Contacts of the helix formed by residues 457 - 465 (chain A) in PDB entry 5E9W
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 SER 457 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339A GLU* 5.1 2.4 + - - -
340A ILE* 4.9 0.3 - - - +
456A LEU* 1.3 75.0 - - - +
458A LYS* 1.3 60.6 + - - +
459A SER* 3.7 7.3 + - - -
460A GLU* 2.9 40.3 + - - +
461A TRP* 2.9 26.6 + - - -
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Residues in contact with LYS 458 (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 LEU* 3.6 23.2 - - + +
456A LEU 4.0 0.4 + - - -
457A SER* 1.3 73.4 - - - +
459A SER* 1.3 60.0 + - - +
461A TRP* 3.3 6.6 + - - +
462A GLU* 3.0 51.6 + - - +
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Residues in contact with SER 459 (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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338A ASN* 3.3 30.3 + - - +
339A GLU* 2.8 44.5 + - - +
340A ILE* 4.2 5.9 - - - +
457A SER* 3.2 5.3 + - - -
458A LYS* 1.3 79.7 + - - +
460A GLU* 1.3 64.1 + - - +
462A GLU* 3.3 5.2 + - - -
463A ALA* 3.1 19.9 + - - +
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Residues in contact with GLU 460 (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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168A ARG 4.4 11.3 - - - +
169A ILE* 5.6 0.4 - - - -
171A TYR* 4.1 23.8 + - - +
172A LEU* 3.8 16.5 + - + +
340A ILE* 3.4 22.0 - - + +
455A THR 4.6 0.3 - - - +
456A LEU* 3.4 31.0 - - + +
457A SER* 2.9 38.9 + - - +
459A SER* 1.3 75.8 - - - +
461A TRP* 1.3 57.8 + - - +
463A ALA* 3.1 6.7 + - - +
464A THR* 2.9 29.6 + - - +
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Residues in contact with TRP 461 (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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175A PHE* 3.8 18.4 - + - -
395A PHE 5.2 0.7 - - - -
396A LEU* 3.9 25.8 - - + -
399A TYR* 3.4 39.7 - + + -
451A LEU* 3.7 18.4 - - + -
452A PRO* 3.3 38.3 + - + +
454A GLY 2.6 30.5 + - - -
455A THR* 4.7 0.7 - - - -
456A LEU* 3.1 34.9 + - + +
457A SER 2.9 11.5 + - - -
458A LYS* 3.5 10.5 - - - +
460A GLU* 1.3 78.1 - - - +
462A GLU* 1.3 51.1 + - - +
464A THR* 3.4 29.0 - - + +
465A SER* 2.7 42.7 + - - -
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Residues in contact with GLU 462 (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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327A ARG* 2.7 38.0 + - - +
338A ASN* 2.6 37.8 + - - +
341A TYR* 4.1 7.6 - - + +
451A LEU* 4.4 12.3 - - + -
458A LYS* 3.0 49.7 + - - +
459A SER* 3.5 10.1 + - - +
460A GLU 3.3 0.2 - - - -
461A TRP* 1.3 77.5 - - - +
463A ALA* 1.3 61.7 + - - +
465A SER* 3.3 7.6 + - - -
466A ILE* 3.8 0.7 - - - +
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Residues in contact with ALA 463 (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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172A LEU* 3.9 22.7 - - + -
340A ILE* 4.2 9.0 - - + -
341A TYR* 3.8 28.0 - - + -
360A PHE* 5.8 2.8 - - + -
362A LEU* 5.2 1.3 - - + -
459A SER 3.1 11.3 + - - +
460A GLU 3.1 9.0 + - - +
462A GLU* 1.3 79.6 - - - +
464A THR* 1.3 61.6 + - - +
466A ILE* 3.3 21.9 - - - +
467A TYR* 4.3 7.7 - - - -
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Residues in contact with THR 464 (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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172A LEU* 3.8 14.8 - - - -
175A PHE* 3.6 14.2 - - + -
176A ASN* 3.7 7.4 + - - -
395A PHE* 3.1 35.1 - - + +
456A LEU* 3.9 7.6 - - + -
460A GLU 2.9 15.4 + - - +
461A TRP* 3.4 38.8 - - + +
463A ALA* 1.3 72.5 - - - +
465A SER* 1.3 62.5 + - - +
466A ILE 3.0 10.4 + - - -
467A TYR* 3.1 16.2 + - - +
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Residues in contact with SER 465 (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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320A ASN* 5.3 2.1 + - - +
323A GLU* 3.9 13.4 - - - +
327A ARG* 2.8 28.4 + - - -
394A THR* 5.3 4.3 - - - -
395A PHE* 4.6 7.6 + - - -
396A LEU* 5.1 22.7 - - - +
451A LEU* 5.6 6.6 - - - +
461A TRP* 2.7 24.1 + - - -
462A GLU* 3.3 2.9 + - - -
464A THR* 1.3 78.8 - - - +
466A ILE* 1.3 61.1 + - - +
467A TYR 3.2 6.6 + - - +
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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