Contacts of the helix formed by residues 383 - 399 (chain C) in PDB entry 2IHU
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 383 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378C TYR* 3.6 44.7 - - + -
380C ASP* 2.9 29.5 + - - -
381C GLY 2.9 27.7 + - - -
382C MET* 1.3 75.9 + - - +
384C VAL* 1.3 66.5 + - - +
385C HIS* 3.3 27.4 - - + +
386C GLN* 3.0 25.5 + - - +
387C VAL* 3.3 11.0 + - - +
560C ASN* 3.4 41.6 + - - +
561C TYR* 5.6 1.6 + - - +
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Residues in contact with VAL 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383C ARG* 1.3 72.1 - - - +
385C HIS* 1.3 63.3 + - - +
387C VAL* 3.0 9.7 + - + +
388C ILE* 3.0 28.7 + - + +
413C PHE* 4.0 19.5 - - + +
416C TYR* 3.6 40.2 - - + -
460C ILE* 4.5 10.5 - - + -
488C VAL* 5.1 2.2 - - + -
559C VAL* 4.4 14.8 - - + -
560C ASN 5.3 0.4 + - - +
561C TYR* 3.4 38.4 - - + +
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Residues in contact with HIS 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371C PHE* 3.1 74.6 - + + +
372C LEU* 3.7 15.5 - - + +
374C ASP* 2.8 32.9 + - + +
378C TYR* 4.7 1.6 - - - -
383C ARG* 3.4 30.1 - - + +
384C VAL* 1.3 77.4 - - - +
386C GLN* 1.3 67.5 + - + +
388C ILE* 3.6 3.0 + - - +
389C ASP* 3.0 29.6 + - - +
416C TYR* 3.5 17.7 + - + -
420C PHE* 5.1 0.2 - - - -
536C ARG* 5.0 0.2 - - - -
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Residues in contact with GLN 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C ASP* 3.1 16.7 + - - +
376C GLU 2.7 28.9 + - - +
378C TYR* 3.6 22.4 + - - -
382C MET* 3.8 23.2 - - + +
383C ARG 3.0 27.8 + - - +
385C HIS* 1.3 86.8 - - + +
387C VAL* 1.3 60.8 + - - +
389C ASP* 3.5 1.9 + - - +
390C SER* 2.9 33.2 + - - -
536C ARG* 3.5 34.5 + - - +
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Residues in contact with VAL 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C MET* 4.1 9.2 - - + -
383C ARG 3.7 12.1 - - - +
384C VAL* 3.0 13.8 + - - +
386C GLN* 1.3 74.5 - - - +
388C ILE* 1.3 59.0 + - - +
390C SER* 3.3 4.5 + - - -
391C MET* 3.0 32.7 + - + +
460C ILE* 3.9 18.2 - - + -
486C VAL* 3.9 28.0 - - + -
488C VAL* 4.0 9.0 - - + -
539C LEU* 3.7 17.4 - - + +
557C VAL* 4.0 24.7 - - + -
559C VAL* 4.3 2.0 - - + -
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Residues in contact with ILE 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384C VAL* 3.0 22.3 + - + +
385C HIS* 4.0 5.2 - - - +
387C VAL* 1.3 71.5 - - - +
389C ASP* 1.3 61.6 + - - +
391C MET* 3.2 10.9 + - + +
392C ASN* 2.9 34.4 + - - +
406C ILE* 5.8 2.0 - - + -
413C PHE 5.1 0.7 - - - +
416C TYR* 3.9 20.0 - - + +
417C GLY* 3.9 21.3 - - - +
420C PHE* 3.9 12.1 - - + -
421C ALA* 3.8 36.3 - - + +
460C ILE* 4.0 29.8 - - + -
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Residues in contact with ASP 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C LEU* 3.0 43.5 - - + +
373C ALA* 4.8 2.7 - - - -
385C HIS 3.0 16.5 + - - +
386C GLN 3.7 4.3 - - - +
388C ILE* 1.3 77.7 - - - +
390C SER* 1.3 61.7 + - - +
392C ASN* 3.3 12.5 + - - +
393C THR* 3.1 31.3 + - - -
536C ARG* 2.7 21.7 + - - +
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Residues in contact with SER 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C GLN 2.9 21.9 + - - -
387C VAL 3.5 4.9 - - - -
388C ILE 3.2 0.2 - - - -
389C ASP* 1.3 74.7 - - - +
391C MET* 1.3 64.8 + - - +
393C THR* 3.3 5.1 + - - -
394C VAL* 3.2 27.2 + - - +
536C ARG* 4.2 18.2 + - - +
539C LEU* 3.7 26.7 - - - +
540C LEU* 3.9 26.2 - - - +
543C LEU* 3.8 2.9 - - - -
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Residues in contact with MET 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387C VAL* 3.0 31.1 + - + +
