Contacts of the helix formed by residues 347 - 361 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335E ALA* 4.1 3.3 - - - +
346E CYS* 1.3 79.3 - - - +
348E GLY* 1.3 61.2 + - - -
349E SER* 3.1 6.8 + - - -
350E ALA* 3.5 10.9 + - - +
351E GLY 3.7 5.2 + - - -
376E ASP* 3.0 14.8 + - - -
377E SER 3.0 12.1 + - - -
378E VAL* 4.6 0.4 - - - -
381E TYR* 3.6 18.2 - - - -
385E PHE* 3.5 11.4 - - - -
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Residues in contact with GLY 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303E VAL* 4.3 6.5 - - - -
331E ALA* 4.0 2.9 - - - +
332E PHE* 3.8 24.9 - - - -
335E ALA* 4.0 15.0 - - - -
347E GLY* 1.3 69.8 - - - -
349E SER* 1.3 65.0 + - - +
350E ALA 3.2 0.2 - - - -
351E GLY* 2.9 10.7 + - - -
352E SER* 2.9 17.8 + - - -
381E TYR* 3.7 11.6 - - - -
385E PHE* 3.5 6.0 - - - -
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Residues in contact with SER 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254E SER* 4.2 6.2 + - - -
303E VAL* 4.5 8.9 - - - +
304E GLU 4.7 0.2 - - - -
306E ILE* 4.8 4.3 - - - -
347E GLY 4.0 2.8 - - - -
348E GLY* 1.3 77.8 - - - +
350E ALA* 1.3 59.3 + - - +
352E SER* 3.4 5.2 + - - -
353E THR* 2.4 28.3 + - - -
375E PRO* 3.6 10.4 - - - +
376E ASP* 2.6 37.4 + - - -
381E TYR* 3.6 14.5 + - - -
1510E PLP 3.6 24.9 - - - -
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Residues in contact with ALA 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338E LEU* 4.3 2.7 - - + -
346E CYS* 3.5 26.0 - - + -
347E GLY 3.5 1.5 + - - +
348E GLY 3.2 0.4 - - - -
349E SER* 1.3 76.9 + - - +
351E GLY* 1.3 53.2 + - - +
353E THR* 2.6 22.9 + - - -
354E VAL* 2.6 29.6 + - - +
374E LEU* 3.3 45.3 - - + +
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Residues in contact with GLY 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331E ALA* 3.4 21.1 - - - -
334E PHE* 4.1 0.7 - - - +
335E ALA* 4.0 5.2 - - - -
338E LEU* 4.0 16.5 - - - +
347E GLY 3.7 2.4 + - - -
348E GLY 2.9 11.9 + - - -
350E ALA* 1.3 77.0 - - - +
352E SER* 1.3 54.9 + - - -
355E ALA* 2.7 39.0 + - - +
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Residues in contact with SER 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254E SER* 5.2 3.1 - - - -
280E VAL* 3.8 17.9 - - - +
303E VAL* 4.1 5.4 - - - +
306E ILE* 3.7 25.7 - - - +
326E SER* 3.5 17.8 + - - -
327E ASN 4.3 0.5 + - - -
331E ALA* 2.8 29.7 - - - +
348E GLY 2.9 9.9 + - - -
349E SER* 3.8 7.9 - - - -
351E GLY* 1.3 75.1 - - - +
353E THR* 1.3 65.2 + - - +
355E ALA* 3.7 4.6 - - - +
356E VAL* 3.5 13.7 + - - +
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Residues in contact with THR 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E VAL* 3.5 30.1 - - + +
253E ALA 4.1 1.3 - - - +
254E SER* 3.5 30.1 - - - +
280E VAL* 4.6 5.8 - - + +
349E SER 2.4 27.0 + - - -
350E ALA* 2.6 14.3 + - - -
351E GLY 3.0 0.2 - - - -
352E SER* 1.3 73.9 - - - +
354E VAL* 1.3 65.1 + - - -
356E VAL* 3.1 14.0 + - - +
357E ALA* 3.2 10.2 + - - +
372E VAL* 4.3 6.3 - - + -
373E ILE 3.5 22.2 + - - +
375E PRO* 4.4 0.3 - - - +
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Residues in contact with VAL 354 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ILE* 5.3 7.6 - - + -
95E ILE* 4.3 9.0 - - + +
105E LEU* 5.3 9.6 - - + -
107E ALA* 5.6 0.4 - - + -
