Contacts of the helix formed by residues 380 - 393 (chain C) in PDB entry 3IW4
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 ASP 380 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375C VAL* 3.0 23.0 + - + +
378C ASP* 2.8 34.6 + - - +
379C ASP* 1.3 77.3 - - - +
381C VAL* 1.3 65.9 + - - +
382C GLU 3.3 2.5 - - - -
383C CYS* 3.1 20.2 - - - -
384C THR* 2.8 25.1 + - - +
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Residues in contact with VAL 381 (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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375C VAL* 3.6 22.5 - - + +
376C ILE* 3.9 17.3 - - + -
379C ASP* 3.5 2.9 - - - -
380C ASP* 1.3 76.1 - - - +
382C GLU* 1.3 68.2 + - + +
384C THR* 2.9 7.3 + - - -
385C MET* 2.9 25.2 + - + +
652C ASP* 3.6 53.2 - - + +
653C PHE* 4.0 5.2 - - + -
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Residues in contact with GLU 382 (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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379C ASP 5.0 3.8 + - - +
380C ASP 3.3 0.6 - - - -
381C VAL* 1.3 81.1 - - + +
383C CYS* 1.3 69.8 + - + +
385C MET* 3.0 7.8 + - - +
386C VAL* 3.0 38.9 + - + +
389C ARG* 4.3 7.8 + - - -
486C LYS* 6.0 2.1 + - - -
487C GLU* 5.5 0.2 - - - +
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Residues in contact with CYS 383 (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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379C ASP 4.9 1.6 - - - -
380C ASP* 3.1 42.1 - - - -
382C GLU* 1.3 84.8 - - + +
384C THR* 1.3 62.0 + - - +
386C VAL* 3.8 10.1 - - + +
387C GLU* 3.1 22.7 + - - +
483C GLY* 4.0 26.2 - - - +
484C MET* 5.5 2.0 - - - -
485C CYS 5.8 2.9 - - - +
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Residues in contact with THR 384 (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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370C LEU* 3.7 19.5 - - + +
375C VAL* 3.9 12.1 - - - +
380C ASP* 2.8 18.8 + - - +
381C VAL* 2.9 11.6 + - - -
383C CYS* 1.3 77.6 - - - +
385C MET* 1.3 66.4 + - - +
387C GLU* 3.4 8.2 + - - +
388C LYS* 3.2 18.9 + - - +
413C LEU* 3.7 27.8 - - + -
415C PHE* 4.0 18.3 - - + -
653C PHE* 5.6 1.1 - - - -
656C PHE* 4.0 5.8 - - + -
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Residues in contact with MET 385 (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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381C VAL* 2.9 20.4 + - + +
382C GLU* 3.0 7.6 + - - +
384C THR* 1.3 75.3 - - - +
386C VAL* 1.3 60.3 + - - +
388C LYS* 3.3 9.1 + - + +
389C ARG* 2.8 62.1 + - - +
652C ASP 3.7 21.3 - - - +
653C PHE* 4.2 12.8 - - - +
654C GLU 3.4 24.9 - - - +
655C GLY 4.1 3.4 - - - +
656C PHE* 3.8 41.7 - - + +
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Residues in contact with VAL 386 (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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382C GLU* 3.0 35.6 + - + +
383C CYS* 3.9 9.0 - - - +
385C MET* 1.3 75.4 - - - +
387C GLU* 1.3 56.3 + - - +
389C ARG* 3.0 13.9 + - - +
390C VAL* 2.7 38.7 + - + +
482C PHE 5.2 0.2 - - - +
485C CYS* 3.7 41.5 - - + +
487C GLU* 3.5 32.3 - - + +
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Residues in contact with GLU 387 (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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368C LYS* 2.6 36.0 + - - +
383C CYS 3.1 15.2 + - - +
384C THR* 3.7 8.0 - - - +
385C MET 3.3 0.2 - - - -
386C VAL* 1.3 78.0 - - - +
