Contacts of the helix formed by residues 358 - 377 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C GLU* 3.9 28.2 + - + +
339C LEU 3.1 14.4 - - - +
340C THR* 4.3 11.4 - - - +
341C ILE* 4.2 2.2 - - - -
356C GLY 5.2 2.7 - - - +
357C GLU* 1.3 80.1 + - - +
359C VAL* 1.3 64.0 + - - +
360C ASP* 3.5 3.3 + - - +
361C PHE* 3.2 37.6 + - - +
362C VAL* 3.5 9.7 + - - +
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Residues in contact with VAL 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C LEU* 2.9 24.4 + - + +
340C THR 5.6 0.4 - - - -
341C ILE* 4.4 8.3 - - + +
357C GLU 4.2 0.2 + - - -
358C THR* 1.3 72.5 - - - +
360C ASP* 1.3 56.8 + - - +
362C VAL* 3.2 11.0 + - - +
363C ASN* 3.0 22.2 + - - +
121D ILE* 3.4 31.0 - - + +
123D SER* 3.8 15.3 - - - +
126D MSE 3.5 34.5 - - + -
154D LEU* 4.3 11.2 - - + -
158D ILE* 4.0 16.2 - - + -
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Residues in contact with ASP 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C GLU* 4.4 4.5 - - - +
331C LYS* 5.5 0.7 + - - -
332C VAL 5.2 5.4 - - - +
333C GLY 4.5 9.4 - - - +
335C SER* 3.8 27.1 + - - -
338C GLU* 3.7 23.0 + - - +
358C THR* 3.1 4.2 + - - +
359C VAL* 1.3 78.2 - - - +
361C PHE* 1.3 59.0 + - - +
363C ASN* 3.3 18.6 + - - +
364C THR* 2.8 43.3 + - - -
121D ILE 5.0 0.6 - - - +
123D SER* 4.2 12.6 + - - +
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Residues in contact with PHE 361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C LEU* 4.1 2.5 - - + -
357C GLU* 3.5 41.5 - - + +
358C THR* 3.2 27.3 + - - +
360C ASP* 1.3 76.3 - - - +
362C VAL* 1.3 66.3 + - + +
364C THR* 3.2 6.9 + - - -
365C LYS* 3.0 57.3 + - + +
432D LEU 4.4 4.0 - - - -
433D LEU* 3.9 37.9 - - + -
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Residues in contact with VAL 362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C ILE* 3.7 23.3 - - + -
354C LEU* 4.2 10.8 - - + -
358C THR 3.6 13.5 - - - +
359C VAL* 3.4 9.2 - - - +
361C PHE* 1.3 77.9 - - + +
363C ASN* 1.3 59.2 + - - +
365C LYS* 3.2 3.1 + - - +
366C ALA* 2.9 27.9 + - - +
121D ILE* 3.8 24.2 - - + -
150D THR* 4.3 19.1 - - + -
154D LEU* 4.5 6.1 - - + -
429D MSE 5.0 1.6 - - - +
433D LEU* 3.6 28.8 - - + +
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Residues in contact with ASN 363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C TYR* 3.1 48.1 + - - +
275C GLU* 4.0 13.3 + - - +
308C SER 5.0 1.7 + - - -
331C LYS* 6.0 0.2 - - - -
359C VAL 3.0 8.0 + - - +
360C ASP* 3.3 18.5 + - - +
362C VAL* 1.3 76.6 - - - +
364C THR* 1.3 56.7 + - - +
366C ALA* 3.3 6.1 + - - +
367C TYR* 3.1 26.9 + - - +
121D ILE* 3.3 47.4 + - - +
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Residues in contact with THR 364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331C LYS* 3.8 28.0 + - - +
360C ASP* 2.8 29.5 + - - -
361C PHE* 3.5 8.7 - - - +
362C VAL 3.1 0.2 - - - -
363C ASN* 1.3 74.7 - - - +
365C LYS* 1.3 69.0 + - - +
367C TYR* 3.3 9.0 + - + +
368C GLU* 3.0 46.2 + - + +
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Residues in contact with LYS 365 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C PHE* 3.0 44.6 + - + +
362C VAL 3.2 0.4 + - - +
364C THR* 1.3 79.9 - - - +
366C ALA* 1.3 65.8 + - - +
368C GLU* 2.9 33.1 + - - +
369C GLY* 3.0 21.8 + - - -
429D MSE 4.1 8.6 - - - +
432D LEU* 3.8 29.9 - - + +
433D LEU* 3.5 33.9 - - + -
446D GLU* 5.0 10.3 + - - -
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Residues in contact with ALA 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C TYR* 4.2 11.7 - - + -
308C SER* 4.9 5.6 - - - -
311C LEU* 5.8 1.1 - - + -
362C VAL 2.9 14.8 + - - +
363C ASN 3.4 9.4 - - - +
364C THR 3.2 0.2 - - - -
365C LYS* 1.3 77.2 - - - +
367C TYR* 1.3 59.9 + - - +
369C GLY* 4.1 0.3 - - - -
370C THR* 2.7 35.3 + - - +
121D ILE* 3.9 16.2 - - + -
429D MSE 3.8 28.1 - - - +
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Residues in contact with TYR 367 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C TYR* 3.5 28.0 + + + -
329C VAL* 3.7 35.0 - - + -
331C LYS* 3.4 42.4 - - + +
363C ASN 3.1 10.0 + - - +
364C THR* 3.4 13.2 - - + +
365C LYS 3.3 0.2 - - - -
366C ALA* 1.3 79.6 - - - +
368C GLU* 1.3 77.6 + - + +
370C THR* 3.9 1.2 - - - -
371C LEU* 2.9 51.9 + - + +
383C ILE* 3.1 37.2 - - - +
385C ASN* 4.9 0.7 + - - -