334E PHE* 4.2 14.8 - - + -
338E LEU* 3.4 40.8 - - + -
350E ALA 2.6 21.5 + - - +
353E THR* 1.3 67.9 - - - +
355E ALA* 1.3 60.5 + - - +
356E VAL 2.9 7.4 + - - -
357E ALA* 3.2 17.0 + - + +
358E VAL* 3.5 19.8 + - + +
372E VAL* 4.2 8.7 - - + -
374E LEU* 3.6 20.4 - - + -
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Residues in contact with ALA 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E GLU* 3.8 44.0 - - + +
334E PHE* 3.7 23.4 - - + -
351E GLY 2.7 25.1 + - - +
352E SER* 3.7 7.0 - - - +
353E THR 3.2 0.2 - - - -
354E VAL* 1.3 72.4 - - - +
356E VAL* 1.3 59.5 + - - +
358E VAL* 3.2 15.7 - - - +
359E LYS* 4.9 2.4 + - - +
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Residues in contact with VAL 356 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E VAL* 3.7 7.9 - - + -
280E VAL* 3.6 28.3 - - + -
324E PHE* 3.8 37.2 - - + -
325E LYS 5.5 0.2 - - - -
326E SER* 4.0 22.0 - - - -
330E GLU* 4.9 2.9 - - - +
352E SER 3.5 10.9 + - - +
353E THR 3.1 7.9 + - - +
354E VAL 2.9 0.4 - - - -
355E ALA* 1.3 79.8 - - - +
357E ALA* 1.3 56.8 + - - +
358E VAL 3.0 2.2 - - - -
359E LYS* 2.6 34.6 + - + +
360E ALA* 2.8 16.9 + - + +
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Residues in contact with ALA 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E LEU* 3.7 3.3 - - - +
105E LEU* 4.7 12.3 - - + -
252E VAL* 3.8 17.0 - - + +
353E THR 3.2 9.4 + - - +
354E VAL* 3.2 10.7 + - - +
356E VAL* 1.3 78.2 - - - +
358E VAL* 1.3 55.6 + - - +
359E LYS 3.0 3.7 + - - -
360E ALA 4.5 0.7 - - - +
361E ALA* 3.1 30.8 + - - +
370E CYS* 4.6 4.3 - - - -
372E VAL* 3.5 32.5 - - + -
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Residues in contact with VAL 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E ILE 4.2 12.6 - - - +
96E GLY* 4.8 6.1 - - - +
99E PHE* 3.9 41.2 - - + +
101E LEU* 4.2 12.6 - - + -
105E LEU* 5.6 3.4 - - + -
334E PHE* 3.9 20.6 - - + -
354E VAL* 3.6 16.4 - - + +
355E ALA 3.2 26.0 - - - +
357E ALA* 1.3 76.1 - - + +
359E LYS* 1.3 58.7 + - + +
362E GLN* 3.8 22.7 + - - +
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Residues in contact with LYS 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324E PHE* 3.2 43.5 - - + +
325E LYS 5.2 7.5 + - - +
330E GLU* 5.9 0.8 + - - -
355E ALA 4.9 1.3 - - - +
356E VAL* 2.6 26.2 + - - +
357E ALA 3.0 0.2 - - - -
358E VAL* 1.3 77.6 - - + +
360E ALA* 1.3 65.6 + - - +
361E ALA 3.2 1.1 - - - -
362E GLN* 3.1 24.6 + - + +
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Residues in contact with ALA 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250E MET* 3.5 15.0 - - + +
252E VAL* 4.3 5.8 - - + -
278E ILE* 4.0 14.8 - - + -
324E PHE* 3.4 35.6 - - + -
356E VAL* 2.8 19.3 + - + +
359E LYS* 1.3 74.3 - - - +
361E ALA* 1.3 59.5 + - - +
362E GLN 3.2 0.9 + - - -
363E GLU* 3.5 25.3 + - - +
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Residues in contact with ALA 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E LEU* 3.4 15.3 - - + +
103E CYS* 3.7 25.4 - - - -
250E MET* 3.8 10.1 - - - -
357E ALA 3.1 19.8 + - - +
360E ALA* 1.3 74.8 - - - +
362E GLN* 1.3 57.7 + - - +
363E GLU 2.8 13.0 + - - -
364E LEU* 3.0 30.0 + - + +
370E CYS* 4.2 8.3 - - - -
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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