388C ILE* 3.6 16.4 - - + +
390C SER* 1.3 76.2 - - - +
392C ASN* 1.3 57.6 + - - +
395C MET* 2.9 33.1 + - - +
406C ILE* 4.3 19.5 - - + -
458C PHE* 3.8 36.7 - - + -
459C LEU 4.0 12.3 - - - +
460C ILE* 4.0 32.8 - - + +
486C VAL* 4.3 13.0 - - + -
539C LEU* 5.6 0.2 - - + -
543C LEU* 3.9 22.7 - - + -
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Residues in contact with ASN 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C LEU* 4.9 7.5 - - - +
388C ILE* 2.9 22.2 + - - +
389C ASP* 3.5 13.8 + - - +
390C SER 3.3 0.2 - - - -
391C MET* 1.3 75.5 - - - +
393C THR* 1.3 56.8 + - - +
395C MET* 3.9 2.0 - - - +
396C GLU* 3.0 31.0 + - - +
406C ILE* 3.7 6.2 - - - +
420C PHE* 2.8 27.9 + - - +
421C ALA* 3.5 4.7 - - - -
422C ARG* 2.8 41.4 + - + +
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Residues in contact with THR 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389C ASP* 3.1 20.7 + - - -
390C SER* 3.3 9.3 + - - -
392C ASN* 1.3 77.3 - - - +
394C VAL* 1.3 59.3 + - - +
396C GLU* 3.3 5.7 + - - +
397C GLU* 3.1 48.3 + - + +
540C LEU* 4.0 13.1 - - + +
544C ARG* 4.0 11.7 - - - +
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Residues in contact with VAL 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C SER 3.2 14.9 + - - +
393C THR* 1.3 72.7 - - + +
395C MET* 1.3 61.1 + - - +
397C GLU* 3.3 11.0 + - + +
398C ALA* 2.8 28.6 + - + +
458C PHE* 4.1 13.0 - - + -
540C LEU* 3.8 20.0 - - + +
543C LEU* 3.7 30.3 - - + +
544C ARG* 3.7 43.7 - - + +
547C ALA* 4.2 6.3 - - + -
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Residues in contact with MET 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C MET 2.9 20.7 + - - +
392C ASN 3.9 3.1 - - - +
394C VAL* 1.3 73.6 - - - +
396C GLU* 1.3 60.3 + - - +
398C ALA* 4.7 0.7 - - - -
399C ALA* 2.8 44.2 + - + +
403C GLU 5.2 1.1 - - - +
404C GLY* 3.8 25.1 - - - -
405C THR 3.5 28.0 - - - +
406C ILE* 4.1 13.7 - - + -
422C ARG* 4.0 18.6 - - + +
456C PRO* 3.7 20.0 - - + +
458C PHE* 3.6 38.2 - - + -
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Residues in contact with GLU 396 (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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392C ASN 3.0 19.1 + - - +
393C THR* 3.3 6.0 + - - +
395C MET* 1.3 75.5 - - - +
397C GLU* 1.3 67.5 + - - +
399C ALA* 3.4 6.9 - - - +
422C ARG* 3.6 39.7 + - - +
602C K 2.9 19.6 - - - -
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Residues in contact with GLU 397 (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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393C THR* 3.1 24.2 + - + +
394C VAL* 3.5 11.0 - - + +
395C MET 3.2 0.2 - - - -
396C GLU* 1.3 84.4 - - - +
398C ALA* 1.3 59.4 - - - +
544C ARG* 2.7 53.0 + - - +
602C K 2.9 17.9 - - - -
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Residues in contact with ALA 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C VAL* 2.8 21.7 + - + +
395C MET* 4.2 2.2 - - - +
397C GLU* 1.3 76.1 - - - +
399C ALA* 1.3 59.6 + - - +
400C GLU* 4.0 4.5 + - - +
456C PRO* 3.7 23.8 - - + +
458C PHE* 4.9 0.7 - - + -
547C ALA* 4.0 27.4 - - + +
548C GLU* 6.4 0.7 - - + -
602C K 4.6 0.2 - - - -
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Residues in contact with ALA 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C MET* 2.8 34.1 + - + +
396C GLU* 3.4 6.3 - - - +
398C ALA* 1.3 73.6 - - - +
400C GLU* 1.3 63.0 + - - +
401C PRO 3.9 0.2 - - - -
403C GLU 3.5 31.2 - - - +
422C ARG* 5.8 2.0 - - - +
456C PRO* 3.8 13.2 - - + -
602C K 2.7 26.7 - - - -
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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