Contacts of the helix formed by residues 347 - 361 (chain C) in PDB entry 1M54
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 GLY 347 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C ALA* 4.2 2.4 - - - +
346C CYS* 1.3 78.6 - - - +
348C GLY* 1.3 67.1 + - - -
349C SER* 3.0 3.8 + - - -
350C ALA* 2.9 20.1 + - - +
351C GLY 3.4 2.3 + - - -
376C ASP* 3.2 18.9 + - - -
377C SER 3.4 13.6 + - - -
381C TYR* 3.6 16.4 - - - -
385C PHE* 4.2 2.9 - - - -
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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
----------------------------------------------------------
303C VAL* 4.3 8.1 - - - -
331C ALA* 3.2 10.0 - - - +
332C PHE* 4.0 22.4 - - - -
335C ALA* 4.0 15.7 - - - -
347C GLY* 1.3 67.7 - - - -
349C SER* 1.3 66.6 + - - +
351C GLY* 2.7 11.3 + - - -
352C SER 2.8 10.4 + - - -
381C TYR* 4.5 9.2 - - - -
385C PHE* 3.7 9.1 - - - -
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Residues in contact with SER 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C SER* 4.6 3.3 - - - -
303C VAL* 4.2 11.1 - - - +
304C GLU 4.5 1.9 + - - -
306C ILE* 5.1 4.0 - - - -
347C GLY* 3.0 2.8 + - - -
348C GLY* 1.3 75.2 - - - +
350C ALA* 1.3 65.5 + - - +
352C SER* 3.0 27.9 + - - -
353C THR* 3.1 12.2 + - - -
375C PRO* 3.6 18.6 - - - +
376C ASP* 3.6 17.8 + - - -
381C TYR* 5.4 1.0 + - - -
1310C PLP 3.2 38.5 - - - +
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Residues in contact with ALA 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C LEU* 3.5 3.1 - - + +
346C CYS* 3.4 30.1 - - + -
347C GLY 2.9 11.4 + - - +
349C SER* 1.3 80.6 + - - +
351C GLY* 1.3 66.3 + - - +
352C SER 3.4 0.2 + - - -
353C THR* 4.1 1.6 - - - +
354C VAL* 3.3 27.9 + - - +
374C LEU* 3.2 36.7 - - + +
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Residues in contact with GLY 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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331C ALA* 2.7 28.9 - - - -
334C PHE* 3.3 8.9 - - - +
335C ALA* 3.4 16.7 - - - +
347C GLY 3.4 2.4 + - - -
348C GLY 2.7 10.3 + - - -
350C ALA* 1.3 75.6 - - - +
352C SER* 1.3 62.0 + - - +
355C ALA* 3.0 25.1 + - - +
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Residues in contact with SER 352 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C SER* 5.5 0.9 - - - -
280C VAL* 4.0 17.9 - - - -
303C VAL* 4.4 3.6 - - - +
306C ILE* 3.8 20.2 - - - +
326C SER* 3.5 13.9 + - - -
327C ASN 4.8 0.2 + - - -
331C ALA* 2.8 26.3 - - - +
348C GLY 2.8 6.3 + - - -
349C SER 3.0 12.0 + - - -
351C GLY* 1.3 74.4 - - - +
353C THR* 1.3 69.6 + - - +
355C ALA* 3.0 15.7 + - - +
356C VAL* 3.2 13.0 + - - +
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Residues in contact with THR 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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252C VAL* 3.5 35.8 - - + +
253C ALA* 4.1 1.1 - - - +
254C SER* 3.4 30.0 + - - -
280C VAL* 3.5 10.7 - - + +
349C SER 3.1 7.3 + - - -
350C ALA 4.3 3.1 - - - -
352C SER* 1.3 75.7 - - - +
354C VAL* 1.3 51.1 + - - +
356C VAL* 2.8 9.9 + - - +
357C ALA* 2.7 30.3 + - - +
372C VAL* 3.4 27.4 - - + -
373C ILE 3.7 11.5 + - - +
374C LEU* 4.9 0.2 - - - -
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Residues in contact with VAL 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ILE* 6.2 4.9 - - + -
95C ILE* 4.5 11.7 - - + -
105C LEU* 5.5 7.9 - - + -
334C PHE* 3.7 22.0 - - + -
338C LEU* 3.7 25.8 - - + -
350C ALA 3.3 18.0 + - - +
351C GLY 4.2 0.2 - - - +
352C SER 3.3 0.6 - - - -
353C THR* 1.3 70.2 - - - +
