Contacts of the helix formed by residues 320 - 331 (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 ASN 320 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318C THR 3.4 1.6 + - - -
319C PRO* 1.3 69.2 - - - +
321C SER* 1.3 64.0 + - - +
322C PHE* 3.1 29.0 + - - +
323C GLU* 3.2 23.9 + - + +
324C LEU* 3.1 22.7 + - - +
326C ARG* 5.1 3.2 - - - +
375C PHE* 6.0 0.2 - - - +
392C LYS* 5.1 5.1 - - - +
394C THR* 4.0 23.0 - - - +
465C SER 5.4 1.2 + - - -
466C ILE 2.7 20.9 + - - +
467C TYR 4.4 1.6 - - - +
468C LEU* 3.7 32.1 - - + +
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Residues in contact with SER 321 (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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319C PRO 3.4 5.6 + - - -
320C ASN* 1.3 73.6 + - - +
322C PHE* 1.3 66.5 + - - +
324C LEU* 3.3 2.7 + - - +
325C ILE* 2.9 36.0 + - - +
372C LEU* 3.6 35.0 - - - -
373C VAL 3.2 23.5 + - - -
374C TYR* 3.7 22.9 - - - -
375C PHE* 4.3 2.5 + - - +
468C LEU* 5.1 0.6 - - - +
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Residues in contact with PHE 322 (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* 3.1 17.8 + - - +
321C SER* 1.3 88.0 + - - +
323C GLU* 1.3 57.8 + - - +
325C ILE* 4.0 4.6 - - - +
326C ARG* 3.0 51.3 + - - +
374C TYR* 3.8 36.1 - + - -
375C PHE* 5.3 4.0 - - + -
376C PRO* 4.2 19.1 - - + -
392C LYS* 5.0 15.3 - - - -
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Residues in contact with GLU 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C ASN* 3.2 26.9 + - + +
322C PHE* 1.3 78.6 - - - +
324C LEU* 1.3 63.1 + - - +
326C ARG* 3.5 26.4 + - - +
327C ARG* 2.5 81.0 + - - +
465C SER* 4.0 13.2 - - - +
466C ILE* 4.1 8.7 - - + +
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Residues in contact with LEU 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C PRO* 3.8 15.0 - - + +
320C ASN 3.1 15.4 + - - +
321C SER* 3.6 7.4 - - - +
323C GLU* 1.3 77.7 - - - +
325C ILE* 1.3 61.9 + - - +
327C ARG* 3.6 0.4 + - - +
328C LEU* 3.1 22.7 + - - +
336C PHE* 3.7 27.9 - - + -
343C VAL* 4.3 17.0 - - + -
345C PHE* 4.4 6.7 - - + -
358C TYR* 3.5 34.8 - - + +
360C PHE* 5.8 0.7 - - + -
372C LEU* 3.8 21.8 - - + -
466C ILE* 3.9 27.6 - - + -
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Residues in contact with ILE 325 (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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321C SER* 2.9 22.7 + - - +
322C PHE* 4.1 4.3 - - - +
324C LEU* 1.3 72.7 - - - +
326C ARG* 1.3 59.0 + - - +
328C LEU* 3.0 4.7 + - + +
329C GLU* 2.7 61.1 + - + +
345C PHE* 4.3 13.9 - - + -
351C TYR* 3.5 45.1 - - + +
372C LEU* 4.0 18.6 - - + -
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Residues in contact with ARG 326 (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* 5.1 3.2 - - - +
322C PHE* 3.0 44.9 + - - +
323C GLU* 3.5 28.6 + - - +
325C ILE* 1.3 78.4 - - - +
327C ARG* 1.3 61.9 + - + +
329C GLU* 3.6 4.8 + - - +
330C ALA* 3.1 30.5 + - + +
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Residues in contact with ARG 327 (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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323C GLU* 2.5 50.3 + - - +
326C ARG* 1.3 77.3 - - + +
328C LEU* 1.3 66.3 + - - +
330C ALA* 3.8 5.8 - - - +
331C SER* 3.1 23.2 + - - -
336C PHE* 3.7 34.4 - - + +
341C TYR* 3.0 20.5 + - - -
462C GLU* 2.7 30.3 + - - +
465C SER* 2.7 28.7 + - - -
466C ILE* 3.2 19.1 - - - +
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Residues in contact with LEU 328 (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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324C LEU 3.1 14.7 + - - +
325C ILE* 3.0 11.6 + - + +
327C ARG* 1.3 78.2 - - - +
329C GLU* 1.3 57.5 + - - +
331C SER* 3.1 18.5 + - - +
333C THR 4.1 1.1 - - - +
334C GLU* 3.4 40.2 - - - +
336C PHE* 3.8 12.0 - - + -
345C PHE* 3.7 32.5 - - + -
348C LYS* 3.1 34.2 + - + -
351C TYR* 3.3 33.2 - - + +
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Residues in contact with GLU 329 (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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325C ILE* 2.7 33.3 + - + +
326C ARG* 4.3 4.2 - - - +
328C LEU* 1.3 75.7 - - + +
330C ALA* 1.3 60.5 + - - +
331C SER 3.2 5.9 + - - +
332C GLU* 5.4 1.4 - - - +
348C LYS* 4.3 12.8 + - + +
349C GLY* 4.7 5.1 + - - +
351C TYR* 3.4 33.4 + - - +
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Residues in contact with ALA 330 (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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326C ARG* 3.1 20.9 + - + +
327C ARG* 3.8 7.0 - - - +
328C LEU 3.2 0.2 - - - -
329C GLU* 1.3 78.0 - - - +
331C SER* 1.3 60.3 + - - +
332C GLU* 4.0 10.0 + - - +
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Residues in contact with SER 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327C ARG 3.1 13.6 + - - -
328C LEU* 3.1 11.4 + - - -
329C GLU 3.6 3.8 - - - +
330C ALA* 1.3 80.8 - - - +
332C GLU* 1.3 57.2 + - - +
333C THR* 2.9 19.4 + - - -
335C SER 2.7 29.1 + - - -
336C PHE* 4.3 6.5 - - - -
348C LYS* 2.5 28.4 + - - -
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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