Contacts of the helix formed by residues 354 - 369 (chain C) in PDB entry 5MG3
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 TRP 354 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348C HIS* 5.1 1.6 + - - -
352C GLY* 3.7 15.1 - - - -
353C ASN* 1.3 89.6 - - - +
355C GLY* 1.4 60.6 + - - +
356C PHE 3.0 6.4 + - - -
357C SER* 3.1 22.4 + - - -
358C ILE* 3.9 7.3 + - - +
445C GLU* 3.1 57.9 - - + +
448C GLN* 3.4 43.5 - - + +
449C ALA 4.3 10.5 - - - -
450C PRO* 4.4 13.7 - - + -
451C PHE* 5.7 11.7 - + - -
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Residues in contact with GLY 355 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C ASN 3.2 1.6 + - - -
354C TRP* 1.4 76.0 - - - +
356C PHE* 1.3 61.4 + - - +
358C ILE* 3.5 12.0 + - - +
359C ILE* 3.4 25.8 + - - +
440C LEU* 6.1 0.2 - - - -
445C GLU* 4.0 3.8 + - - +
446C LEU* 4.4 20.9 - - - -
450C PRO* 4.0 8.1 - - - +
453C LEU* 4.6 5.6 - - - -
458C LEU* 4.6 7.6 - - - +
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Residues in contact with PHE 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C VAL* 5.0 5.8 - - + -
353C ASN* 3.4 34.9 + - + +
354C TRP 3.0 0.2 + - - -
355C GLY* 1.3 72.0 - - - +
357C SER* 1.4 70.2 + - - +
359C ILE* 3.1 24.1 - - + +
360C ILE* 3.2 37.7 + - + +
450C PRO* 3.9 17.7 - - + +
452C ALA* 3.6 30.5 - - + -
453C LEU* 4.0 19.5 - - + +
44F ARG* 5.2 19.3 - - - -
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Residues in contact with SER 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C HIS* 3.1 49.2 - - - +
351C VAL* 3.8 19.9 - - - +
353C ASN 4.5 0.4 + - - -
354C TRP 3.1 14.7 + - - -
356C PHE* 1.4 79.6 - - - +
358C ILE* 1.3 53.4 + - - +
360C ILE* 3.3 6.7 + - - +
361C ILE* 2.8 39.8 + - - +
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Residues in contact with ILE 358 (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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344C LEU 5.5 0.2 - - - +
345C LYS* 4.4 15.7 - - - -
348C HIS* 4.6 5.6 - - + +
354C TRP 4.5 8.7 - - - +
355C GLY* 3.5 12.3 + - - +
356C PHE 3.4 0.4 - - - -
357C SER* 1.3 74.2 - - - +
359C ILE* 1.4 59.1 + - + +
361C ILE* 3.5 16.2 - - + +
362C THR* 2.6 40.2 + - - +
436C LEU* 3.8 13.6 - - + +
439C MET* 3.9 35.0 - - + -
440C LEU* 3.8 38.6 - - + -
445C GLU* 5.9 1.3 - - - +
446C LEU* 6.4 0.2 - - + -
516C TYR* 4.8 2.5 - - + -
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Residues in contact with ILE 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355C GLY 3.4 12.3 + - - +
356C PHE* 3.1 19.7 - - + +
358C ILE* 1.4 81.2 - - + +
360C ILE* 1.4 63.4 + - + +
362C THR* 3.5 5.3 - - - -
363C PHE* 3.0 22.3 + - - +
453C LEU* 3.8 29.6 - - + -
512C GLY 5.7 0.9 - - - +
515C LEU* 4.7 12.8 - - + +
516C TYR* 4.3 28.9 - - + +
519C VAL* 3.4 42.4 - - + +
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Residues in contact with ILE 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C PHE* 3.2 48.6 + - + +
357C SER* 3.6 9.2 - - - +
359C ILE* 1.4 81.2 - - + +
361C ILE* 1.4 67.5 + - + +
363C PHE* 3.2 9.4 + - + +
364C ILE* 3.1 37.7 + - + +
519C VAL* 6.3 0.9 - - + -
190F LEU* 4.5 26.2 - - + +
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Residues in contact with ILE 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C LEU* 3.4 38.8 - - + +
347C ILE* 3.8 33.4 - - + +
348C HIS* 3.8 23.3 - - + +
357C SER* 2.8 26.0 + - - +
358C ILE* 3.5 20.6 - - + +
360C ILE* 1.4 72.7 - - + +
362C THR* 1.4 61.0 + - - +
364C ILE* 3.7 10.7 - - + +
365C VAL* 2.8 37.3 + - + +
436C LEU* 4.6 8.1 - - + -
191F PHE* 4.9 6.5 - - + -
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Residues in contact with THR 362 (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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358C ILE 2.6 25.2 + - - -
359C ILE* 3.5 8.5 - - - +
361C ILE* 1.4 77.6 - - - +
363C PHE* 1.4 58.2 + - - +
365C VAL* 4.1 4.2 - - - +
