Contacts of the helix formed by residues 445 - 452 (chain A) in PDB entry 4X61
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 LEU 445 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A PRO* 5.1 0.4 - - + -
315A LEU* 4.0 12.1 - - + -
442A ASP 3.3 9.4 + - - +
444A GLU* 1.3 81.5 - - - +
446A SER* 1.3 64.6 + - - +
447A PRO* 3.3 1.8 - - - -
448A GLU* 3.4 22.0 + - + +
449A CYS* 3.1 26.0 + - - -
604A ARG* 3.8 4.9 - - - +
611A VAL* 3.5 30.7 - - + -
635A ILE* 3.7 43.5 - - + +
636A GLY 3.8 14.4 - - - +
637A LEU* 3.7 24.5 - - + -
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Residues in contact with SER 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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434A SER* 5.1 0.5 + - - -
436A LEU* 3.3 41.6 + - - +
437A LEU* 4.5 5.2 - - - +
441A ALA 4.8 2.9 - - - -
442A ASP 4.4 0.4 + - - -
444A GLU 3.3 3.4 - - - -
445A LEU* 1.3 73.6 - - - +
447A PRO* 1.4 72.2 - - - +
449A CYS 3.4 0.2 + - - -
450A LEU* 3.1 37.8 + - - +
465A PRO* 5.6 1.0 - - - +
468A TYR* 2.8 32.5 + - - -
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Residues in contact with PRO 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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442A ASP* 3.7 29.8 - - + -
445A LEU* 3.5 4.3 - - - -
446A SER* 1.4 91.2 - - - +
448A GLU* 1.3 61.7 + - - +
451A ASP* 3.0 35.2 + - - +
468A TYR* 3.1 17.0 - - - +
521A PHE* 3.7 29.8 - - + -
523A HIS* 3.7 9.2 - - + -
532A ASN* 3.5 20.9 - - - +
604A ARG* 3.9 4.3 - - - +
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Residues in contact with GLU 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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421A ARG* 4.0 9.3 - - - +
445A LEU* 3.5 17.9 - - + +
446A SER 3.3 0.4 - - - -
447A PRO* 1.3 75.4 - - - +
449A CYS* 1.3 63.4 + - - +
451A ASP* 3.5 5.0 - - - +
452A GLY* 3.4 14.4 + - - -
532A ASN* 3.4 21.2 + - - +
604A ARG* 2.7 46.7 + - - -
606A SER* 5.2 2.8 - - - -
611A VAL* 4.1 14.4 - - + +
637A LEU* 3.7 33.2 - - + -
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Residues in contact with CYS 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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315A LEU* 3.8 22.4 - - - -
420A MET* 3.7 17.6 - - - +
421A ARG* 3.6 18.4 - - - +
436A LEU* 3.7 21.1 - - + -
444A GLU 5.1 2.0 - - - -
445A LEU* 3.1 22.7 + - - +
446A SER 3.8 0.4 - - - +
448A GLU* 1.3 74.9 - - - +
450A LEU* 1.3 65.3 + - - +
452A GLY 3.2 10.7 + - - -
453A ALA* 3.5 7.3 + - - +
701A SAM 3.2 31.9 - - - -
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Residues in contact with LEU 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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364A LEU* 4.5 10.3 - - + -
420A MET* 4.1 9.0 - - - -
432A ILE* 4.8 13.8 - - + +
434A SER* 3.4 37.0 - - - +
436A LEU* 3.8 12.3 - - + -
446A SER* 3.1 25.9 + - - +
449A CYS* 1.3 75.3 - - - +
451A ASP* 1.3 59.5 + - - +
453A ALA* 3.1 5.4 + - - +
454A GLN* 3.0 32.3 + - - +
463A SER* 4.4 9.2 - - - +
465A PRO* 4.9 4.9 - - + -
523A HIS* 3.7 40.8 - - + +
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Residues in contact with ASP 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 PRO 3.0 24.6 + - - +
448A GLU* 3.5 8.5 - - - +
449A CYS 3.2 0.2 - - - -
450A LEU* 1.3 77.3 - - - +
452A GLY* 1.3 57.2 + - - +
453A ALA 3.1 4.0 + - - -
454A GLN* 3.5 26.1 + - - +
455A HIS* 4.8 1.6 + - - +
523A HIS* 3.9 15.1 + - - -
525A ASN* 4.5 9.2 - - - +
530A ILE* 3.1 35.2 - - + +
532A ASN* 3.3 19.5 + - - +
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Residues in contact with GLY 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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420A MET 3.6 9.7 - - - +
421A ARG* 3.6 23.5 - - - +
448A GLU 3.4 3.8 + - - -
449A CYS 3.2 9.4 + - - -
451A ASP* 1.3 77.0 - - - +
453A ALA* 1.3 57.6 + - - +
455A HIS* 3.3 22.1 + - - -
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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