Contacts of the helix formed by residues 358 - 377 (chain E) in PDB entry 3IFS
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 THR 358 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338E GLU* 3.9 23.2 + - + +
339E LEU 3.2 15.3 - - - +
340E THR* 4.1 13.7 - - - +
341E ILE* 4.1 3.1 - - - -
356E GLY 5.0 2.7 - - - +
357E GLU* 1.3 79.6 - - - +
359E VAL* 1.3 63.6 + - - +
360E ASP* 3.4 5.5 + - - +
361E PHE* 3.1 37.4 + - - +
362E VAL* 3.4 10.0 + - - +
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Residues in contact with VAL 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339E LEU* 2.8 24.6 + - + +
340E THR 5.5 0.2 - - - -
341E ILE* 4.2 17.7 - - + -
358E THR* 1.3 71.3 - - - +
360E ASP* 1.3 62.3 + - - +
362E VAL* 3.1 7.6 + - - +
363E ASN* 3.0 18.5 + - - +
121F ILE* 3.5 26.2 - - + +
123F SER* 3.9 14.4 - - - +
126F MSE 3.1 36.3 - - + -
154F LEU* 4.4 8.7 - - + -
158F ILE* 3.9 20.2 - - + -
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Residues in contact with ASP 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E GLU* 4.5 4.5 - - - +
331E LYS* 5.3 2.1 + - - -
332E VAL 5.3 4.6 - - - +
333E GLY 4.6 8.5 - - - +
335E SER* 3.9 30.5 + - - -
338E GLU* 3.7 22.5 + - - +
358E THR* 3.2 3.8 + - - +
359E VAL* 1.3 81.4 - - - +
361E PHE* 1.3 55.0 + - - +
363E ASN* 3.3 18.4 + - - +
364E THR* 2.9 42.3 + - - -
121F ILE 5.0 0.9 - - - -
123F SER* 4.3 8.9 + - - +
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Residues in contact with PHE 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354E LEU* 4.1 7.2 - - + -
357E GLU* 3.6 47.3 - - + +
358E THR* 3.1 27.1 + - - +
360E ASP* 1.3 76.7 - - - +
362E VAL* 1.3 67.1 + - + +
364E THR* 3.3 7.1 + - - -
365E LYS* 3.1 56.7 + - + +
432F LEU 4.5 1.6 - - - -
433F LEU* 3.8 33.9 - - + -
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Residues in contact with VAL 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341E ILE* 3.8 20.4 - - + -
354E LEU* 4.0 17.5 - - + -
358E THR 3.4 12.3 + - - +
359E VAL 3.1 8.4 + - - +
361E PHE* 1.3 80.3 - - + +
363E ASN* 1.3 63.1 + - - +
365E LYS* 3.2 3.3 + - - +
366E ALA* 2.9 21.8 + - - +
121F ILE* 3.8 24.7 - - + -
150F THR* 4.2 20.0 - - + -
154F LEU* 4.5 6.5 - - + -
429F MSE 5.2 2.0 - - - -
433F LEU* 3.8 23.2 - - + +
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Residues in contact with ASN 363 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E TYR* 3.1 48.7 + - - +
275E GLU* 4.0 12.9 + - - +
308E SER 4.9 2.1 + - - -
331E LYS* 5.8 0.2 - - - -
359E VAL 3.0 7.8 + - - +
360E ASP* 3.3 18.8 + - - +
362E VAL* 1.3 75.6 - - - +
364E THR* 1.3 58.4 + - - +
366E ALA* 3.4 2.1 + - - +
367E TYR* 3.0 27.4 + - - +
121F ILE* 3.3 48.3 + - - +
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Residues in contact with THR 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331E LYS* 3.8 29.6 + - - +
360E ASP* 2.9 26.6 + - - -
361E PHE* 3.5 7.8 - - - -
362E VAL 3.2 0.2 - - - -
363E ASN* 1.3 78.4 - - - +
365E LYS* 1.3 63.3 + - + +
367E TYR* 3.2 8.8 + - + +
368E GLU* 2.9 46.7 + - + +
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Residues in contact with LYS 365 (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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361E PHE* 3.1 44.9 + - + +
362E VAL 3.2 0.6 + - - +
364E THR* 1.3 77.4 - - + +
366E ALA* 1.3 61.7 + - - +
368E GLU* 3.6 26.4 + - - +
369E GLY* 2.9 27.0 + - - -
429F MSE 4.1 6.2 - - - +
432F LEU* 3.6 35.8 + - + +
433F LEU* 3.6 33.0 - - + -
446F GLU* 5.2 6.7 + - - +
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Residues in contact with ALA 366 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E TYR* 4.3 9.9 - - + -
308E SER* 5.0 5.6 - - - -
311E LEU* 5.8 1.3 - - + -
362E VAL 2.9 12.7 + - - +
363E ASN* 3.5 8.7 - - - +
365E LYS* 1.3 75.0 - - - +
367E TYR* 1.3 63.4 + - - +
369E GLY 3.9 0.2 - - - -
370E THR* 2.8 34.5 + - - +
121F ILE* 3.9 16.2 - - + -
425F TYR* 5.9 0.2 - - - -
429F MSE 3.7 30.8 - - - +
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Residues in contact with TYR 367 (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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274E TYR* 3.5 27.8 + + + -
329E VAL* 3.8 33.2 - - + -
331E LYS* 3.6 41.3 - - + +
363E ASN 3.0 14.2 + - - +
364E THR* 3.2 13.2 + - + +
366E ALA* 1.3 77.8 - - - +
368E GLU* 1.3 82.9 + - + +
370E THR* 3.8 1.2 - - - -
371E LEU* 3.0 50.4 + - + +
383E ILE* 3.3 35.4 - - + +
385E ASN* 4.9 0.9 + - - -
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Residues in contact with GLU 368 (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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364E THR* 2.9 32.5 + - - +