366C ARG* 2.8 29.2 + - + +
433C PHE* 4.2 10.7 - - + -
436C LEU* 3.7 12.4 - - - +
516C TYR* 3.6 28.8 - - + +
520C SER* 3.7 40.4 - - - +
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Residues in contact with PHE 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C ILE 3.0 15.6 + - - +
360C ILE* 3.2 12.1 + - + +
362C THR* 1.4 74.6 - - - +
364C ILE* 1.3 51.0 + - - +
366C ARG* 3.7 1.4 - - - +
367C GLY* 2.8 28.8 + - - -
519C VAL* 4.4 14.7 - - + +
522C LEU* 4.3 21.3 - - + -
523C VAL* 3.7 32.2 - - + +
526C ILE* 3.6 33.2 - - + -
33F LEU* 5.0 5.2 - - + -
36F ALA* 5.8 2.7 - - + -
40F ILE* 4.6 15.0 - - + -
187F ILE* 3.9 23.3 - - + +
190F LEU* 4.0 17.3 - - + -
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Residues in contact with ILE 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C ILE* 3.1 29.0 + - + +
361C ILE* 3.7 11.0 - - + +
362C THR 3.4 0.2 - - - -
363C PHE* 1.3 71.7 - - - +
365C VAL* 1.3 62.1 + - + +
367C GLY* 3.0 4.0 + - - -
368C ILE* 2.9 33.5 + - + +
187F ILE* 3.4 24.0 - - + +
188F LEU* 6.1 1.1 - - + -
190F LEU* 3.8 24.2 - - + +
191F PHE* 3.5 66.9 - - + -
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Residues in contact with VAL 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344C LEU* 5.0 10.3 - - + -
347C ILE* 5.4 5.2 - - + -
361C ILE* 2.8 27.7 + - + +
362C THR* 4.1 4.0 - - - +
364C ILE* 1.3 71.0 - - + +
366C ARG* 1.4 65.3 + - - +
368C ILE* 3.1 25.4 + - + +
369C MET* 3.1 31.9 + - + +
432C ILE* 4.0 34.8 - - + -
433C PHE* 4.3 13.5 - - + -
436C LEU* 5.7 1.6 - - + -
191F PHE* 6.5 0.7 - - + -
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Residues in contact with ARG 366 (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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362C THR* 2.8 21.3 + - + +
363C PHE* 3.9 4.0 - - - +
365C VAL* 1.4 78.1 - - - +
367C GLY* 1.4 54.8 + - - +
369C MET* 3.1 27.6 - - - +
370C TYR* 3.4 1.4 + - - -
373C THR* 3.4 44.1 + - - +
429C GLN* 3.4 15.4 + - - +
433C PHE* 3.3 42.5 - - + -
520C SER* 3.0 44.6 + - - +
521C ASN* 4.9 4.4 + - - -
523C VAL* 3.6 27.8 - - + +
524C THR* 5.6 1.3 - - - +
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Residues in contact with GLY 367 (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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363C PHE 2.8 16.0 + - - -
364C ILE 3.0 6.4 + - - -
366C ARG* 1.4 73.1 - - - +
368C ILE* 1.3 61.9 + - - +
369C MET 3.3 0.2 - - - -
370C TYR* 3.2 23.5 - - - +
523C VAL* 4.6 7.8 - - - +
33F LEU* 6.5 0.7 - - - -
184F THR* 4.7 7.3 - - - +
187F ILE* 3.7 31.1 - - - +
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Residues in contact with ILE 368 (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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364C ILE* 2.9 25.0 + - + +
365C VAL* 3.1 18.8 + - + +
367C GLY* 1.3 76.4 - - - +
369C MET* 1.4 72.2 + - + +
370C TYR 3.2 4.4 + - - -
371C PRO* 4.0 6.4 - - - +
372C LEU* 3.8 12.1 - - + +
184F THR* 6.0 0.6 - - - +
187F ILE* 4.9 4.9 - - + -
188F LEU* 5.8 3.8 - - + -
191F PHE* 5.8 7.0 - - + -
271F GLU* 5.8 4.5 - - - +
275F LEU* 3.9 41.7 - - + -
279F ILE* 4.5 9.6 - - - +
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Residues in contact with MET 369 (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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365C VAL* 3.1 34.0 + - + +
366C ARG* 3.1 14.5 - - - +
367C GLY 3.3 0.2 - - - -
368C ILE* 1.4 88.1 - - + +
370C TYR* 1.3 56.0 + - - -
371C PRO 3.7 1.8 - - - -
372C LEU* 3.7 35.7 - - + -
373C THR* 2.8 43.5 + - - +
428C ILE* 5.0 7.2 - - + -
429C GLN* 3.4 23.3 - - + +
432C ILE* 4.2 18.2 - - + -
433C PHE* 4.9 6.7 - - + -
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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
------------------------------------------------------------
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