Contacts of the helix formed by residues 352 - 366 (chain C) in PDB entry 3IAD
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 352 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351C PHE* 1.3 77.6 - - - +
353C ASP* 1.3 60.0 + - - +
354C LEU* 3.5 8.1 + - - +
355C GLU* 2.7 42.6 + - - +
356C ILE* 3.1 29.4 + - - +
472C ARG* 4.6 10.5 - - - +
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Residues in contact with ASP 353 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C ARG 5.6 1.4 - - - +
297C LEU* 4.5 8.6 - - + +
300C THR* 3.9 21.5 + - + +
301C PHE* 3.7 22.5 - - + -
352C THR* 1.3 72.9 - - - +
354C LEU* 1.3 61.9 + - - +
356C ILE* 3.4 14.2 + - - +
357C LEU* 2.9 29.5 + - - +
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Residues in contact with LEU 354 (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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301C PHE* 3.7 25.7 - - + -
352C THR* 3.3 7.9 + - - +
353C ASP* 1.3 79.4 - - - +
355C GLU* 1.3 57.3 + - + +
357C LEU* 3.4 4.2 + - + +
358C ALA* 2.9 27.7 + - - +
418C LEU* 3.9 18.6 - - + -
422C GLN* 4.0 27.8 - - + +
425C SER* 3.6 31.9 - - - +
426C LEU* 3.8 11.6 - - + +
429C MET* 4.0 10.9 - - + +
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Residues in contact with GLU 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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351C PHE* 3.4 14.1 - - + -
352C THR* 2.7 46.4 + - - +
354C LEU* 1.3 75.1 - - + +
356C ILE* 1.3 59.4 + - - +
358C ALA* 3.2 3.0 + - - +
359C ALA* 3.0 29.3 + - - +
429C MET* 3.7 29.5 - - + +
469C TYR* 5.9 2.3 - - - -
472C ARG* 2.7 47.4 + - - +
476C LEU* 4.4 13.9 - - + +
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Residues in contact with ILE 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C ARG* 3.8 35.4 - - + +
297C LEU* 4.9 7.9 - - + -
342C LEU* 3.8 32.8 - - + -
351C PHE* 4.1 22.2 - - + +
352C THR 3.1 21.2 + - - +
353C ASP* 3.7 15.3 - - - +
355C GLU* 1.3 76.1 - - - +
357C LEU* 1.3 62.1 - - - +
359C ALA* 3.2 4.3 + - - +
360C ILE* 3.0 28.5 + - + +
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Residues in contact with LEU 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C PHE* 3.8 34.1 - - + -
297C LEU* 4.4 12.5 - - + +
301C PHE* 3.8 40.2 - - + -
303C ILE* 5.1 1.8 - - + -
353C ASP 2.9 18.3 + - - +
354C LEU* 3.5 5.4 - - + +
356C ILE* 1.3 76.2 - - - +
358C ALA* 1.3 58.1 + - - +
360C ILE* 4.2 2.6 - - - +
361C PHE* 2.9 35.8 + - + +
415C PHE* 3.9 32.3 - - + -
418C LEU* 4.4 4.3 - - + -
426C LEU* 4.1 13.2 - - + -
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Residues in contact with ALA 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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354C LEU 2.9 15.1 + - - +
355C GLU* 3.4 11.9 - - - +
356C ILE 3.2 0.2 - - - -
357C LEU* 1.3 76.6 - - - +
359C ALA* 1.3 52.9 + - - +
362C ALA* 2.7 39.2 + - - +
426C LEU* 3.5 18.5 - - + +
429C MET* 3.9 28.0 - - + -
430C VAL* 3.6 10.9 - - + +
433C ILE* 4.3 4.5 - - + -
476C LEU* 5.7 0.2 - - + -
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Residues in contact with ALA 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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338C THR* 4.1 16.6 - - + -
342C LEU* 4.4 7.6 - - + -
355C GLU 3.0 12.7 + - - +
356C ILE 3.2 8.0 + - - +
358C ALA* 1.3 75.2 - - - +
360C ILE* 1.3 54.1 + - - +
362C ALA* 3.5 2.3 + - - +
363C SER* 2.7 36.7 + - - -
433C ILE* 3.9 14.8 - - + +
476C LEU* 4.2 21.1 - - + -
479C MET* 5.3 0.9 - - - -
480C VAL* 4.0 7.1 - - + +
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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
----------------------------------------------------------
