Contacts of the helix formed by residues 347 - 356 (chain C) in PDB entry 6N0M
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 HIS 347 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340C GLN 5.5 2.5 - - - -
341C ASP 3.8 19.0 + - - -
342C TYR* 3.4 44.6 + + + +
343C THR 3.4 3.4 + - - +
346C ASP* 1.3 91.1 - - + +
348C GLY* 1.3 67.7 + - - +
349C TYR 3.5 0.7 - - - -
350C SER* 3.2 7.2 - - - -
351C LEU* 3.1 24.4 + - - +
476C THR* 5.4 8.0 - - + +
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Residues in contact with GLY 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C TYR* 3.6 17.9 - - - -
343C THR 3.2 10.1 + - - -
344C TRP* 3.5 14.8 - - - -
347C HIS* 1.3 77.7 - - - +
349C TYR* 1.3 61.4 + - - +
351C LEU* 3.2 5.7 + - - +
352C ILE* 3.1 24.4 + - - +
469C LEU* 4.2 1.3 - - - -
472C LEU* 3.9 14.1 - - - +
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Residues in contact with TYR 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C TRP* 2.9 47.7 + + + +
345C GLU* 4.8 8.5 - - - +
348C GLY* 1.3 67.6 - - - +
350C SER* 1.3 59.9 + - - +
352C ILE* 3.4 1.4 + - - +
353C GLN* 2.7 79.2 + - - +
360C GLY* 3.5 27.1 - - - -
361C GLN* 3.5 16.5 + - - -
364C ASP* 3.2 35.2 - - + +
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Residues in contact with SER 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345C GLU 5.5 0.4 + - - -
346C ASP 3.5 19.2 + - - -
347C HIS* 3.2 13.0 - - - -
349C TYR* 1.3 83.1 - - - +
351C LEU* 1.3 57.5 + - - -
353C GLN* 3.9 2.9 - - - +
354C ARG* 3.2 33.5 + - - +
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Residues in contact with LEU 351 (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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342C TYR* 3.5 4.7 - - - +
347C HIS 3.1 15.8 + - - +
348C GLY 3.6 3.8 - - - +
350C SER* 1.3 73.5 - - - +
352C ILE* 1.3 65.3 + - - +
353C GLN 3.2 1.3 - - - -
354C ARG* 3.4 29.0 + - - +
355C LEU* 3.3 42.3 + - + +
472C LEU* 3.4 27.6 - - + +
475C ILE* 4.2 8.5 - - + -
476C THR* 3.3 40.4 - - + +
479C MET* 3.9 12.6 - - - -
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Residues in contact with ILE 352 (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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195C ILE* 3.8 34.3 - - + -
199C VAL* 4.1 16.8 - - + -
344C TRP* 4.2 13.7 - - + -
348C GLY 3.1 12.8 + - - +
349C TYR 4.0 4.7 - - - +
351C LEU* 1.3 75.5 - - - +
353C GLN* 1.3 57.5 + - - +
355C LEU* 3.1 3.2 + - - -
356C TYR* 2.7 44.8 + - + +
359C GLY 4.2 2.7 - - - -
360C GLY* 3.3 34.5 - - - +
363C LEU* 4.5 6.1 - - + -
468C LEU* 4.3 9.0 - - + -
472C LEU* 3.6 22.0 - - + -
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Residues in contact with GLN 353 (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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349C TYR* 2.7 61.7 + - + +
350C SER* 3.9 3.1 - - - +
352C ILE* 1.3 76.0 - - - +
354C ARG* 1.3 61.2 + - - +
356C TYR 4.3 0.4 - - - -
357C PRO* 3.6 42.7 - - + +
360C GLY* 4.5 3.4 - - - -
361C GLN* 3.5 17.8 + - - -
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Residues in contact with ARG 354 (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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350C SER* 3.2 23.9 + - - +
351C LEU* 3.4 30.3 - - - +
352C ILE 3.3 0.6 - - - -
353C GLN* 1.3 78.0 - - - +
355C LEU* 1.3 70.2 + - + +
356C TYR 3.8 0.2 + - - -
357C PRO* 4.7 4.3 - - - +
476C THR* 5.6 2.0 - - - +
479C MET* 3.6 22.0 - - - +
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Residues in contact with LEU 355 (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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106C PRO* 6.0 0.9 - - - +
191C LEU* 3.6 43.3 - - + +
192C ALA* 4.0 20.5 - - - +
195C ILE* 3.9 29.4 - - + -
351C LEU* 3.3 41.5 + - + +
352C ILE 3.1 2.3 + - - +
354C ARG* 1.3 87.8 - - + +
356C TYR* 1.3 60.0 + - - +
357C PRO* 4.1 3.5 - - - +
475C ILE* 4.5 8.5 - - + -
479C MET* 4.7 6.7 - - + -
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Residues in contact with TYR 356 (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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99C LEU* 3.4 31.3 + - + +
100C LEU* 3.6 19.7 - - + +
105C GLY* 5.9 0.4 - - - -
106C PRO* 4.6 17.5 - - + -
192C ALA 5.0 1.6 - - - +
195C ILE* 3.3 30.3 - - + -
196C GLN* 3.7 41.0 + - + +
199C VAL* 4.2 15.3 - - + -
352C ILE* 2.7 20.3 + - + +
355C LEU* 1.3 76.0 - - - +
357C PRO* 1.3 75.1 - - + +
358C GLU* 3.3 3.8 - - + -
359C GLY* 3.7 26.2 - - - -
360C GLY 3.2 14.9 + - - -
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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