Contacts of the helix formed by residues 380 - 393 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A VAL* 2.6 30.5 + - + +
378A ASP* 3.3 25.7 - - - +
379A ASP* 1.3 78.0 - - - +
381A VAL* 1.3 64.3 + - - +
382A GLU 3.2 2.7 - - - -
383A CYS* 3.2 22.3 - - - -
384A THR* 2.9 26.9 + - - +
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Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A VAL* 3.6 20.9 - - + -
376A ILE* 3.8 27.8 - - + -
379A ASP* 3.5 3.3 - - - -
380A ASP* 1.3 78.3 - - - +
382A GLU* 1.3 65.5 + - - +
384A THR* 3.2 2.9 + - - -
385A MET* 3.0 26.4 + - + +
652A ASP* 3.4 49.4 - - + +
653A PHE* 4.3 4.3 - - + -
347B LYS 5.7 6.3 - - - +
348B GLY* 6.5 0.7 - - - -
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Residues in contact with GLU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ASP 5.1 1.2 + - - +
380A ASP 3.2 1.0 - - - -
381A VAL* 1.3 81.7 - - - +
383A CYS* 1.3 60.0 + - + +
385A MET* 3.2 6.6 + - - +
386A VAL* 2.9 41.0 + - + +
389A ARG* 3.9 10.3 + - - -
487A GLU* 4.1 5.5 - - - +
347B LYS* 5.0 17.7 - - - +
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Residues in contact with CYS 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ASP 4.9 1.8 - - - -
380A ASP* 3.2 42.2 - - - -
382A GLU* 1.3 75.7 - - + +
384A THR* 1.3 60.4 + - - +
386A VAL* 3.6 11.3 - - + +
387A GLU* 2.9 28.8 + - - +
462A ARG* 6.2 0.9 - - - +
483A GLY* 3.6 29.2 - - - +
484A MET* 4.8 4.9 - - - +
485A CYS 5.5 3.4 - - - +
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Residues in contact with THR 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A LEU* 4.3 7.5 - - + +
375A VAL* 3.7 18.6 - - + +
380A ASP* 2.9 23.3 + - - +
381A VAL* 3.4 7.9 - - - +
383A CYS* 1.3 78.8 - - - +
385A MET* 1.3 69.2 + - - +
387A GLU* 3.3 9.5 + - - +
388A LYS* 3.1 21.7 + - - +
413A LEU* 3.7 28.9 - - + -
415A PHE* 4.2 15.6 - - + -
653A PHE* 5.1 2.0 - - + -
656A PHE* 4.6 4.9 - - + -
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Residues in contact with MET 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A VAL* 3.0 17.7 + - + +
382A GLU* 3.4 13.0 - - - +
384A THR* 1.3 82.6 - - - +
386A VAL* 1.3 60.5 + - - +
388A LYS* 3.5 10.3 + - + +
389A ARG* 3.1 46.5 + - - +
652A ASP 3.9 21.3 - - - +
653A PHE* 4.2 15.5 - - - -
654A GLU 3.4 26.0 - - - +
655A GLY 4.2 3.4 - - - +
656A PHE* 4.2 31.6 - - + -
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Residues in contact with VAL 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLU* 2.9 37.0 + - + +
383A CYS* 3.9 9.4 - - - +
384A THR 3.2 0.2 - - - -
385A MET* 1.3 75.0 - - - +
387A GLU* 1.3 55.1 + - - +
389A ARG* 3.1 27.3 + - - +
390A VAL* 2.6 49.3 + - + +
482A PHE 5.2 0.2 - - - +
485A CYS* 4.1 27.6 - - + +
487A GLU* 3.7 23.3 - - + +
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Residues in contact with GLU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A LYS* 2.4 36.7 + - - +
