Contacts of the helix formed by residues 457 - 465 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339D GLU* 4.8 2.0 + - - -
456D LEU* 1.3 75.6 - - - +
458D LYS* 1.3 60.2 + - - +
459D SER* 3.5 7.2 + - - -
460D GLU* 3.0 44.2 + - - +
461D TRP* 2.8 27.3 + - - -
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Residues in contact with LYS 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451D LEU* 4.1 14.1 - - + +
452D PRO 5.9 0.7 - - - -
456D LEU 3.9 0.4 + - - -
457D SER* 1.3 74.2 - - - +
459D SER* 1.3 58.9 + - - +
461D TRP* 3.3 10.1 + - - +
462D GLU* 3.0 52.3 + - - +
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Residues in contact with SER 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D ASN* 3.1 33.9 + - - +
339D GLU* 3.0 40.6 + - - +
340D ILE* 3.9 6.0 - - - +
457D SER* 3.2 6.1 + - - -
458D LYS* 1.3 81.2 - - - +
460D GLU* 1.3 60.7 + - - +
462D GLU* 3.3 5.5 + - - -
463D ALA* 3.2 15.1 + - - +
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Residues in contact with GLU 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ARG 3.5 20.7 - - - +
169D ILE* 5.5 0.2 - - + -
171D TYR* 4.0 20.5 - - - +
172D LEU* 3.9 16.3 + - + +
340D ILE* 3.5 23.3 - - + -
455D THR 5.0 0.2 - - - +
456D LEU* 3.7 26.4 - - + +
457D SER* 3.0 38.7 + - - +
459D SER* 1.3 76.9 - - - +
461D TRP* 1.3 62.1 + - - +
463D ALA* 3.3 4.1 + - - +
464D THR* 3.1 24.4 + - - +
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Residues in contact with TRP 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D PHE* 3.8 16.4 - + - -
395D PHE 5.2 0.2 - - - -
396D LEU* 4.8 17.0 - - + -
399D TYR* 3.6 38.8 - + - -
451D LEU* 4.2 16.2 - - + -
452D PRO* 3.3 47.1 + - + -
454D GLY 3.0 28.1 + - - -
455D THR* 4.6 0.9 - - - -
456D LEU* 3.2 36.9 + - + +
457D SER 2.8 15.1 + - - +
458D LYS* 3.6 7.6 - - - +
460D GLU* 1.3 77.0 - - - +
462D GLU* 1.3 51.2 + - - +
464D THR* 3.4 30.0 - - + +
465D SER* 2.8 46.5 + - - -
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Residues in contact with GLU 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D ARG* 2.9 40.0 + - - +
337D GLY 5.4 0.5 - - - +
338D ASN* 2.9 27.9 + - - +
341D TYR* 4.3 3.4 - - + +
451D LEU* 3.7 16.4 - - + +
458D LYS* 3.0 45.3 + - - +
459D SER* 3.6 8.4 + - - +
460D GLU 3.3 0.2 - - - -
461D TRP* 1.3 76.6 - - - +
463D ALA* 1.3 63.4 + - - +
465D SER* 3.2 7.2 + - - -
466D ILE* 3.9 0.3 - - - +
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Residues in contact with ALA 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D LEU* 4.1 13.7 - - + -
340D ILE* 4.0 19.3 - - + -
341D TYR* 3.9 28.0 - - + -
360D PHE* 5.7 4.8 - - + -
362D LEU* 5.5 4.3 - - + +
459D SER 3.2 12.7 + - - +
460D GLU* 3.7 7.6 - - - +
461D TRP 3.2 0.2 - - - -
462D GLU* 1.3 79.8 - - - +
464D THR* 1.3 61.7 + - - +
466D ILE* 3.5 19.3 - - - +
467D TYR* 4.9 4.0 - - - -
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Residues in contact with THR 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D LEU* 3.8 15.3 - - - -
175D PHE* 3.6 14.1 - - + -
176D ASN* 3.7 7.8 + - - -
395D PHE* 3.3 25.1 - - + +
456D LEU* 3.9 8.3 - - + -
460D GLU 3.1 13.9 + - - +
461D TRP* 3.4 39.0 - - + +
463D ALA* 1.3 74.6 - - - +
465D SER* 1.3 61.3 + - - +
466D ILE 3.0 9.8 + - - -
467D TYR* 3.1 23.9 + - - +
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Residues in contact with SER 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D ASN* 5.3 1.9 + - - +
323D GLU* 3.9 13.2 - - - +
327D ARG* 2.9 26.6 + - - -
394D THR* 5.3 5.0 - - - -
395D PHE* 4.6 7.6 + - - -
396D LEU* 5.1 13.7 - - - +
451D LEU* 4.4 16.2 - - - +
461D TRP* 2.8 27.2 + - - -
462D GLU* 3.2 4.0 + - - -
464D THR* 1.3 75.9 - - - +
466D ILE* 1.3 62.6 + - - +
467D TYR 3.1 7.9 + - - +
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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