Contacts of the helix formed by residues 320 - 329 (chain C) in PDB entry 1M6X
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 LEU 320 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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367B ILE* 5.8 0.4 - - + -
315C LEU* 2.7 27.3 + - + +
318C LYS* 4.4 7.2 - - + -
319C GLY* 1.3 76.3 - - - +
321C THR* 1.3 65.1 + - - +
322C GLU* 3.1 22.2 - - - +
323C LEU* 3.0 42.7 + - + +
324C THR 3.8 1.9 + - - -
353C HIS* 4.8 9.4 - - + +
357C LEU* 3.7 31.2 - - + -
364C TYR* 3.5 49.4 - - + +
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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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315C LEU 4.7 0.7 - - - -
316C SER* 3.6 35.0 - - - +
319C GLY* 3.8 1.2 - - - -
320C LEU* 1.3 78.1 - - - +
322C GLU* 1.3 64.9 + - - +
324C THR* 2.9 31.2 + - - +
325C ASN* 4.1 5.7 + - - -
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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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366B PRO 3.8 17.8 - - - +
367B ILE 4.4 6.2 - - - +
369B LYS* 3.8 30.5 + - - +
319C GLY 5.5 0.9 - - - +
320C LEU* 4.1 19.2 - - - +
321C THR* 1.3 81.7 + - - +
323C LEU* 1.3 74.4 + - + +
325C ASN* 4.4 8.5 + - - +
326C VAL* 3.9 12.1 - - - +
334C ARG* 5.7 2.6 + - - -
353C HIS* 4.3 12.5 + - - -
364C TYR* 5.4 2.5 + - - -
369C LYS* 5.6 3.8 + - - -
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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
----------------------------------------------------------
315C LEU* 4.4 7.2 - - + -
320C LEU* 3.0 30.1 + - + +
321C THR 3.0 0.8 - - - -
322C GLU* 1.3 93.7 - - + +
324C THR* 1.3 65.2 + - - +
325C ASN 3.4 0.2 - - - -
326C VAL* 3.0 9.1 + - + +
327C VAL* 2.8 33.3 + - + +
351C PRO* 3.4 39.7 - - + -
353C HIS* 3.9 26.2 - - + +
354C TYR* 4.2 26.7 - - + -
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Residues in contact with THR 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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189C CYS* 5.4 1.1 - - - -
312C THR* 4.4 22.5 + - + +
315C LEU* 3.8 26.1 - - + +
316C SER* 5.7 0.2 - - - -
320C LEU 3.8 0.8 + - - -
321C THR* 2.9 28.6 + - - +
323C LEU* 1.3 76.8 - - - +
325C ASN* 1.3 68.0 + - - +
328C GLY 2.8 22.5 + - - -
330C TRP* 3.4 27.6 - - + -
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Residues in contact with ASN 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 4.1 7.1 + - - -
322C GLU* 4.4 5.4 + - - +
323C LEU 3.2 0.8 + - - -
324C THR* 1.3 79.1 - - - +
326C VAL* 1.3 58.6 + - + +
329C ASN* 2.8 27.9 + - - -
330C TRP* 3.1 47.5 + - - +
331C SER 5.0 2.9 - - - +
332C ASP* 6.2 2.5 - - - -
334C ARG* 5.9 5.1 - - - +
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Residues in contact with VAL 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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228C ARG* 5.5 0.5 - - - -
322C GLU 3.9 15.3 - - - +
323C LEU* 3.0 13.2 + - + +
325C ASN* 1.3 75.8 - - + +
327C VAL* 1.3 67.9 + - - +
329C ASN* 3.1 13.9 + - - +
334C ARG* 5.4 9.2 - - - +
348C THR* 4.1 26.9 - - + +
349C ALA 3.9 27.1 - - - +
350C ILE* 3.7 13.1 - - + +
351C PRO* 4.4 11.2 - - + -
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Residues in contact with VAL 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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188C ASN* 3.1 21.7 - - - +
189C CYS* 3.8 17.7 - - + -
228C ARG* 3.2 17.1 + - - +
315C LEU* 4.3 9.4 - - + -
323C LEU* 2.8 30.5 + - + +
324C THR 4.0 1.8 - - - +
326C VAL* 1.3 76.9 - - + +
328C GLY* 1.3 58.5 + - - +
350C ILE* 3.2 23.7 - - + +
351C PRO* 5.3 0.7 - - + -
354C TYR* 3.5 55.6 - - + +
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Residues in contact with GLY 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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189C CYS* 3.6 28.7 - - - +
194C ASP* 5.2 1.4 - - - +
228C ARG* 4.0 6.1 + - - -
308C ARG* 3.0 23.7 + - - -
324C THR 2.8 16.8 + - - -
325C ASN 3.8 0.2 - - - -
327C VAL* 1.3 74.3 - - - +
329C ASN* 1.3 68.6 + - - +
330C TRP* 3.8 8.3 - - - -
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Residues in contact with ASN 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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191C ARG* 4.7 4.2 + - - -
222C THR* 5.1 3.0 + - - +
224C THR* 4.5 9.3 + - - +
226C VAL* 3.0 44.5 + - - +
227C SER 3.8 3.6 + - - -
228C ARG* 3.3 36.4 - - + +
308C ARG* 3.8 6.3 + - - +
325C ASN 2.8 12.2 + - - -
326C VAL* 3.1 9.9 + - - +
328C GLY* 1.3 85.4 - - - +
330C TRP* 1.3 68.5 + - - +
331C SER* 4.8 1.2 + - - -
15G T 5.3 0.5 + - - -
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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