Contacts of the helix formed by residues 347 - 361 (chain C) in PDB entry 1IRI
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 ARG 347 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162C LEU* 4.8 6.2 - - + +
165C LEU* 3.5 34.5 - - + +
166C MET* 3.5 21.2 - - + +
169C GLU* 4.6 2.9 - - + -
344C TYR 4.7 0.8 + - - -
345C LEU* 3.0 1.2 - - - +
346C HIS* 1.3 120.4 + - + +
348C PHE* 1.3 64.2 + - - +
349C ALA 3.4 2.7 - - - -
350C ALA* 3.4 23.3 + - + +
351C TYR* 3.1 18.0 + - - +
382C GLU* 4.9 5.3 + - - -
347D ARG* 3.8 23.4 - - - +
382D GLU* 3.0 36.2 + - - -
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Residues in contact with PHE 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C MET* 3.7 21.8 - - + +
338C MET* 3.6 28.0 - - + -
340C PRO* 4.6 13.7 - - + -
345C LEU* 3.0 45.4 + - + +
347C ARG* 1.3 78.2 - - - +
349C ALA* 1.3 62.6 + - - +
351C TYR* 3.3 4.5 + - - +
352C PHE* 3.2 48.6 + + - +
407C LEU* 4.5 15.3 - - + -
487C LEU* 4.6 6.3 - - + -
490C LEU* 4.9 13.5 - - + -
491C VAL* 4.3 16.8 - - + -
494C TYR* 4.1 16.2 - + - -
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Residues in contact with ALA 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338C MET* 3.7 34.8 - - + +
340C PRO* 5.1 5.1 - - + +
345C LEU 4.5 1.4 + - - -
346C HIS 5.1 4.2 + - - +
347C ARG 3.4 0.4 - - - -
348C PHE* 1.3 75.9 - - - +
350C ALA* 1.3 61.0 + - - +
352C PHE* 3.5 1.7 + - - -
353C GLN* 2.9 27.6 + - - +
379C VAL* 4.2 6.2 - - - +
380C TRP* 4.5 3.9 - - - -
381C GLY* 3.6 32.3 - - - +
382C GLU* 5.3 1.3 - - - -
383C PRO* 6.4 0.2 - - + -
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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
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162C LEU* 4.0 18.7 - - + +
346C HIS 5.4 0.6 + - - -
347C ARG* 3.4 43.7 + - - +
348C PHE 3.4 0.4 - - - -
349C ALA* 1.3 79.5 - - - +
351C TYR* 1.3 62.9 + - - +
353C GLN* 3.0 26.6 - - - +
354C GLN* 3.3 4.3 + - - +
382D GLU* 3.9 12.6 - - + +
390D ALA* 6.0 0.3 - - - +
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Residues in contact with TYR 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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162C LEU* 3.7 15.4 - - + +
163C GLY* 3.1 43.5 - - - -
166C MET* 3.9 24.5 - - + -
273C ARG* 3.1 28.2 + - - -
274C TYR* 4.7 1.7 - - - -
275C SER 5.3 0.2 + - - -
276C LEU* 3.5 20.0 - - + +
347C ARG 3.1 14.5 + - - +
348C PHE 3.6 7.6 - - - +
349C ALA 3.2 0.4 - - - -
350C ALA* 1.3 77.5 - - - +
352C PHE* 1.3 90.5 + + - +
354C GLN* 3.2 11.8 + - - +
355C GLY* 2.9 21.5 + - - -
491C VAL* 4.2 7.6 - - + -
495C GLU* 4.3 9.9 + - - +
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Residues in contact with PHE 352 (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 MET* 4.0 27.8 - - + -
348C PHE* 3.2 48.6 + + - +
349C ALA 4.5 0.2 - - - +
351C TYR* 1.3 96.8 - + - +
353C GLN* 1.3 65.4 + - - +
354C GLN 3.0 1.3 - - - -
355C GLY* 3.7 5.8 - - - +
356C ASP* 2.8 31.8 + - + +
379C VAL* 4.1 3.9 - - + +
491C VAL* 3.2 39.5 - - + -
494C TYR* 3.3 26.0 - + + -
495C GLU* 4.0 13.0 - - + -
498C ILE* 3.8 19.7 - - + -
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Residues in contact with GLN 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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349C ALA 2.9 13.7 + - - +
350C ALA* 3.0 18.1 + - - +
352C PHE* 1.3 79.7 - - - +
354C GLN* 1.3 57.9 + - - +
357C MET* 3.0 42.5 + - - +
379C VAL* 2.9 35.3 + - - +
380C TRP* 4.2 10.6 - - - +
380D TRP* 3.2 26.2 - - - +
381D GLY 4.9 3.0 + - - +
382D GLU* 3.6 18.5 + - - +
390D ALA* 6.2 0.2 - - + -
391D PHE* 3.5 29.6 - - + +
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Residues in contact with GLN 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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158C GLY* 3.6 17.0 + - - -
