Contacts of the helix formed by residues 408 - 421 (chain D) in PDB entry 1M6X
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 408 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200D PRO 5.1 0.2 + - - -
201D LYS 5.7 2.7 + - - -
203D PHE* 3.6 24.4 + - - +
204D LYS* 5.6 0.2 - - - -
406D ILE 3.6 4.4 + - - -
407D ILE* 1.3 78.1 - - - +
409D GLN* 1.3 64.6 + - - +
410D GLU* 3.3 24.3 + - - +
411D VAL* 3.1 12.0 + - - +
412D LEU* 3.0 17.5 + - - +
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Residues in contact with GLN 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397D SER* 4.0 25.0 + - - +
404D ASN* 6.2 0.2 - - - +
407D ILE 3.3 4.4 + - - -
408D SER* 1.3 69.8 + - - +
410D GLU* 1.3 68.1 - - - +
411D VAL 2.9 0.3 + - - -
412D LEU* 3.0 10.7 + - + -
413D ASP* 2.8 48.4 + - - +
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Residues in contact with GLU 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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204D LYS* 5.4 1.6 - - - -
205D LEU* 3.7 40.7 + - + +
408D SER* 3.3 12.3 + - - +
409D GLN* 1.3 79.6 - - - +
411D VAL* 1.3 61.5 + - - +
413D ASP* 3.7 8.7 + - - +
414D TYR* 3.3 15.8 + - - +
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Residues in contact with VAL 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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203D PHE* 3.8 24.7 - - + +
204D LYS* 4.0 15.0 - - - +
205D LEU* 4.1 8.7 - - + -
215D ILE* 4.1 31.2 - - + -
245D LEU* 6.1 0.7 - - + -
407D ILE* 4.1 15.0 - - + -
408D SER* 3.1 25.3 + - - +
409D GLN 3.0 0.4 - - - -
410D GLU* 1.3 75.6 - - + +
412D LEU* 1.3 68.7 + - + +
413D ASP 3.0 1.6 - - - -
414D TYR* 3.0 7.4 + - - +
415D LEU* 2.9 25.8 + - + +
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Residues in contact with LEU 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D LEU* 4.5 6.1 - - + -
396D GLY* 3.6 12.4 - - - -
397D SER* 4.7 5.6 - - - +
400D TYR* 3.6 41.9 - - + +
403D TRP* 4.0 15.3 - - + +
404D ASN* 4.2 18.2 - - - +
405D GLY 5.0 0.4 - - - +
407D ILE* 3.1 46.4 - - + +
408D SER 3.0 9.8 + - - +
409D GLN* 3.0 12.7 + - + +
411D VAL* 1.3 79.8 - - + +
413D ASP* 1.3 57.2 + - - +
415D LEU* 4.7 1.6 - - + +
416D SER* 2.9 30.3 + - - -
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Residues in contact with ASP 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395D GLU 4.3 5.5 + - - +
396D GLY* 3.3 22.1 + - - +
409D GLN* 2.8 49.5 + - - +
410D GLU* 3.8 8.0 - - - +
412D LEU* 1.3 74.5 - - - +
414D TYR* 1.3 57.0 - - - +
416D SER* 3.0 5.9 + - - -
417D SER* 2.7 41.7 + - - +
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Residues in contact with TYR 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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205D LEU* 3.6 27.6 - - + -
211D LEU 5.4 1.4 + - - -
213D VAL* 3.8 27.2 + - + +
214D ILE* 5.6 0.4 - - - -
215D ILE* 4.2 24.7 - - + -
234D SER* 5.0 3.6 + - - -
242D LEU* 4.0 24.0 - - + +
384D TRP* 3.7 31.4 - + + +
387D ILE* 4.0 27.1 - - + -
410D GLU 3.3 11.8 + - - +
411D VAL 3.0 7.3 + - - +
413D ASP* 1.3 79.2 - - - +
415D LEU* 1.3 65.2 + - - +
417D SER* 3.6 3.8 - - - -
418D TYR* 2.9 39.0 + + + +
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Residues in contact with LEU 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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215D ILE* 4.5 7.2 - - + -
242D LEU* 3.6 46.4 - - + +
245D LEU* 3.8 20.0 - - + -
246D ASP* 4.0 6.5 - - - -
249D LEU* 3.7 22.7 - - + -
400D TYR* 3.2 29.2 - - + +
411D VAL* 2.9 16.9 + - + +
412D LEU* 4.1 3.8 - - - +
414D TYR* 1.3 77.5 - - + +
416D SER* 1.3 68.3 + - - +
418D TYR* 3.5 4.8 - - + +
419D ILE* 2.8 33.7 + - + +
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Residues in contact with SER 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395D GLU* 3.4 20.4 + - - +
396D GLY* 3.6 15.2 - - - -
399D ARG* 3.8 13.6 - - - +
400D TYR* 3.9 13.1 + - - -
412D LEU 2.9 20.6 + - - -
413D ASP* 3.3 4.0 - - - -
415D LEU* 1.3 77.8 - - - +
417D SER* 1.3 64.9 + - - +
419D ILE* 3.3 2.5 + - - +
420D ASN* 2.9 36.3 + - - -
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Residues in contact with SER 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387D ILE* 3.4 31.3 + - - +
413D ASP* 2.7 26.3 + - - +
414D TYR* 3.6 0.4 - - - -
416D SER* 1.3 72.0 - - - +
418D TYR* 1.3 68.8 + - - +
419D ILE 2.8 1.6 + - - -
420D ASN* 3.6 4.9 - - - +
421D ARG* 2.7 28.2 + - - -
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Residues in contact with TYR 418 (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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234D SER* 2.7 29.4 + - - -
240D ASP* 2.4 31.2 + - - -
242D LEU* 3.5 37.0 - - + -
243D VAL* 4.9 2.9 - - + -
383D GLU* 4.0 16.8 - - - -
387D ILE* 3.6 27.9 - - + +
414D TYR* 2.9 30.3 + - + +
415D LEU* 3.5 6.7 - - + +
417D SER* 1.3 76.1 - - - +
419D ILE* 1.3 80.1 + - + +
421D ARG* 3.5 4.4 - - - +
422D ARG* 3.0 40.0 + - - +
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Residues in contact with ILE 419 (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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242D LEU 4.1 10.1 - - - +
243D VAL* 4.4 12.1 - - + -
246D ASP* 3.6 24.9 - - + +
399D ARG* 3.3 32.8 - - - +
400D TYR* 3.8 16.6 - - - +
415D LEU* 2.8 23.3 + - + +
416D SER 3.4 7.4 - - - +
417D SER 2.8 3.2 + - - -
418D TYR* 1.3 84.8 - - + +
420D ASN* 1.3 60.5 + - - +
422D ARG* 2.8 28.6 + - - +
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Residues in contact with ASN 420 (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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395D GLU* 4.3 15.8 + - - +
399D ARG* 3.9 19.6 + - - +
416D SER* 2.9 32.9 + - - -
417D SER* 2.9 8.8 + - - +
419D ILE* 1.3 73.6 - - - +
421D ARG* 1.3 54.6 + - - +
422D ARG 2.5 25.6 + - - -
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Residues in contact with ARG 421 (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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383D GLU* 3.2 44.4 + - - +
386D HIS* 2.7 44.8 + - - +
387D ILE* 3.9 16.6 - - + -
417D SER* 2.7 26.9 + - - +
418D TYR* 3.5 9.2 - - - +
420D ASN* 1.3 71.1 - - - +
422D ARG* 1.3 56.7 + - - +
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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