Contacts of the helix formed by residues 433 - 446 (chain D) in PDB entry 4B2Q
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 ARG 433 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135D GLU* 3.4 29.1 + - - +
431D LEU* 4.0 19.9 + - + +
432D VAL* 1.3 76.1 - - - +
434D LEU* 1.3 55.4 + - - +
435D LYS* 4.3 23.4 - - + +
436D ASP* 3.0 14.4 + - + +
437D THR* 2.8 34.2 + - - -
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Residues in contact with LEU 434 (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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133D ILE* 3.6 33.0 - - + -
135D GLU* 2.8 31.9 + - + +
142D ASP* 3.1 45.7 + - + +
143D LEU 4.4 0.2 - - - +
367D HIS* 3.5 20.6 - - + +
432D VAL 3.9 2.4 + - - -
433D ARG* 1.3 71.6 - - - +
435D LYS* 1.3 65.0 + - + +
437D THR* 3.9 8.3 - - - -
438D VAL* 3.2 31.4 + - + +
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Residues in contact with LYS 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLU* 4.9 6.3 - - - +
433D ARG* 3.1 21.5 - - + +
434D LEU* 1.3 79.4 - - + +
436D ASP* 1.3 60.3 + - - +
438D VAL* 4.2 3.3 + - - +
439D ALA* 3.7 17.3 + - - +
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Residues in contact with ASP 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432D VAL* 4.3 7.7 - - + +
433D ARG* 3.0 17.2 + - + +
435D LYS* 1.3 78.8 - - - +
437D THR* 1.3 58.9 + - - +
439D ALA* 3.1 9.4 + - - +
440D SER* 2.6 35.9 + - - -
462D GLY* 4.0 22.7 - - - -
463D ILE* 3.8 16.9 + - - +
464D GLU* 5.9 2.7 - - - +
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Residues in contact with THR 437 (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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138D ILE 5.4 0.2 - - - -
139D LYS* 3.8 27.3 - - + +
142D ASP* 5.2 2.2 + - + +
143D LEU* 4.0 19.3 - - + +
432D VAL* 3.0 21.7 + - - +
433D ARG 2.8 28.9 + - - -
434D LEU* 3.6 11.8 - - - -
436D ASP* 1.3 72.7 - - - +
438D VAL* 1.3 63.7 + - + +
440D SER* 3.0 16.7 + - - -
441D PHE* 3.2 39.5 - - + -
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Residues in contact with VAL 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D LEU* 4.2 15.0 - - + -
366D GLU* 4.8 11.2 - - + +
367D HIS* 3.4 47.1 - - + +
370D VAL* 4.0 27.4 - - + +
434D LEU* 3.2 21.0 + - + +
435D LYS* 4.6 3.4 - - - +
437D THR* 1.3 75.4 - - - +
439D ALA* 1.3 57.6 + - - +
441D PHE* 3.8 0.6 + - - +
442D LYS* 3.1 29.4 + - + +
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Residues in contact with ALA 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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435D LYS 3.7 13.4 + - - +
436D ASP* 3.1 16.4 + - - +
438D VAL* 1.3 79.3 - - - +
440D SER* 1.3 61.3 + - - +
442D LYS* 3.9 10.0 - - - +
443D ALA* 3.4 20.6 + - - +
463D ILE* 5.6 1.7 - - + +
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Residues in contact with SER 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D LYS* 6.0 1.2 - - - +
413D PHE* 3.8 18.3 - - - -
432D VAL* 5.6 0.5 - - - +
436D ASP* 2.6 23.1 + - - -
437D THR* 3.0 10.4 + - - -
439D ALA* 1.3 76.0 - - - +
441D PHE* 1.3 67.3 + - - +
443D ALA* 3.2 6.6 + - - +
444D VAL* 3.1 26.0 + - - +
462D GLY* 5.3 0.3 - - - -
463D ILE* 3.3 42.6 + - - +
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Residues in contact with PHE 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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139D LYS* 4.4 11.2 - - + -
143D LEU* 3.5 30.3 - - + -
370D VAL* 4.2 10.8 - - + -
374D VAL* 4.1 9.4 - - + -
410D ILE* 3.5 26.9 - - + +
413D PHE* 3.3 41.3 - + - -
414D LEU* 3.5 32.3 - - + -
437D THR* 3.2 30.7 + - + +
438D VAL 4.5 0.2 - - - +
440D SER* 1.3 75.7 - - - +
442D LYS* 1.3 57.5 + - - +
444D VAL* 2.9 10.1 + - + +
445D LEU* 2.7 40.5 + - + +
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Residues in contact with LYS 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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366D GLU* 2.9 31.6 + - - +
370D VAL* 3.9 26.7 - - + +
438D VAL* 3.1 21.1 + - + +
439D ALA* 3.9 10.1 - - - +
441D PHE* 1.3 80.4 - - - +
443D ALA* 1.3 63.3 + - - +
445D LEU* 3.0 14.3 + - - +
446D GLU* 3.2 40.6 + - + +
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Residues in contact with ALA 443 (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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439D ALA 3.4 11.7 + - - +
440D SER* 3.2 11.1 + - - +
441D PHE 3.2 0.2 - - - -
442D LYS* 1.3 80.1 - - - +
444D VAL* 1.3 60.1 + - - +
446D GLU* 3.4 16.8 + - - +
448D LYS* 3.3 32.4 + - + +
449D TYR* 3.8 23.6 - - + +
463D ILE* 5.5 1.3 - - + -
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Residues in contact with VAL 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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406D ARG* 4.2 15.5 - - + +
409D LYS* 4.9 12.6 - - + -
410D ILE* 4.3 23.3 - - + +
413D PHE* 5.0 7.2 - - + -
440D SER 3.1 17.0 + - - +
441D PHE* 2.9 11.5 + - + +
443D ALA* 1.3 75.1 - - - +
445D LEU* 1.3 62.7 + - - +
447D GLY* 3.3 12.6 + - - +
448D LYS 4.9 0.9 - - - +
449D TYR* 3.9 26.0 + - + +
450D ASP* 4.7 1.4 - - - +
457D PHE* 4.1 27.6 - - + -
463D ILE* 4.4 5.4 - - + -
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Residues in contact with LEU 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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370D VAL* 3.6 44.6 - - + +
373D LYS* 3.7 25.1 - - + +
374D VAL* 3.8 12.6 - - + +
377D THR* 4.4 12.8 - - + +
406D ARG* 3.3 24.4 + - - +
410D ILE* 3.6 31.9 - - + -
441D PHE 2.7 24.5 + - - +
442D LYS* 3.0 7.1 + - - +
444D VAL* 1.3 73.4 - - - +
446D GLU* 1.3 59.3 + - + +
447D GLY 3.2 1.1 - - - -
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Residues in contact with GLU 446 (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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406D ARG* 4.4 5.1 + - - -
442D LYS* 3.2 41.5 + - + +
443D ALA* 3.7 16.2 - - - +
444D VAL 3.2 0.4 - - - -
445D LEU* 1.3 78.4 - - + +
447D GLY* 1.3 62.1 + - - +
448D LYS* 3.4 34.9 + - + +
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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