159C GLY* 3.3 7.6 + - - -
162C LEU* 3.3 27.4 - - + +
273C ARG* 3.7 17.7 - - + +
350C ALA 3.3 5.0 + - - +
351C TYR* 3.2 11.7 + - + +
353C GLN* 1.3 78.6 - - - +
355C GLY* 1.3 68.8 + - - +
356C ASP 3.1 1.6 - - - -
358C GLU* 3.0 47.4 + - - +
603C E4P 3.3 10.4 - - - +
389D HIS 3.1 15.3 - - - +
390D ALA* 3.7 25.1 - - + +
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Residues in contact with GLY 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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273C ARG* 3.8 19.0 - - - -
274C TYR* 4.1 4.1 + - - -
351C TYR* 2.9 17.3 + - - -
352C PHE* 3.3 12.0 + - - -
354C GLN* 1.3 78.8 - - - +
356C ASP* 1.3 57.5 + - - +
359C SER* 2.5 32.9 + - - -
498C ILE* 3.8 9.8 - - - +
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Residues in contact with ASP 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C HIS* 5.4 0.9 - - - -
338C MET* 5.9 1.4 - - - +
352C PHE* 2.8 19.4 + - + +
355C GLY* 1.3 77.0 - - - +
357C MET* 1.3 65.0 + - - +
359C SER* 3.0 5.4 + - - -
360C ASN* 3.0 34.0 + - - +
376C GLY* 4.9 0.3 - - - -
377C PRO* 4.0 23.4 - - - +
379C VAL* 3.6 25.3 - - + +
497C LYS* 4.5 12.8 + - - +
498C ILE* 3.7 27.5 - - + +
501C GLN* 4.4 8.4 - - - +
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Residues in contact with MET 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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353C GLN* 3.0 31.1 + - - +
356C ASP* 1.3 81.7 - - - +
358C GLU* 1.3 57.0 + - - +
360C ASN 5.2 0.2 - - - -
361C GLY* 2.9 29.4 + - - +
377C PRO 3.5 17.0 - - - +
378C ILE* 3.7 29.6 - - + -
379C VAL* 3.6 24.5 - - + +
380D TRP* 3.9 14.1 - - + -
390D ALA 4.9 0.2 - - - -
391D PHE* 3.7 29.8 - - + +
393D GLN* 4.1 2.1 - - - +
394D LEU* 3.9 33.7 - - + +
395D ILE* 5.5 0.4 - - + -
402D ILE* 5.4 0.4 - - + -
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Residues in contact with GLU 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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273C ARG* 3.3 31.8 + - - +
354C GLN* 3.0 40.3 + - - +
357C MET* 1.3 78.2 - - - +
359C SER* 1.3 57.8 + - - +
362C LYS* 3.2 18.2 + - - -
511C ASP 3.6 1.0 - - - +
512C GLN* 3.4 25.0 - - + +
515C VAL* 4.6 4.5 - - + +
603C E4P 3.5 17.8 - - - +
389D HIS 3.4 12.8 - - - +
390D ALA 3.3 17.8 + - - +
393D GLN* 3.4 25.3 - - + +
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Residues in contact with SER 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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273C ARG* 2.9 10.9 + - - +
274C TYR* 2.8 19.1 + - - -
355C GLY 2.5 25.5 + - - -
356C ASP 3.0 3.5 + - - -
358C GLU* 1.3 79.6 - - - +
360C ASN* 1.3 63.6 + - - +
362C LYS* 2.7 27.0 + - - +
498C ILE* 3.6 18.6 - - - -
509C SER* 3.3 25.9 + - - -
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Residues in contact with ASN 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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356C ASP* 3.0 14.4 + - - +
357C MET* 5.2 0.2 - - - -
359C SER* 1.3 83.3 - - - +
361C GLY* 1.3 57.6 + - - +
362C LYS* 2.8 13.7 + - - +
375C THR* 3.2 5.7 + - - -
376C GLY* 3.0 25.9 + - - -
498C ILE* 3.2 25.2 + - - +
501C GLN* 4.0 3.3 - - - +
502C GLY* 4.0 1.9 + - - -
505C TRP* 3.7 31.3 - - + -
507C ILE* 3.3 16.8 - - + +
509C SER* 2.6 31.1 + - - -
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Residues in contact with GLY 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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357C MET 2.9 19.5 + - - -
359C SER 3.7 1.0 - - - -
360C ASN* 1.3 72.0 - - - +
362C LYS* 1.3 58.9 + - - +
375C THR* 4.5 0.4 - - - -
393D GLN* 2.9 29.8 + - - +
394D LEU* 3.5 30.4 - - - +
397D GLN 3.4 6.9 - - - +
398D GLY* 3.6 10.1 - - - -
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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