355C ALA* 1.3 58.7 + - - +
356C VAL 2.8 11.0 + - - -
357C ALA* 2.8 19.8 + - + -
358C VAL* 3.0 23.4 + - + +
372C VAL* 4.3 11.7 - - + -
374C LEU* 4.1 13.5 - - + -
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Residues in contact with ALA 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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330C GLU* 3.3 33.8 - - + +
334C PHE* 3.5 28.8 - - + -
351C GLY 3.0 19.4 + - - +
352C SER 3.0 8.3 + - - +
354C VAL* 1.3 74.8 - - - +
356C VAL* 1.3 57.0 + - - +
358C VAL* 3.7 4.6 - - - +
359C LYS* 3.2 28.2 - - - +
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Residues in contact with VAL 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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252C VAL* 4.0 14.8 - - + -
278C ILE* 4.4 1.8 - - + -
280C VAL* 3.5 33.7 - - + -
324C PHE* 3.4 47.8 - - + -
325C LYS 5.6 0.2 - - - -
326C SER* 4.4 11.7 - - - -
330C GLU* 4.5 2.2 - - - +
352C SER 3.2 4.5 + - - +
353C THR 2.8 10.0 + - - +
355C ALA* 1.3 81.5 - - - +
357C ALA* 1.3 50.9 + - - +
358C VAL 3.3 1.8 - - - -
359C LYS* 2.7 31.4 + - - +
360C ALA* 2.8 17.4 + - + -
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Residues in contact with ALA 357 (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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101C LEU* 4.4 2.2 - - + -
105C LEU* 4.9 11.4 - - + -
252C VAL* 4.0 25.8 - - + -
353C THR 2.7 11.5 + - - +
354C VAL* 3.4 18.2 - - + +
356C VAL* 1.3 72.3 - - - +
358C VAL* 1.3 57.3 + - - +
359C LYS 2.8 11.2 + - - -
360C ALA 4.4 0.7 - - - +
361C ALA* 2.9 31.6 + - - +
370C CYS* 5.3 0.9 - - - -
372C VAL* 4.2 15.7 - - + -
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Residues in contact with VAL 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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95C ILE* 4.8 7.9 - - + +
96C GLY* 5.4 2.0 - - - -
99C PHE* 3.8 44.3 - - + +
101C LEU* 3.3 31.5 - - + +
105C LEU* 5.6 0.9 - - + -
334C PHE* 3.9 23.1 - - + -
354C VAL* 3.0 26.2 + - + +
355C ALA 3.7 14.4 - - - +
357C ALA* 1.3 73.5 - - + +
359C LYS* 1.3 64.1 + - + +
362C GLN* 3.8 11.7 - - - +
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Residues in contact with LYS 359 (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 PHE* 4.3 27.1 - - + -
325C LYS 4.9 8.1 + - - -
330C GLU* 3.3 22.0 + - - -
355C ALA 3.2 24.9 - - - +
356C VAL* 2.7 16.1 + - - +
357C ALA 2.8 0.2 - - - -
358C VAL* 1.3 84.8 - - + +
360C ALA* 1.3 64.8 + - - +
361C ALA 3.1 1.6 + - - -
362C GLN* 3.3 12.8 + - - +
363C GLU* 4.8 1.2 + - - +
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Residues in contact with ALA 360 (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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250C MET* 3.5 22.5 - - + +
252C VAL* 4.8 6.5 - - + -
278C ILE* 4.0 15.3 - - + -
324C PHE* 3.8 27.9 - - + -
356C VAL 2.8 15.1 + - - +
357C ALA 4.4 1.1 - - - +
359C LYS* 1.3 73.7 - - - +
361C ALA* 1.3 58.9 + - - +
363C GLU* 2.8 33.1 - - - +
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Residues in contact with ALA 361 (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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101C LEU* 3.8 22.3 - - + +
102C LYS 4.9 1.6 + - - -
103C CYS* 4.0 16.5 - - - -
250C MET* 3.9 9.6 - - - -
357C ALA* 2.9 17.9 + - - +
360C ALA* 1.3 75.7 - - - +
362C GLN* 1.3 55.0 + - - +
363C GLU 2.3 20.5 + - - -
364C LEU* 2.8 25.0 + - + +
370C CYS* 4.6 8.7 - - - -
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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