Contacts of the helix formed by residues 439 - 455 (chain D) in PDB entry 6M04
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 SER 439 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D PHE* 4.9 1.4 - - - -
409D ILE* 3.3 17.7 - - - +
410D PRO 3.1 17.8 + - - -
411D ASP* 3.7 22.9 - - - +
435D GLY 4.0 1.0 + - - -
436D VAL* 3.1 15.8 + - - +
437D PHE 3.3 3.3 - - - +
438D LEU* 1.3 76.9 - - - +
440D GLU* 1.3 59.9 + - - +
441D VAL* 3.3 18.5 - - - +
442D SER* 3.4 4.6 + - - -
443D GLU* 3.0 23.1 + - - +
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Residues in contact with GLU 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D PRO 5.0 3.8 + - - +
411D ASP 6.4 0.9 - - - -
412D VAL* 5.0 9.7 - - + +
438D LEU 3.5 4.4 + - - +
439D SER* 1.3 71.1 + - - +
441D VAL* 1.3 73.6 + - - +
442D SER 3.2 0.4 - - - -
443D GLU* 3.2 22.1 - - - +
444D ASN* 2.9 24.8 + - - +
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Residues in contact with VAL 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409D ILE* 3.8 14.1 - - + -
410D PRO* 4.2 18.2 - - + +
439D SER* 3.3 14.1 + - - +
440D GLU* 1.3 91.2 - - - +
442D SER* 1.3 60.9 + - - +
444D ASN* 3.1 13.8 + - + +
445D LYS* 2.9 45.2 + - - +
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Residues in contact with SER 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D TRP* 3.1 38.6 - - - -
212D ALA* 5.0 2.9 - - - +
288D PHE* 4.7 1.3 - - - -
409D ILE* 3.8 24.1 - - - +
436D VAL* 4.3 13.5 + - - +
437D PHE* 6.2 0.2 - - - -
439D SER* 3.4 13.8 + - - -
440D GLU 3.2 0.4 - - - -
441D VAL* 1.3 80.2 - - - +
443D GLU* 1.3 58.3 + - - +
445D LYS* 3.2 14.9 - - - +
446D LEU* 3.0 21.7 + - - +
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Residues in contact with GLU 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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285D LYS* 3.8 13.9 + - - +
288D PHE* 3.6 34.0 - - + +
292D ARG* 3.0 34.3 + - - -
439D SER 3.0 12.6 + - - +
440D GLU* 3.2 23.3 - - - +
442D SER* 1.3 77.4 - - - +
444D ASN* 1.3 57.0 + - - +
446D LEU* 3.2 3.1 + - - +
447D ARG* 2.9 54.1 + - - +
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Residues in contact with ASN 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440D GLU* 2.9 14.9 + - - +
441D VAL* 3.1 19.1 + - + +
443D GLU* 1.3 72.7 - - - +
445D LYS* 1.3 60.0 + - - +
447D ARG* 3.3 24.5 - - - +
448D GLU* 2.9 30.7 + - - +
502D GLU* 3.5 30.1 + - - +
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Residues in contact with LYS 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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208D TRP* 4.6 8.5 - - + +
215D GLU* 6.0 2.2 - - - -
409D ILE* 6.1 4.0 - - + +
441D VAL* 2.9 38.5 + - - +
442D SER* 3.2 19.1 - - - +
444D ASN* 1.3 75.8 - - - +
446D LEU* 1.3 57.1 + - - +
448D GLU* 3.3 3.3 + - + -
449D ILE* 2.9 49.4 + - + +
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Residues in contact with LEU 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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208D TRP* 3.5 59.5 - - + +
281D GLY* 4.3 24.0 - - - +
284D ALA* 3.7 17.0 - - + -
285D LYS* 4.9 4.9 - - + +
288D PHE* 3.5 28.9 - - + -
442D SER 3.0 8.7 + - - +
443D GLU 3.2 7.6 + - - +
445D LYS* 1.3 76.9 - - - +
447D ARG* 1.3 56.8 + - - +
449D ILE* 4.9 8.7 - - + -
450D SER* 2.9 36.6 + - - +
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Residues in contact with ARG 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D LYS* 3.4 27.7 - - + +
443D GLU* 2.9 42.7 + - - +
444D ASN* 3.3 36.4 - - - +
446D LEU* 1.3 75.2 - - - +
448D GLU* 1.3 56.9 + - - +
450D SER* 4.4 5.2 - - - -
451D LEU* 3.3 20.4 - - - +
478D MET* 6.3 1.2 - - - +
480D SER* 3.1 43.6 + - - +
502D GLU* 5.2 5.4 - - + -