388C LYS* 1.3 53.9 + - - +
390C VAL* 3.3 3.9 + - - +
391C LEU* 2.7 55.5 + - + +
415C PHE* 4.6 8.6 - - + -
481C ASP* 4.4 1.0 - - - +
482C PHE* 3.4 40.0 + - + +
483C GLY* 3.8 13.2 - - - -
901C LW4 3.5 20.4 - - - -
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Residues in contact with LYS 388 (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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384C THR 3.2 10.5 + - - +
385C MET* 3.4 13.7 - - + +
386C VAL 3.1 0.2 - - - -
387C GLU* 1.3 76.0 - - - +
389C ARG* 1.3 76.9 + - + +
390C VAL 3.1 0.3 + - - -
391C LEU* 3.1 4.3 + - - +
392C ALA* 2.7 33.4 + - + +
403C LEU* 4.7 0.2 - - - +
406C CYS* 3.8 17.5 - - - -
415C PHE* 3.7 14.7 - - + -
655C GLY 2.8 25.6 + - - +
656C PHE* 2.8 37.7 + - + +
657C SEP 3.9 5.9 + - - -
658C TYR* 3.7 22.9 - - - +
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Residues in contact with ARG 389 (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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382C GLU* 4.3 7.9 + - - -
385C MET* 2.8 50.3 + - - +
386C VAL* 3.6 19.3 - - - +
388C LYS* 1.3 83.2 - - + +
390C VAL* 1.3 63.4 + - + +
392C ALA* 3.2 4.5 + - - +
393C LEU* 3.2 27.2 + - + +
487C GLU* 2.8 43.0 + - - +
488C HIS* 5.7 2.1 + - - -
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Residues in contact with VAL 390 (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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386C VAL* 2.7 28.8 + - + +
387C GLU* 3.7 5.8 - - - +
389C ARG* 1.3 72.3 - - + +
391C LEU* 1.3 65.4 + - - +
392C ALA 3.3 0.3 + - - -
393C LEU* 3.4 22.7 + - - +
396C LYS* 3.8 6.2 - - - +
400C LEU* 6.1 1.1 - - + +
454C LEU* 4.0 23.5 - - + +
459C ILE* 3.2 24.7 - - + -
482C PHE* 4.0 29.2 - - + -
485C CYS* 4.0 21.5 - - + -
487C GLU* 5.1 3.6 - - + -
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Residues in contact with LEU 391 (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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387C GLU* 2.7 39.7 + - + +
388C LYS 3.9 1.6 - - - +
390C VAL* 1.3 74.0 - - - +
392C ALA* 1.3 59.3 + - - +
393C LEU 3.3 0.6 - - - +
396C LYS* 3.0 27.0 + - - +
401C THR* 4.0 9.0 - - - +
403C LEU* 3.7 22.9 - - + +
415C PHE* 3.7 29.8 - - + -
417C MET* 3.6 36.6 - - + -
481C ASP 6.0 0.4 - - - +
482C PHE* 3.4 35.9 - - + -
658C TYR* 5.4 0.2 - - - -
901C LW4 5.6 2.0 - - + -
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Residues in contact with ALA 392 (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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388C LYS* 2.7 27.7 + - - +
389C ARG* 3.7 6.1 - - - +
390C VAL 3.1 0.4 - - - -
391C LEU* 1.3 77.1 - - - +
393C LEU* 1.3 68.4 + - - +
394C LEU* 3.6 3.1 + - - +
403C LEU* 4.0 7.0 - - + -
658C TYR* 3.7 47.7 + - + -
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Residues in contact with LEU 393 (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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389C ARG* 3.2 13.2 + - + +
390C VAL* 3.4 18.6 - - - +
391C LEU 3.3 1.8 - - - +
392C ALA* 1.3 85.5 - - - +
394C LEU* 1.3 64.6 + - - +
395C ASP 4.1 0.3 + - - -
396C LYS* 3.5 22.7 + - + +
453C PHE* 4.2 18.8 - - + -
454C LEU* 4.2 5.2 - - + -
457C ARG* 3.9 27.1 - - + +
459C ILE* 3.8 28.3 - - + -
658C TYR* 5.2 0.9 + - - -
660C ASN* 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
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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