288C MET* 3.8 23.1 - - - -
291C ILE* 3.8 26.0 - - + -
292C PHE* 3.9 14.4 - - + -
295C ARG* 3.8 24.7 - - - +
297C LEU* 4.5 7.4 - - + -
335C VAL* 4.0 12.9 - - + +
338C THR* 4.4 8.3 - - + -
339C HIS* 4.9 7.0 - - + +
342C LEU* 4.2 11.2 - - + -
356C ILE* 3.0 25.3 + - + +
357C LEU* 4.2 3.4 - - - +
359C ALA* 1.3 73.9 - - - +
361C PHE* 1.3 60.7 + - - +
363C SER* 3.3 7.7 + - - -
364C ALA* 3.1 25.1 + - - +
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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
----------------------------------------------------------
288C MET* 5.1 8.3 - - + -
292C PHE* 5.6 2.9 - + + -
311C TYR* 3.4 42.8 - + - -
357C LEU* 2.9 24.5 + - + +
358C ALA* 3.9 2.2 - - - +
360C ILE* 1.3 76.1 - - - +
362C ALA* 1.3 64.3 + - - +
364C ALA* 3.2 15.1 + - + +
365C ILE* 3.2 36.4 + - + +
403C GLY 4.1 6.7 - - - -
404C PHE* 4.2 16.2 - + - -
407C LEU* 4.5 5.2 - - + -
414C ILE* 4.1 8.5 - - + -
415C PHE* 3.6 41.7 - + + -
426C LEU* 5.4 1.6 - - + -
430C VAL* 3.9 19.3 - - + -
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Residues in contact with ALA 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 ALA 2.7 23.9 + - - +
359C ALA 3.6 4.7 - - - +
361C PHE* 1.3 73.7 - - - +
363C SER* 1.3 56.9 + - - +
365C ILE* 3.4 1.2 + - - +
366C HIS* 3.0 32.9 + - - +
430C VAL* 4.0 13.9 - - + -
433C ILE* 3.8 32.5 - - + -
434C VAL* 3.7 18.1 - - + +
480C VAL* 5.3 1.3 - - - -
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Residues in contact with SER 363 (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* 3.9 5.4 - - - +
334C VAL* 4.0 9.9 - - - -
335C VAL* 3.7 26.9 - - - +
338C THR* 3.2 20.1 + - - -
359C ALA 2.7 22.1 + - - -
360C ILE* 3.5 7.4 - - - -
361C PHE 3.2 0.4 - - - -
362C ALA* 1.3 75.8 - - - +
364C ALA* 1.3 60.3 + - - +
366C HIS* 2.8 30.7 + - - -
480C VAL* 3.5 12.6 - - - +
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Residues in contact with ALA 364 (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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284C LEU* 4.1 6.3 - - + +
288C MET* 3.8 26.9 - - + -
315C LEU* 3.8 18.0 - - + +
319C TYR* 2.7 31.9 + - - -
331C ALA* 4.0 3.2 - - - +
335C VAL* 3.5 13.9 - - + -
360C ILE 3.1 12.7 + - - +
361C PHE* 3.2 10.2 + - + +
363C SER* 1.3 78.4 - - - +
365C ILE* 1.3 55.1 + - + +
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Residues in contact with ILE 365 (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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311C TYR* 3.5 24.9 - - - +
315C LEU* 4.1 10.3 - - + -
319C TYR* 3.6 2.0 - - - -
361C PHE* 3.2 32.9 + - + +
362C ALA* 3.7 6.1 - - - +
364C ALA* 1.3 77.7 - - + +
366C HIS* 1.3 60.8 - - - +
367C ASP 2.9 10.2 + - - -
368C VAL* 3.0 22.1 + - + +
399C HIS* 3.5 10.6 - - - +
400C LEU* 4.1 17.9 - - + +
403C GLY* 3.9 27.8 - - - -
404C PHE* 4.7 2.0 - - + +
430C VAL* 4.0 23.3 - - + -
434C VAL* 4.2 6.1 - - + -
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Residues in contact with HIS 366 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C TYR* 4.8 0.4 + - - -
330C HIS* 3.6 6.5 - + - -
331C ALA* 4.6 4.9 - - - -
334C VAL* 3.5 34.9 - - + +
362C ALA 3.0 17.0 + - - +
363C SER* 2.8 22.3 + - - -
364C ALA 3.5 2.0 - - - -
365C ILE* 1.3 74.9 - - - +
367C ASP* 1.3 71.7 + - + +
368C VAL 3.8 0.2 - - - -
399C HIS* 2.9 21.9 - - - +
434C VAL* 4.1 22.9 - - + +
437C THR* 4.3 22.7 + - + -
480C VAL* 5.4 2.5 - - + -
484C ASP* 3.1 13.3 + - - -
620C ZN 2.2 35.3 - - - -
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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
------------------------------------------------------------
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