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Residues in contact with GLU 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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444D ASN* 2.9 21.0 + - - +
445D LYS* 3.7 5.6 - - + +
446D LEU 3.1 0.2 - - - -
447D ARG* 1.3 77.6 - - - +
449D ILE* 1.3 80.7 + - - +
450D SER 3.3 0.2 - - - -
451D LEU* 3.3 4.7 + - - +
452D ASN* 2.4 65.3 + - - +
481D GLY* 6.1 5.6 - - - +
484D ASP* 4.0 7.8 - - - +
504D LYS* 6.2 5.2 - - + -
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Residues in contact with ILE 449 (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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208D TRP* 5.5 4.9 - - - +
211D LYS* 4.9 16.2 - - - +
215D GLU* 5.9 3.1 - - - +
445D LYS* 2.9 41.5 + - + +
446D LEU* 4.4 11.2 - - + +
448D GLU* 1.3 97.3 - - - +
450D SER* 1.3 58.5 + - - +
452D ASN* 3.7 4.1 - - + +
453D HIS* 2.9 33.9 + - + +
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Residues in contact with SER 450 (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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281D GLY* 5.4 11.3 - - - -
282D GLU* 5.3 9.2 + - - +
446D LEU* 2.9 21.5 + - - +
447D ARG* 4.6 5.2 - - - -
449D ILE* 1.3 79.3 - - - +
451D LEU* 1.3 60.6 + - - +
453D HIS* 3.4 4.4 + - - +
454D GLU* 2.9 37.4 + - - +
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Residues in contact with LEU 451 (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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447D ARG* 3.3 11.9 - - + +
448D GLU* 3.3 8.0 + - - +
450D SER* 1.3 80.5 - - - +
452D ASN* 1.3 65.2 + - - +
454D GLU* 3.3 26.9 - - - +
455D TRP* 3.2 29.2 + - + +
478D MET* 5.0 4.5 - - + +
479D LEU* 3.7 27.1 - - + -
480D SER* 3.3 37.0 - - - +
481D GLY* 3.3 19.7 - - - +
482D VAL 5.6 0.9 - - - +
483D PRO* 4.6 5.9 - - + +
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Residues in contact with ASN 452 (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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448D GLU* 2.4 52.4 + - - +
449D ILE* 4.2 4.7 - - - +
451D LEU* 1.3 75.3 - - - +
453D HIS* 1.3 57.7 + - - +
455D TRP 4.0 12.2 - - - +
456D THR* 5.6 0.7 - - - -
482D VAL 3.5 5.1 + - - +
483D PRO* 3.4 7.5 - - - +
484D ASP* 2.7 45.1 + - - -
485D ALA* 4.5 4.0 + - - +
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Residues in contact with HIS 453 (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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277D ASP* 5.0 8.7 - - + +
278D LYS* 3.6 37.0 + - + +
449D ILE* 2.9 22.4 + - + +
450D SER* 3.9 4.7 - - - +
451D LEU 3.1 0.2 - - - -
452D ASN* 1.3 79.1 - - - +
454D GLU* 1.3 66.3 + - + +
455D TRP 3.4 0.7 - - - -
456D THR* 3.6 19.6 - - + +
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Residues in contact with GLU 454 (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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450D SER* 2.9 24.0 + - - +
451D LEU* 3.3 33.6 - - - +
453D HIS* 1.3 81.7 - - + +
455D TRP* 1.3 80.9 + - + +
456D THR* 3.4 3.7 + - - +
459D LYS* 2.9 30.9 + - - +
479D LEU* 4.4 1.7 - - - +
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Residues in contact with TRP 455 (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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451D LEU 3.2 11.4 + - - +
452D ASN* 4.0 10.7 - - - +
453D HIS 4.4 1.8 - - - -
454D GLU* 1.3 105.6 + - + +
456D THR* 1.3 66.4 + - - +
459D LYS* 3.6 44.6 - - + -
460D LEU* 4.1 17.9 - - + -
463D HIS* 6.2 4.9 - + + -
474D LEU* 5.3 19.5 - - + -
475D HIS 6.2 0.7 - - - -
479D LEU* 3.6 25.4 - - + +
483D PRO* 3.8 34.4 - - + +
485D ALA* 3.5 15.2 - - - +
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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