Contacts of the strand formed by residues 445 - 453 (chain A) in PDB entry 1HMU
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 GLY 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A HIS* 3.7 14.9 + - - -
439A VAL* 3.1 16.2 - - - -
440A SER* 4.3 0.2 - - - -
444A TYR* 1.3 78.8 - - - +
446A ALA* 1.3 61.2 + - - -
464A PHE* 3.0 30.8 + - - -
621A GLN* 3.2 13.6 - - - +
646A LEU* 4.6 5.6 - - - -
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Residues in contact with ALA 446 (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 GLY* 3.1 2.1 - - - -
439A VAL* 2.9 38.6 + - + +
445A GLY* 1.3 74.1 - - - -
447A SER* 1.3 63.2 + - - +
462A TRP 3.1 12.3 - - - +
463A PHE* 3.8 18.6 - - + -
464A PHE* 4.1 1.1 - - - -
621A GLN* 3.4 23.8 - - + +
622A ALA 5.2 1.1 - - - +
623A ILE* 4.3 13.7 - - + +
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Residues in contact with SER 447 (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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340A HIS* 4.9 1.0 + - - -
342A GLN* 2.6 23.6 + - - +
349A VAL* 3.6 22.5 - - - +
362A MET* 4.1 15.5 - - - -
437A GLY 3.0 12.3 - - - -
438A GLY* 3.8 0.9 - - - -
446A ALA* 1.3 75.4 + - - +
448A ALA* 1.3 62.9 + - - +
461A ALA* 3.3 4.9 - - - +
462A TRP* 2.9 38.3 + - - +
464A PHE* 4.1 4.0 - - - -
623A ILE* 4.3 3.6 - - - +
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Residues in contact with ALA 448 (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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362A MET* 3.7 5.8 - - - +
435A PHE* 3.9 13.2 - - + -
436A ALA* 3.3 3.6 - - - -
437A GLY 2.8 31.6 + - - +
447A SER* 1.3 76.7 - - - +
449A TYR* 1.3 63.0 + - - +
460A LYS 3.3 5.8 - - - +
461A ALA* 4.2 1.1 - - + -
462A TRP* 4.2 1.1 - - - -
623A ILE* 3.5 36.8 - - + +
625A TYR* 3.6 12.1 - - - +
661A PRO* 5.8 0.2 - - + -
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Residues in contact with TYR 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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362A MET* 3.9 15.5 - - + -
363A VAL* 3.2 38.9 - - + +
369A ARG* 3.9 2.3 + - - -
384A SER 4.2 0.9 - - - -
385A ASP* 2.6 46.1 + - - -
386A GLY* 4.0 13.9 - - - -
433A ASN* 3.4 25.9 + - - -
435A PHE* 4.0 2.7 - - - -
436A ALA* 4.3 1.6 - - + -
448A ALA* 1.3 78.1 - - - +
450A ALA* 1.3 59.1 + - - +
451A LEU* 3.4 36.7 + - + +
452A ASP 4.8 0.7 + - - -
458A ALA 3.6 0.2 - - - +
459A LYS* 3.7 1.0 - - - -
460A LYS* 2.7 45.0 + - + +
462A TRP* 3.9 16.2 - - + -
625A TYR* 5.0 2.9 - - - -
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Residues in contact with ALA 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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433A ASN* 2.9 31.1 - - + +
435A PHE* 3.1 37.2 + - + +
449A TYR* 1.3 69.6 - - - +
451A LEU* 1.3 64.2 + - - +
452A ASP* 4.5 1.0 - - - +
458A ALA 3.5 6.3 - - - -
459A LYS* 3.8 26.9 - - + -
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Residues in contact with LEU 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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385A ASP* 3.5 22.4 - - + +
413A THR* 4.0 17.5 - - - +
449A TYR* 3.4 39.0 + - + +
450A ALA* 1.3 75.5 - - - +
452A ASP* 1.3 67.0 + - - +
453A TYR* 4.0 15.0 - - + +
456A LEU* 3.8 37.7 - - + +
457A GLN* 3.2 5.9 - - - +
458A ALA* 2.8 46.1 + - + +
459A LYS* 6.2 0.2 - - - -
460A LYS* 4.8 5.6 - - + -
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Residues in contact with ASP 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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432A SER* 2.6 41.4 + - - +
433A ASN* 5.2 4.0 + - + +
449A TYR* 4.8 0.6 + - - -
450A ALA 3.6 5.0 + - - +
451A LEU* 1.3 78.4 - - - +
453A TYR* 1.3 63.9 + - - +
455A SER* 5.4 1.0 + - - -
456A LEU 3.2 5.8 - - - -
457A GLN* 3.3 29.0 + - + -
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Residues in contact with TYR 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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369A ARG* 3.3 51.1 + - - +
381A ARG* 3.6 28.3 + - - +
382A TYR* 3.9 13.4 - + - -
385A ASP* 4.3 1.1 - - - -
423A LEU* 4.9 4.5 - - - +
429A GLU* 3.4 29.2 + - - -
432A SER* 5.1 5.2 - - - +
449A TYR* 5.4 0.2 - - - +
451A LEU* 4.0 16.8 - - + +
452A ASP* 1.3 79.2 + - - +
454A ASP* 1.3 106.1 + - + +
455A SER 3.2 2.0 - - - -
456A LEU* 3.0 24.8 + - - +
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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