370A LEU* 5.6 0.2 - - - +
383A CYS 2.9 18.3 + - - +
384A THR* 3.6 8.1 - - - +
386A VAL* 1.3 74.6 - - - +
388A LYS* 1.3 54.7 + - - +
390A VAL* 3.6 3.4 - - - +
391A LEU* 2.7 55.5 + - + +
415A PHE* 4.4 12.9 - - + -
481A ASP* 4.4 0.2 - - - -
482A PHE* 3.7 36.5 + - + +
483A GLY* 3.8 16.7 - - - -
901A LW4 3.7 19.2 - - - -
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Residues in contact with LYS 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A THR 3.1 10.4 + - - +
385A MET* 3.7 13.9 - - + +
386A VAL 3.2 0.2 - - - -
387A GLU* 1.3 81.5 - - - +
389A ARG* 1.3 68.2 + - + +
391A LEU* 3.4 4.5 + - - +
392A ALA* 2.9 33.6 + - + +
403A LEU* 4.6 1.1 - - + +
406A CYS* 3.8 15.3 - - - -
415A PHE* 4.0 17.4 - - + -
655A GLY 2.9 24.2 + - - +
656A PHE* 3.2 40.6 - - + +
657A SEP 4.3 3.6 + - - -
658A TYR* 3.8 23.8 - - + +
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Residues in contact with ARG 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A GLU* 3.9 10.3 + - - -
385A MET* 3.1 35.5 + - - +
386A VAL* 3.1 24.9 + - - +
388A LYS* 1.3 84.8 - - + +
390A VAL* 1.3 69.5 + - + +
392A ALA* 2.9 15.5 + - - +
393A LEU* 3.1 20.3 + - + +
487A GLU* 2.7 44.5 + - - +
488A HIS* 5.6 0.8 + - - -
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Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A VAL* 2.6 29.4 + - + +
387A GLU* 3.7 6.7 - - - +
389A ARG* 1.3 75.0 - - + +
391A LEU* 1.3 63.2 + - - +
393A LEU* 3.2 22.8 + - + +
396A LYS* 4.0 5.5 - - - +
400A LEU* 6.6 0.2 - - + -
454A LEU* 4.1 16.6 - - + -
459A ILE* 3.7 20.4 - - + -
482A PHE* 3.8 35.0 - - + -
485A CYS* 3.8 26.2 - - + -
487A GLU* 5.4 2.0 - - - +
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Residues in contact with LEU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A GLU* 2.7 38.3 + - + +
388A LYS 3.8 2.2 - - - +
390A VAL* 1.3 73.0 - - - +
392A ALA* 1.3 61.3 + - - +
393A LEU 3.4 0.5 + - - -
396A LYS* 2.7 30.2 + - - +
401A THR* 4.2 9.9 - - - +
403A LEU* 3.7 22.9 - - + +
415A PHE* 3.7 30.5 - - + -
417A MET* 4.0 34.1 - - + -
482A PHE* 3.5 32.3 - - + -
901A LW4 5.8 1.1 - - + -
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Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A LYS* 2.9 23.2 + - - +
389A ARG* 2.9 10.0 + - - +
391A LEU* 1.3 74.0 - - - +
393A LEU* 1.3 69.3 + - - +
394A LEU* 3.3 5.7 + - - +
403A LEU* 4.2 6.3 - - + -
658A TYR* 3.5 50.1 + - + -
660A ASN* 6.1 0.2 - - - -
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Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389A ARG* 3.1 15.5 + - + +
390A VAL* 3.2 20.2 - - - +
391A LEU 3.2 2.1 - - - +
392A ALA* 1.3 78.7 - - - +
394A LEU* 1.3 60.7 + - - +
395A ASP 4.0 0.2 + - - -
396A LYS* 3.1 27.4 + - + +
453A PHE* 4.1 24.0 - - + -
454A LEU* 4.1 9.4 - - + -
457A ARG* 4.4 19.1 - - + -
459A ILE* 3.6 32.1 - - + -
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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