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Residues in contact with GLU 368 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C THR* 3.0 27.3 + - - +
365C LYS* 2.9 38.9 + - - +
367C TYR* 1.3 93.0 - - + +
369C GLY* 1.3 62.5 + - - +
371C LEU* 3.8 5.7 - - - +
372C LEU* 3.2 28.8 + - - +
432D LEU* 3.7 14.3 - - + +
446D GLU* 5.4 0.3 - - - +
449D LEU* 3.8 33.5 - - + +
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Residues in contact with GLY 369 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365C LYS 3.0 16.6 + - - -
366C ALA 4.1 0.2 - - - -
368C GLU* 1.3 75.8 - - - +
370C THR* 1.3 58.1 + - - +
372C LEU* 3.6 1.8 + - - -
373C ALA* 3.0 24.3 + - - +
425D TYR 4.5 3.1 - - - -
428D ASN* 3.1 33.2 + - - +
429D MSE 4.1 5.2 - - - -
432D LEU* 3.5 10.2 - - - +
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Residues in contact with THR 370 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C TYR* 3.5 17.7 - - - +
307C PHE* 4.4 2.5 - - + -
311C LEU* 3.6 18.6 - - + +
366C ALA 2.7 22.3 + - - -
369C GLY* 1.3 73.5 - - - +
371C LEU* 1.3 61.1 + - - +
374C HIS* 2.8 67.9 + - + +
425D TYR* 3.4 31.3 + - + +
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Residues in contact with LEU 371 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LYS* 4.0 23.8 - - + -
274C TYR* 5.1 0.2 + - - -
329C VAL* 5.2 2.0 - - + -
367C TYR* 2.9 37.6 + - + +
368C GLU* 3.8 5.4 - - - +
369C GLY 3.4 0.2 - - - -
370C THR* 1.3 76.0 - - - +
372C LEU* 1.3 69.7 + - + +
374C HIS* 4.0 1.9 - - - +
375C SER* 2.7 47.3 + - - +
381C ASN* 3.8 30.3 + - + +
383C ILE* 3.6 35.9 - - + -
449D LEU* 5.5 4.9 - - + -
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Residues in contact with LEU 372 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LYS* 5.5 3.6 - - + -
368C GLU 3.2 17.5 + - - +
369C GLY* 5.0 0.2 - - - -
371C LEU* 1.3 84.9 - - + +
373C ALA* 1.3 59.9 + - - +
375C SER* 3.4 4.0 + - - +
376C ASP* 2.9 35.3 + - - +
428D ASN* 3.9 10.8 - - - +
432D LEU* 4.7 3.6 - - + -
445D LEU* 3.7 47.8 - - + +
448D ARG* 3.8 39.9 - - + +
449D LEU* 3.9 24.5 - - + -
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Residues in contact with ALA 373 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C GLN* 3.0 19.8 + - - +
369C GLY 3.0 19.4 + - - +
370C THR 3.7 3.1 - - - +
372C LEU* 1.3 76.3 - - - +
374C HIS* 1.3 63.1 + - + +
376C ASP* 3.1 8.2 + - - +
377C GLY 3.0 17.3 + - - -
424D ALA* 3.8 7.6 - - + -
425D TYR* 3.7 28.9 - - + +
428D ASN* 3.3 13.6 - - - +
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Residues in contact with HIS 374 (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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307C PHE* 4.0 3.1 - + - -
311C LEU* 3.8 17.9 - - + +
315C GLY* 4.7 5.1 + - - -
318C VAL* 3.5 29.4 - - + +
319C GLN* 3.3 26.0 + - - +
327C GLU* 2.8 33.0 + - - +
370C THR* 2.8 49.3 + - + +
373C ALA* 1.3 74.2 - - + +
375C SER* 1.3 64.1 + - - +
377C GLY* 3.0 9.7 + - - +
378C GLY 3.2 0.5 + - - -
379C VAL* 2.9 29.4 + - + +
381C ASN* 3.8 8.8 + - - +
425D TYR* 5.1 4.2 - - + +
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Residues in contact with SER 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LYS 4.3 10.3 + - - -
14C SER* 5.7 1.1 - - - -
15C PHE* 3.5 22.7 - - - -
371C LEU* 2.7 34.0 + - - +
372C LEU* 3.6 7.6 - - - -
374C HIS* 1.3 76.7 - - - +
376C ASP* 1.3 58.5 + - - +
378C GLY* 2.8 18.2 + - - -
379C VAL 3.5 16.9 + - - -
381C ASN* 3.9 6.9 + - - +
448D ARG* 4.6 8.7 - - - -
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Residues in contact with ASP 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C GLN* 4.7 1.8 - - - +
372C LEU 2.9 17.2 + - - +
373C ALA* 3.1 12.5 + - - +
375C SER* 1.3 73.2 - - - +
377C GLY* 1.3 59.0 + - - +
378C GLY 3.3 1.0 + - - -
428D ASN* 4.9 3.6 + - - -
445D LEU* 5.5 0.5 - - - +
448D ARG* 2.8 41.5 + - - -
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Residues in contact with GLY 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C GLN* 3.6 26.4 - - - +
323C ARG* 2.9 30.1 + - - -
373C ALA 3.0 8.7 + - - -
374C HIS 3.0 6.9 + - - -
375C SER 3.0 0.8 - - - -
376C ASP* 1.3 77.9 - - - +
378C GLY* 1.3 56.0 + - - +
379C VAL 3.6 0.2 - - - -
297D GLN* 5.7 1.2 + - - -
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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