Contacts of the helix formed by residues 435 - 448 (chain D) in PDB entry 4O9U
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 435 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306D SER* 2.8 20.7 + - - -
410D ARG* 3.8 14.5 + - + +
434D GLY* 1.3 71.7 - - - -
436D ALA* 1.3 59.2 + - - +
437D GLN* 3.5 4.4 - - - +
438D LYS* 3.0 31.2 + - + +
439D VAL* 2.8 26.7 + - - +
500D NAP 2.7 29.0 + - - -
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Residues in contact with ALA 436 (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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302D GLY 3.7 8.7 - - - +
306D SER* 3.6 10.8 - - - -
308D ALA* 3.6 20.2 - - + -
374D ILE* 3.6 20.5 - - + +
408D ILE* 4.2 3.8 - - - -
435D ASP* 1.3 72.8 - - - +
437D GLN* 1.3 56.8 + - - +
439D VAL* 3.3 6.2 + - - +
440D LEU* 3.2 28.8 + - - +
500D NAP 2.7 27.2 + - + +
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Residues in contact with GLN 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D SER* 3.0 22.7 + - - +
307D GLN* 2.9 24.6 - - - +
308D ALA* 3.6 21.3 - - + +
311D LYS* 4.1 27.3 - - + +
435D ASP* 3.5 3.8 - - - +
436D ALA* 1.3 75.3 - - - +
438D LYS* 1.3 62.9 + - + +
439D VAL 3.2 2.0 - - - -
440D LEU* 3.9 2.0 - - - +
441D THR* 2.6 34.0 + - - -
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Residues in contact with LYS 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434D GLY* 5.7 4.3 - - - -
435D ASP* 3.0 35.7 + - + +
437D GLN* 1.3 80.9 - - + +
439D VAL* 1.3 57.5 + - + +
441D THR* 4.5 3.9 - - - -
442D GLU* 3.4 45.6 + - + +
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Residues in contact with VAL 439 (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 VAL* 4.4 1.4 - - - +
408D ILE* 3.7 30.7 - - + -
432D LEU* 3.6 37.2 - - + -
433D TYR 3.9 9.6 - - - +
434D GLY* 3.8 26.9 - - - +
435D ASP 2.8 14.3 + - - +
436D ALA 3.4 7.9 - - - +
437D GLN 3.2 0.2 - - - -
438D LYS* 1.3 79.8 - - + +
440D LEU* 1.3 61.5 + - - +
441D THR 3.4 0.2 - - - -
442D GLU* 3.2 12.3 + - - +
443D LEU* 2.9 26.3 + - + +
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Residues in contact with LEU 440 (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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297D PHE* 5.2 1.3 - - + -
308D ALA* 3.8 23.3 - - + +
311D LYS* 3.3 34.3 - - + +
312D LEU* 3.8 23.8 - - + +
315D LEU* 3.8 26.0 - - + -
374D ILE* 4.2 7.4 - - + -
408D ILE* 3.9 24.7 - - + -
436D ALA 3.2 16.0 + - - +
437D GLN 3.7 0.6 + - - +
439D VAL* 1.3 76.2 - - - +
441D THR* 1.3 57.3 + - - +
443D LEU* 3.0 8.4 + - + +
444D ILE* 2.8 40.5 + - - +
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Residues in contact with THR 441 (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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311D LYS* 3.3 36.4 - - + +
437D GLN* 2.6 24.1 + - - +
438D LYS* 4.9 3.6 - - - -
440D LEU* 1.3 77.4 - - - +
442D GLU* 1.3 57.8 + - - +
444D ILE* 3.9 10.1 - - + +
445D GLN* 3.0 56.2 + - + +
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Residues in contact with GLU 442 (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 VAL* 3.3 39.8 - - + +
283D GLU* 4.6 0.5 - - - +
438D LYS* 3.4 39.6 + - + +
439D VAL* 3.2 12.8 + - - +
441D THR* 1.3 77.2 - - - +
443D LEU* 1.3 58.9 + - - +
445D GLN* 4.7 4.9 - - - +
446D ALA* 3.2 28.6 + - - +
449D ARG* 4.4 4.7 + - - +
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Residues in contact with LEU 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D VAL* 3.9 7.4 - - + +
285D ALA* 3.7 26.2 - - + -
286D ALA* 3.7 14.9 - - - +
289D LEU* 3.6 22.9 - - + -
315D LEU* 3.8 28.9 - - + -
372D VAL* 5.1 6.7 - - + -
406D ILE* 5.7 1.8 - - + -
408D ILE* 4.6 4.3 - - + -
432D LEU* 4.1 20.6 - - + -
439D VAL* 2.9 16.1 + - + +
440D LEU* 3.0 22.2 + - + +
442D GLU* 1.3 76.4 - - - +
444D ILE* 1.3 59.4 + - - +
446D ALA* 3.9 1.3 - - - -
447D LEU* 3.0 31.0 + - - +
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Residues in contact with ILE 444 (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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311D LYS* 3.5 31.0 - - + +
314D GLU* 3.8 35.0 - - + +
315D LEU* 4.0 26.5 - - + +
318D LEU* 3.9 12.5 - - + +
440D LEU 2.8 26.6 + - - +
441D THR* 3.9 10.5 - - + +
443D LEU* 1.3 72.6 - - - +
445D GLN* 1.3 55.1 - - + +
447D LEU* 3.1 5.0 + - - +
448D LYS* 2.7 58.3 + - - +
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Residues in contact with GLN 445 (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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311D LYS* 5.8 0.6 - - - +
441D THR* 3.0 40.5 + - + +
442D GLU* 4.7 4.4 - - - +
444D ILE* 1.3 79.3 - - + +
446D ALA* 1.3 53.7 + - - +
448D LYS* 3.8 21.6 - - + +
449D ARG* 2.7 46.2 + - - +
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Residues in contact with ALA 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D VAL 4.0 7.0 - - - +
283D GLU* 3.6 28.3 - - + +
286D ALA* 3.9 17.0 - - + -
442D GLU 3.2 21.6 + - - +
443D LEU 4.0 0.2 - - - +
444D ILE 3.2 0.4 - - - -
445D GLN* 1.3 75.8 - - - +
447D LEU* 1.3 63.5 + - - +
448D LYS 3.3 0.4 - - - -
449D ARG* 3.2 20.8 + - - +
450D LEU* 3.4 19.3 - - + +
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Residues in contact with LEU 447 (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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286D ALA* 3.7 18.1 - - + +
289D LEU* 3.7 37.2 - - + -
290D ALA* 3.8 15.5 - - + -
315D LEU* 3.7 15.5 - - + +
318D LEU* 4.1 15.2 - - + +
319D LEU* 4.0 11.4 - - + -
322D ARG* 3.6 32.7 + - - +
443D LEU 3.0 16.8 + - - +
444D ILE 3.5 4.7 - - - +
446D ALA* 1.3 72.7 - - - +
448D LYS* 1.3 64.0 + - - +
449D ARG 3.1 1.8 - - - -
450D LEU* 3.2 22.2 + - + +
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Residues in contact with LYS 448 (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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314D GLU* 4.6 10.6 + - - -
318D LEU* 4.0 24.7 - - + +
444D ILE* 2.7 40.3 + - + +
445D GLN* 3.8 21.2 - - + +
447D LEU* 1.3 72.9 - - - +
449D ARG* 1.3 57.8 + - + +
450D LEU 3.2 6.1 + - - +
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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