Contacts of the helix formed by residues 316 - 327 (chain C) in PDB entry 5D0A
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 ALA 316 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273C LYS* 4.2 14.6 - - + -
276C LEU* 4.7 2.7 - - + -
308C LEU* 3.7 31.9 - - + -
313C ASP* 3.2 17.1 + - - +
314C ALA 3.1 1.0 - - - -
315C SER* 1.3 78.9 + - - +
317C LEU* 1.3 64.3 + - - +
318C PRO* 3.4 2.0 - - - -
319C GLU* 3.3 8.5 + - - +
320C LEU* 2.9 32.7 + - + +
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Residues in contact with LEU 317 (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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313C ASP 4.0 0.2 + - - -
314C ALA* 2.9 33.1 + - + +
316C ALA* 1.3 76.6 - - - +
318C PRO* 1.4 64.1 - - + +
320C LEU* 3.3 3.0 + - + +
321C THR* 2.9 27.5 + - - -
340C ILE* 4.0 33.2 - - + +
343C ILE* 3.8 31.4 - - + -
345C ASP* 3.5 35.9 - - + +
348C TYR* 3.5 30.3 - - + +
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Residues in contact with PRO 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C ALA 3.9 3.6 - - - +
315C SER* 3.6 14.4 - - - +
316C ALA 3.5 3.4 - - - -
317C LEU* 1.4 91.4 - - + +
319C GLU* 1.3 63.4 + - - +
321C THR* 3.1 9.4 + - - -
322C GLU* 3.0 21.1 + - - +
348C TYR* 3.7 17.0 - - + +
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Residues in contact with GLU 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C LYS* 5.1 5.2 - - + +
276C LEU* 3.5 34.2 - - + +
277C ALA* 4.1 16.7 - - - +
315C SER 5.7 0.7 - - - +
316C ALA* 3.3 10.0 + - - +
318C PRO* 1.3 78.9 - - - +
320C LEU* 1.3 62.8 + - - +
322C GLU* 3.2 23.9 + - - +
323C LEU* 3.0 37.6 + - - +
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Residues in contact with LEU 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C LEU* 4.1 14.6 - - + -
305C ILE* 3.8 38.6 - - + -
308C LEU* 4.9 6.1 - - + -
316C ALA* 2.9 31.7 + - + +
317C LEU* 3.8 5.2 - - - +
319C GLU* 1.3 76.3 - - - +
321C THR* 1.3 56.6 - - - +
323C LEU* 3.3 7.9 + - + +
324C MET* 2.8 29.6 + - - +
336C ALA* 3.5 13.2 - - + +
339C ALA* 4.1 13.0 - - + -
340C ILE* 3.9 16.2 - - + -
343C ILE* 3.7 30.5 - - + -
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Residues in contact with THR 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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317C LEU 2.9 16.5 + - - -
318C PRO* 3.3 11.9 - - - -
320C LEU* 1.3 75.5 - - - +
322C GLU* 1.3 66.3 + - - +
324C MET* 3.4 6.7 + - + +
325C HIS* 3.2 38.9 + - + -
340C ILE* 3.7 13.7 - - - +
348C TYR* 3.4 24.1 - - + -
351C GLU* 4.0 20.4 - - + +
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Residues in contact with GLU 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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318C PRO 3.0 11.7 + - - +
319C GLU* 3.2 27.1 + - - +
321C THR* 1.3 78.3 - - - +
323C LEU* 1.3 58.5 + - + +
325C HIS* 3.2 6.5 + - - +
326C LYS* 2.8 41.5 + - + +
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Residues in contact with LEU 323 (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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276C LEU* 3.5 52.3 - - + +
277C ALA* 5.6 0.2 - - - -
305C ILE* 4.3 16.8 - - + -
319C GLU* 3.0 25.1 + - - +
320C LEU* 3.5 13.7 - - + +
321C THR 3.2 0.2 - - - -
322C GLU* 1.3 75.8 - - + +
324C MET* 1.3 66.4 + - - +
326C LYS* 5.3 0.2 - - - -
327C ASP* 3.0 53.5 + - + +
329C ARG* 5.6 0.2 - - - +
332C ILE* 4.3 8.5 - - + -
333C ARG* 3.5 5.9 - - - +
336C ALA* 4.2 6.5 - - + -
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Residues in contact with MET 324 (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 LEU 2.8 16.7 + - - +
321C THR* 3.6 12.8 - - + +
323C LEU* 1.3 75.1 - - - +
325C HIS* 1.3 74.8 + - + +
333C ARG* 3.3 40.8 - - + +
336C ALA* 4.0 3.9 - - + +
337C ALA* 3.6 20.0 - - + +
340C ILE* 4.1 12.8 - - + -
351C GLU* 4.2 8.7 - - + +
352C LEU* 3.5 29.4 - - + -
355C ALA* 3.7 31.9 - - + -
359C GLU* 4.2 5.0 - - - +
368C ILE* 4.5 7.4 - - + +
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Residues in contact with HIS 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 THR* 3.2 26.8 + - + -
322C GLU* 3.2 8.6 + - - +
323C LEU 3.1 1.0 - - - -
324C MET* 1.3 87.9 + - + +
326C LYS* 1.3 80.7 + - + +
327C ASP 3.9 0.2 - - - -
333C ARG* 4.1 7.7 - - - -
351C GLU* 2.7 30.9 + - - -
354C LYS 5.2 0.2 - - - -
355C ALA* 3.7 34.0 - - + +
358C LYS* 5.1 18.3 + - + +
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Residues in contact with LYS 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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322C GLU* 2.8 31.6 + - + +
325C HIS* 1.3 91.1 + - + +
327C ASP* 1.3 68.2 + - - +
328C PRO* 3.3 7.4 - - - +
358C LYS* 6.2 0.4 - - - +
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Residues in contact with ASP 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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322C GLU 4.3 0.2 + - - -
323C LEU* 3.0 35.3 + - + +
326C LYS* 1.3 76.5 - - - +
328C PRO* 1.3 67.8 - - - +
329C ARG* 2.7 66.9 + - - +
332C ILE* 3.4 24.6 - - + +
333C ARG* 3.0 31.7 + - + +
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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