + +
455A GLN* 1.3 83.3 - - + +
457A THR* 1.3 57.3 + - + +
458A ASN* 3.1 7.9 + - - +
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Residues in contact with THR 457 (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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453A TRP* 2.4 66.1 + - + +
454A ALA 3.8 0.5 + - - -
456A LYS* 1.3 75.1 - - + +
458A ASN* 1.3 70.8 + - - +
459A THR* 2.9 18.0 + - - -
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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