Contacts of the helix formed by residues 405 - 417 (chain D) in PDB entry 5I94
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 405 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403D GLY 3.8 4.2 + - - -
404D THR* 1.3 69.9 - - - +
406D MET* 1.3 56.9 + - - +
407D VAL* 3.5 9.1 + - - +
408D GLY* 2.7 44.8 + - - -
409D ILE* 3.0 13.1 + - - +
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Residues in contact with MET 406 (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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388D PHE* 5.1 0.2 - - + -
391D GLY* 3.5 34.8 - - - +
392D TYR* 3.4 53.6 - - + -
395D LYS* 4.1 22.4 - - + +
400D PHE* 3.8 18.6 - - + -
404D THR* 3.0 18.0 + - - +
405D ASP* 1.3 70.3 + - - +
407D VAL* 1.3 76.9 + - + +
409D ILE* 3.0 16.1 + - - +
410D LEU* 3.0 26.6 + - + +
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Residues in contact with VAL 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388D PHE* 4.5 22.9 - - + -
392D TYR* 4.3 11.7 - - - +
405D ASP* 3.3 7.6 + - - +
406D MET* 1.3 93.6 - - + +
408D GLY* 1.3 67.3 + - - +
410D LEU* 3.2 13.3 + - - +
411D ASP* 3.2 19.2 + - - +
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Residues in contact with GLY 408 (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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350D ASN* 3.1 31.1 + - - +
405D ASP* 2.7 30.6 + - - -
407D VAL* 1.3 76.4 - - - +
409D ILE* 1.3 63.1 + - - +
411D ASP* 3.5 2.0 + - - +
412D PHE* 3.2 9.7 + - - +
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Residues in contact with ILE 409 (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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338D ILE* 3.7 36.1 - - + +
341D THR* 3.9 11.2 - - + +
342D SER* 3.5 28.5 - - - +
353D LYS* 3.8 25.1 - - - +
400D PHE* 4.3 4.3 - - + -
404D THR* 3.6 29.2 - - + -
405D ASP 3.0 8.1 + - - +
406D MET* 3.3 10.5 - - - +
408D GLY* 1.3 78.1 - - - +
410D LEU* 1.3 59.8 + - - +
412D PHE* 3.3 6.7 + - + +
413D TYR* 2.9 26.1 + - + +
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Residues in contact with LEU 410 (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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338D ILE* 4.1 38.4 - - + -
387D ASN* 4.1 13.5 - - + +
388D PHE* 3.4 56.8 - - + +
391D GLY* 4.9 2.2 - - - -
406D MET* 3.0 29.7 + - - +
407D VAL* 3.2 9.6 + - - +
409D ILE* 1.3 76.2 - - + +
411D ASP* 1.3 61.8 + - - +
413D TYR* 3.0 8.9 + - + +
414D PHE* 2.8 41.8 + - + -
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Residues in contact with ASP 411 (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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350D ASN* 4.2 5.6 - - - +
377D PHE* 3.6 9.6 - - - -
381D ARG* 3.3 40.6 + - - +
388D PHE* 5.1 4.7 - - - -
407D VAL* 3.2 16.5 + - - +
408D GLY* 3.9 7.6 - - - +
410D LEU* 1.3 78.1 - - - +
412D PHE* 1.3 66.3 + - - +
414D PHE* 3.1 17.8 + - - +
415D GLN* 2.9 37.3 + - - +
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Residues in contact with PHE 412 (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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341D THR* 3.4 29.6 - - + -
344D ILE* 4.6 10.1 - - + -
350D ASN* 4.0 14.9 - - - +
353D LYS* 3.6 47.6 - - + -
354D PHE* 3.9 24.2 - + + -
357D VAL* 4.1 14.1 - - + -
408D GLY 3.2 11.8 + - - +
409D ILE* 3.5 11.0 - - + +
411D ASP* 1.3 76.9 - - - +
413D TYR* 1.3 62.2 + - - +
415D GLN* 3.1 15.7 + - + +
416D LEU* 3.1 47.5 + - + +
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Residues in contact with TYR 413 (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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288D LYS* 3.3 16.0 + - - -
291D LYS* 3.4 19.3 - - - -
334D ASN* 3.1 26.3 + - - +
337D ALA* 3.7 23.3 - - + -
338D ILE* 3.6 28.5 - - + -
341D THR* 4.0 15.0 - - + +
380D GLU* 6.0 1.1 - - + -
387D ASN* 3.3 28.0 + - - -
409D ILE* 2.9 14.9 + - + +
410D LEU* 3.0 13.0 + - + +
412D PHE* 1.3 76.4 - - - +
414D PHE* 1.3 75.8 + + - +
415D GLN 3.2 0.2 + - - -
416D LEU* 3.2 6.4 + - - +
417D CYS* 3.2 42.4 + - - -
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Residues in contact with PHE 414 (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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377D PHE* 3.7 21.0 - - + +
380D GLU* 3.4 38.4 - - + +
381D ARG* 3.8 19.3 - - + -
384D GLY* 4.2 4.0 - - - -
387D ASN* 3.2 42.0 - - + -
388D PHE* 3.8 29.4 - + - -
410D LEU* 2.8 38.7 + - + -
411D ASP* 3.6 11.7 - - - +
413D TYR* 1.3 80.4 - + - +
415D GLN* 1.3 58.9 + - - +
417D CYS* 3.6 6.4 + - + +
418D SER* 2.8 27.2 + - - -
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Residues in contact with GLN 415 (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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350D ASN* 4.3 18.2 - - - +
354D PHE* 3.6 40.6 - - + +
372D PHE* 3.7 14.3 - - + -
377D PHE* 3.3 34.7 - - + -
411D ASP* 2.9 31.0 + - - +
412D PHE* 3.1 13.1 + - - +
414D PHE* 1.3 74.8 - - - +
416D LEU* 1.3 58.7 + - - +
418D SER* 2.8 21.1 + - - -
419D ILE* 3.4 9.4 + - - +
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Residues in contact with LEU 416 (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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283D LEU* 4.9 0.5 - - - +
287D VAL* 3.6 31.4 - - + +
291D LYS* 3.8 28.5 - - + +
341D THR* 3.8 15.9 - - + +
344D ILE* 5.5 1.3 - - + -
354D PHE* 4.7 3.6 - - + -
357D VAL* 3.5 34.5 - - + -
412D PHE* 3.1 49.5 + - + +
413D TYR 3.2 5.6 + - - +
415D GLN* 1.3 75.6 - - - +
417D CYS* 1.3 60.6 + - - +
418D SER 3.1 1.1 + - - -
419D ILE* 3.5 27.8 + - + +
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Residues in contact with CYS 417 (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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282D CYS* 3.9 3.5 - - - +
284D GLN* 3.1 67.9 + - - +
287D VAL* 4.5 5.8 - - - -
288D LYS* 4.7 4.0 - - - -
291D LYS* 5.3 0.2 - - - -
380D GLU* 5.2 9.0 - - + -
413D TYR* 3.2 52.4 + - - +
414D PHE* 3.9 8.1 - - - +
415D GLN 3.1 1.0 - - - -
416D LEU* 1.3 77.7 - - - +
418D SER* 1.3 58.6 + - - +
419D ILE 3.4 1.0 + - - -
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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