365E LYS* 3.6 29.8 + - - +
366E ALA 3.3 0.2 - - - -
367E TYR* 1.3 91.7 - - + +
369E GLY* 1.3 66.3 + - - +
371E LEU* 3.4 5.2 + - - +
372E LEU* 3.2 28.2 + - - +
432F LEU* 3.6 15.6 - - + +
449F LEU* 3.7 34.1 - - + +
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Residues in contact with GLY 369 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365E LYS 2.9 19.5 + - - -
366E ALA 4.0 0.4 - - - -
368E GLU* 1.3 73.8 - - - +
370E THR* 1.3 57.5 + - - +
372E LEU* 3.4 1.0 + - - -
373E ALA* 3.0 25.1 + - - +
425F TYR 4.4 4.0 - - - -
428F ASN* 3.2 36.9 + - - +
429F MSE 4.2 2.2 - - - -
432F LEU* 3.4 10.4 - - - +
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Residues in contact with THR 370 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E TYR* 3.4 18.4 - - - +
307E PHE* 4.3 2.9 - - + -
311E LEU* 3.5 27.8 - - + +
366E ALA* 2.8 22.2 + - - -
367E TYR 3.8 0.2 - - - -
369E GLY* 1.3 73.9 - - - +
371E LEU* 1.3 60.5 + - - +
374E HIS* 2.8 62.5 + - + +
425F TYR* 3.5 21.8 + - + +
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Residues in contact with LEU 371 (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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11E LYS* 4.0 24.9 - - + -
329E VAL* 4.9 3.8 - - + -
367E TYR* 3.0 36.1 + - + +
368E GLU* 3.7 6.1 - - - +
370E THR* 1.3 78.8 - - - +
372E LEU* 1.3 72.6 + - + +
374E HIS* 4.0 1.6 - - - +
375E SER* 2.9 38.4 + - - +
381E ASN* 3.8 31.4 + - + +
383E ILE* 3.8 34.5 - - + -
449F LEU* 5.2 5.2 - - + -
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Residues in contact with LEU 372 (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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11E LYS* 5.8 4.0 - - + -
368E GLU 3.2 18.6 + - - +
369E GLY* 3.9 3.6 - - - +
371E LEU* 1.3 87.8 - - + +
373E ALA* 1.3 65.8 + - - +
375E SER* 3.4 4.9 + - - +
376E ASP* 3.0 29.6 + - - +
428F ASN* 4.0 9.4 - - - +
432F LEU* 4.9 2.0 - - + -
445F LEU* 3.9 42.8 - - + +
448F ARG* 3.8 39.2 + - + +
449F LEU* 3.9 23.1 - - + -
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Residues in contact with ALA 373 (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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319E GLN* 2.9 29.0 + - - +
369E GLY 3.0 17.8 + - - +
370E THR 3.3 3.6 + - - +
372E LEU* 1.3 76.5 - - - +
374E HIS* 1.3 62.2 + - + +
376E ASP* 3.2 8.5 + - - +
377E GLY 3.0 8.7 + - - -
424F ALA* 3.7 8.1 - - + -
425F TYR* 3.6 29.6 - - + +
428F ASN* 3.4 13.8 - - - +
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Residues in contact with HIS 374 (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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307E PHE* 4.0 2.9 - + - -
311E LEU* 3.7 20.3 - - + +
315E GLY* 4.5 5.7 + - - -
318E VAL* 3.5 29.7 - - + +
319E GLN* 3.3 25.0 + - - +
327E GLU* 2.9 32.9 + - - +
370E THR* 2.8 47.9 + - + +
371E LEU 4.1 0.2 - - - +
373E ALA* 1.3 73.9 - - + +
375E SER* 1.3 61.8 + - - +
377E GLY* 3.0 12.4 + - - +
378E GLY 3.2 0.5 + - - -
379E VAL* 3.0 26.1 + - + +
381E ASN* 3.8 9.7 + - - +
425F TYR* 5.1 4.8 - - + +
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Residues in contact with SER 375 (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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11E LYS 4.2 14.8 + - - -
14E SER* 5.7 1.1 - - - -
15E PHE* 3.3 24.3 - - - -
371E LEU* 2.9 28.8 + - - +
372E LEU* 3.6 8.7 - - - -
373E ALA 3.3 0.2 - - - -
374E HIS* 1.3 76.1 - - - +
376E ASP* 1.3 62.4 + - - +
378E GLY* 3.0 15.6 + - - -
379E VAL 3.4 16.3 + - - -
381E ASN* 4.1 7.4 + - - +
448F ARG* 4.6 6.1 - - - -
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Residues in contact with ASP 376 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319E GLN* 4.6 1.3 - - - +
372E LEU* 3.0 20.2 + - - +
373E ALA* 3.2 7.5 + - - +
375E SER* 1.3 76.2 - - - +
377E GLY* 1.3 58.3 + - - +
378E GLY 3.2 1.4 + - - -
428F ASN* 5.1 2.9 + - - -
445F LEU* 5.7 0.2 - - - +
448F ARG* 2.8 42.1 + - - -
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Residues in contact with GLY 377 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319E GLN* 3.5 28.3 - - - +
323E ARG* 2.8 29.5 + - - -
373E ALA 3.0 5.9 + - - -
374E HIS* 3.0 10.6 + - - -
376E ASP* 1.3 76.4 - - - +
378E GLY* 1.3 56.5 + - - +
297F GLN* 5.7 1.4 + - - -
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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
------------------------------------------------------------
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