Contacts of the helix formed by residues 457 - 465 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340C ILE* 5.0 0.2 - - - +
456C LEU* 1.3 75.9 - - - +
458C LYS* 1.3 59.8 + - - +
459C SER* 3.7 7.4 + - - -
460C GLU* 2.8 40.1 + - - +
461C TRP* 2.9 27.4 + - - -
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Residues in contact with LYS 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451C LEU* 3.8 29.6 - - + +
457C SER* 1.3 74.0 - - - +
459C SER* 1.3 59.4 + - - +
461C TRP* 3.3 4.2 + - - +
462C GLU* 2.9 52.4 + - - +
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Residues in contact with SER 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C ASN* 3.3 24.5 + - - +
339C GLU* 2.1 36.0 + - - -
340C ILE* 3.8 13.4 - - - +
457C SER* 3.2 6.4 + - - -
458C LYS* 1.3 78.6 - - - +
460C GLU* 1.3 63.9 + - - +
462C GLU* 3.3 5.8 + - - -
463C ALA* 3.2 20.1 + - - +
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Residues in contact with GLU 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ARG 4.3 11.1 - - - +
169C ILE* 6.4 0.4 - - - -
171C TYR* 4.0 26.3 - - - +
172C LEU* 3.6 17.2 + - + +
340C ILE* 3.6 20.8 - - + +
455C THR 4.5 0.5 - - - +
456C LEU* 3.4 29.7 - - + +
457C SER* 2.8 37.8 + - - +
459C SER* 1.3 75.8 - - - +
461C TRP* 1.3 57.4 + - - +
463C ALA* 3.2 5.2 + - - +
464C THR* 3.0 29.5 + - - +
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Residues in contact with TRP 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C PHE* 3.6 17.5 - + - -
395C PHE 5.2 0.9 - - - -
396C LEU* 4.1 28.5 - - + -
399C TYR* 3.5 41.5 - + + -
451C LEU* 3.1 35.0 - - + -
452C PRO* 3.5 20.4 + - + -
454C GLY 2.7 27.8 + - - -
455C THR* 4.5 0.4 - - - -
456C LEU* 3.0 37.8 - - + +
457C SER 2.9 13.6 + - - +
458C LYS 3.4 4.3 - - - +
460C GLU* 1.3 75.5 - - - +
462C GLU* 1.3 58.8 + - - +
464C THR* 3.5 27.7 - - + +
465C SER* 2.8 35.7 + - - -
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Residues in contact with GLU 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327C ARG* 2.7 38.4 + - - +
338C ASN* 2.7 36.7 + - - +
341C TYR* 4.1 9.0 - - + +
451C LEU* 5.3 3.8 - - + -
458C LYS* 2.9 49.6 + - + +
459C SER* 3.3 9.4 + - - +
461C TRP* 1.3 74.8 - - - +
463C ALA* 1.3 65.2 + - - +
465C SER* 3.4 6.0 + - - -
466C ILE* 3.7 0.5 - - - +
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Residues in contact with ALA 463 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C LEU* 4.0 22.2 - - + -
340C ILE* 4.1 7.9 - - + -
341C TYR* 3.8 30.5 - - + -
360C PHE* 5.4 3.7 - - + -
362C LEU* 5.0 2.5 - - + -
459C SER 3.2 10.3 + - - +
460C GLU 3.2 8.0 + - - +
462C GLU* 1.3 77.1 - - - +
464C THR* 1.3 62.7 + - - +
466C ILE* 3.3 22.3 - - - +
467C TYR* 4.1 8.8 - - - -
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Residues in contact with THR 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C LEU* 3.8 14.8 - - - -
175C PHE* 3.6 8.4 - - + -
176C ASN* 3.6 13.6 + - - -
395C PHE* 3.3 33.2 - - + +
456C LEU* 3.8 10.1 - - + -
460C GLU 3.0 14.8 + - - +
461C TRP* 3.5 37.2 - - + +
463C ALA* 1.3 73.1 - - - +
465C SER* 1.3 62.5 + - - +
466C ILE 3.0 9.7 + - - -
467C TYR* 3.1 18.7 + - - -
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Residues in contact with SER 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C ASN* 5.2 1.9 + - - +
323C GLU* 4.0 11.6 - - - +
327C ARG* 2.7 30.2 + - - -
394C THR* 5.1 5.7 - - - +
395C PHE* 4.5 8.7 + - - -
396C LEU* 3.7 34.1 - - - +
461C TRP* 2.8 23.2 + - - -
462C GLU* 3.4 2.3 + - - -
464C THR* 1.3 78.4 - - - +
466C ILE* 1.3 61.2 + - - +
467C TYR 3.1 7.4 + - - +
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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