Contacts of the helix formed by residues 369 - 380 (chain D) in PDB entry 1I43
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 369 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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368D GLY* 1.3 75.0 - - - +
370D LEU* 1.3 69.4 + - - +
371D LEU* 3.0 19.8 + - - +
372D THR* 3.0 23.4 + - - -
373D THR* 2.8 27.0 + - - -
419D ASP* 4.2 3.6 - - - -
420D ASN* 4.0 2.0 - - - +
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Residues in contact with LEU 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ILE* 4.8 9.2 - - + -
369D ASP* 1.3 75.5 - - + +
371D LEU* 1.3 79.3 + - + +
374D ALA* 3.3 20.2 + - + +
398D GLN* 3.5 25.5 + - - +
400D ALA* 4.7 2.9 - - + -
401D ILE* 3.8 25.8 - - + -
405D TRP* 4.3 24.5 - - + -
419D ASP* 3.5 47.5 + - + +
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Residues in contact with LEU 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ILE* 6.1 2.7 - - + -
369D ASP* 3.1 14.3 + - - +
370D LEU* 1.3 94.1 - - + +
372D THR* 1.3 64.4 + - - +
374D ALA* 3.3 9.8 + - + +
375D LYS* 3.1 20.4 + - - +
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Residues in contact with THR 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D VAL* 4.5 4.3 - - + -
367D ASP 4.5 1.1 - - - +
368D GLY* 3.9 17.8 - - - -
369D ASP* 3.0 24.8 + - - -
371D LEU* 1.3 76.2 - - - +
373D THR* 1.3 70.5 + - - +
375D LYS* 2.8 30.8 + - + +
376D PHE* 3.1 5.0 + - - +
445D ILE* 3.9 31.4 - - + +
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Residues in contact with THR 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D VAL* 4.0 13.3 - - + +
368D GLY 4.5 0.2 - - - -
369D ASP 2.8 19.2 + - - -
372D THR* 1.3 75.6 - - - +
374D ALA* 1.3 63.9 + - - +
376D PHE* 3.0 23.4 + - - +
377D VAL* 3.2 7.5 + - + +
398D GLN* 3.3 26.7 - - - +
419D ASP 3.3 8.6 + - - +
420D ASN* 3.4 25.2 + - - +
422D VAL* 3.3 32.5 - - + -
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Residues in contact with ALA 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B THR* 3.5 32.5 - - + +
370D LEU* 3.3 14.1 + - + +
371D LEU* 3.3 15.0 + - + +
372D THR 3.1 0.4 - - - -
373D THR* 1.3 78.5 - - - +
375D LYS* 1.3 58.6 + - - +
377D VAL* 3.2 5.6 + - - +
378D ASP* 2.8 34.6 + - - +
398D GLN* 3.4 11.4 + - - +
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Residues in contact with LYS 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371D LEU* 3.1 12.0 + - - +
372D THR* 2.8 21.4 + - + +
374D ALA* 1.3 77.8 - - - +
376D PHE* 1.3 58.9 + - - +
378D ASP* 3.4 8.5 + - + +
379D ALA* 3.1 22.5 + - - +
444D SER* 4.3 30.4 - - - +
445D ILE* 4.7 9.0 - - + +
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Residues in contact with PHE 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364D PHE* 3.7 31.0 - + - -
366D VAL* 4.0 15.9 - - + -
372D THR 3.1 4.7 + - - +
373D THR* 3.0 14.6 + - - +
375D LYS* 1.3 75.1 - - - +
377D VAL* 1.3 71.6 + - + +
379D ALA* 3.0 15.6 + - - +
380D LEU* 3.3 24.1 + - + +
422D VAL* 4.4 9.0 - - + -
424D PHE* 5.5 1.6 - + - -
438D ILE* 3.6 39.7 - - + -
441D ALA* 3.3 31.3 - - + +
442D LEU* 3.8 13.7 - - + -
444D SER* 6.1 0.2 - - - -
445D ILE* 3.9 21.2 - - + +
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Residues in contact with VAL 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B THR* 3.2 26.2 - - - +
373D THR 3.3 15.3 - - - +
374D ALA 3.2 2.4 + - - +
376D PHE* 1.3 83.6 - - + +
378D ASP* 1.3 68.8 + - - +
379D ALA 3.0 1.3 + - - -
380D LEU* 3.2 34.9 + - + +
385D ILE* 4.1 26.6 - - + +
396D VAL* 5.0 9.6 - - + -
397D ASP* 5.7 5.6 - - - +
398D GLN* 4.1 13.2 - - + +
422D VAL* 4.3 17.9 - - + -
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Residues in contact with ASP 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ASN 5.7 2.2 - - - +
91B LYS* 3.5 26.4 - - + +
92B THR* 2.8 39.9 + - - -
93B SER* 4.4 2.8 + - - -
374D ALA* 2.8 18.6 + - - +
375D LYS* 3.6 10.4 - - + +
377D VAL* 1.3 79.5 - - - +
379D ALA* 1.3 58.6 + - - +
380D LEU 4.1 4.3 - - - +
385D ILE* 4.0 5.1 - - - +
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Residues in contact with ALA 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375D LYS 3.1 11.4 + - - +
376D PHE 3.0 11.9 + - - +
378D ASP* 1.3 76.5 - - - +
380D LEU* 1.3 67.8 + - - +
381D LYS* 3.5 14.2 - - - +
440D GLN* 3.5 13.6 + - - +
441D ALA* 3.3 25.6 - - + +
444D SER* 4.2 13.7 - - - +
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Residues in contact with LEU 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ARG* 5.1 2.9 + - - -
376D PHE* 3.6 27.6 - - + +
377D VAL* 3.2 28.5 + - - +
378D ASP 4.1 5.5 - - - +
379D ALA* 1.3 83.2 - - - +
381D LYS* 1.3 60.6 + - - +
383D PRO* 3.9 13.0 - - + +
396D VAL* 3.7 35.7 - - + -
424D PHE* 4.1 12.1 - - + -
437D ASP* 3.8 16.8 - - - +
438D ILE* 3.9 26.5 - - + -
441D ALA* 3.7 4.7 - - + +
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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