Contacts of the helix formed by residues 326 - 338 (chain D) in PDB entry 1MHL
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 ASN 326 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B PHE* 3.6 24.6 - - + +
30B VAL 2.9 12.4 + - - +
31B ARG* 3.5 21.6 - - + +
602B CL 3.7 11.6 - - + +
162D ASN* 3.0 19.0 + - - -
163D GLN* 2.9 26.3 + - - -
325D ALA* 1.3 69.9 - - - +
327D VAL* 1.3 61.0 + - - +
329D THR* 2.7 29.1 + - - -
330D ASN 3.9 0.3 + - - -
428D HIS* 2.7 31.2 + - - +
430D LEU* 4.1 5.1 - - + +
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Residues in contact with VAL 327 (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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32B TRP* 3.8 24.2 - - + -
602B CL 3.4 6.4 - - + +
325D ALA* 4.2 3.1 - - + -
326D ASN* 1.3 77.1 - - - +
328D PHE* 1.3 60.3 + - - +
330D ASN* 2.9 5.5 + - - +
331D ALA* 2.8 25.2 + - + +
430D LEU* 3.9 12.1 - - + +
436D TRP* 3.6 54.1 - - + +
476D ILE* 4.1 23.1 - - + -
498D ILE* 4.3 18.4 - - + -
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Residues in contact with PHE 328 (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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32B TRP* 5.6 0.7 - - + -
97B LEU* 3.8 27.6 - - + -
98B ASP* 3.6 17.9 - - - -
324D ILE* 3.7 19.7 - - + -
325D ALA* 3.1 9.9 + - + +
327D VAL* 1.3 81.6 - - - +
329D THR* 1.3 62.6 + - - +
331D ALA* 4.2 6.1 - - - -
332D PHE* 3.0 61.7 + + + +
498D ILE* 4.5 7.2 - - + -
499D ILE* 4.3 14.8 - - + -
502D GLN* 3.4 48.5 - - + +
503D PHE* 4.0 13.7 - + - -
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Residues in contact with THR 329 (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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29B PHE* 3.4 39.7 - - + -
98B ASP* 3.7 28.3 - - - +
100B THR* 4.4 2.7 - - - -
605B HEM 3.6 16.4 - - - +
324D ILE* 4.1 5.6 - - + -
326D ASN* 2.7 25.7 + - - +
328D PHE* 1.3 76.0 - - - +
330D ASN* 1.4 58.6 + - - +
333D ARG* 2.9 32.0 + - - +
424D ARG* 6.0 0.2 - - - +
428D HIS* 4.0 11.6 + - - -
430D LEU* 5.6 0.2 - - - +
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Residues in contact with ASN 330 (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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327D VAL 2.9 7.6 + - - +
329D THR* 1.4 82.1 + - - +
331D ALA* 1.3 66.1 + - - +
332D PHE 3.4 0.2 - - - -
333D ARG* 3.1 37.5 + - - +
421D ASN 3.0 27.2 + - - +
424D ARG* 4.2 4.4 - - - +
425D SER* 3.9 18.3 - - - +
430D LEU* 3.9 17.9 - - + -
476D ILE* 3.7 5.5 - - + +
477D TRP* 3.2 42.7 + - - +
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Residues in contact with ALA 331 (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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327D VAL* 2.8 19.1 + - + +
328D PHE* 4.2 1.6 - - - +
330D ASN* 1.3 71.6 - - - +
332D PHE* 1.3 58.8 + - - +
333D ARG 2.9 5.4 + - - -
334D TYR* 3.1 20.3 + - - +
476D ILE* 5.0 7.3 - - + +
477D TRP* 4.8 5.6 - - - +
495D LEU* 4.3 23.5 - - + +
498D ILE* 3.5 36.8 - - + -
499D ILE* 4.9 5.2 - - + -
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Residues in contact with PHE 332 (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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90B GLY 3.6 21.1 - - - -
93B LEU* 4.1 18.8 - - + -
94B ASP* 3.5 32.8 - - + +
97B LEU* 5.5 0.2 - - + -
605B HEM 3.3 23.7 - - + +
296D TYR* 3.5 24.2 - + - -
300D VAL* 5.4 1.1 - - + -
328D PHE* 3.0 49.6 + + + +
331D ALA* 1.3 70.5 - - - +
333D ARG* 1.3 56.9 + - - +
334D TYR* 2.9 31.4 + + - -
499D ILE* 3.8 23.1 - - + +
503D PHE* 4.0 16.2 - + - -
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Residues in contact with ARG 333 (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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100B THR* 5.7 1.8 + - - -
605B HEM 2.8 85.2 + - + +
329D THR* 2.9 29.1 + - - +
330D ASN* 3.2 22.0 - - - +
331D ALA 2.9 2.4 + - - -
332D PHE* 1.3 74.3 - - - +
334D TYR* 1.4 60.5 + - - +
335D GLY 2.9 7.3 + - - -
336D HIS* 2.9 29.5 + - + +
421D ASN* 2.8 37.6 - - - +
424D ARG* 3.3 22.6 - - - +
428D HIS* 5.7 1.2 - - - -
477D TRP* 3.1 17.7 + - + -
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Residues in contact with TYR 334 (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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86B PHE* 4.2 2.9 - - - -
605B HEM 4.5 2.9 - - + +
296D TYR* 3.1 20.1 + - - -
300D VAL* 3.6 20.9 - - + +
331D ALA 3.1 11.1 + - - +
332D PHE* 2.9 33.9 - + - -
333D ARG* 1.4 76.5 - - - +
335D GLY* 1.4 64.9 + - - +
336D HIS 3.1 1.2 + - - -
337D THR* 2.8 33.8 + - - +
338D LEU* 4.0 26.5 - - + +
392D ASN* 6.2 1.1 - - - -
477D TRP* 3.7 11.1 - - + +
481D VAL* 4.0 7.2 - - + -
490D ARG* 4.1 14.1 - - + -
491D VAL* 3.6 22.2 - - + -
495D LEU* 3.7 22.4 - - + -
499D ILE* 3.7 20.4 - - + -
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Residues in contact with GLY 335 (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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605B HEM 3.6 41.1 - - - +
332D PHE 3.6 1.4 + - - -
333D ARG 2.9 2.8 - - - -
334D TYR* 1.4 80.4 - - - +
336D HIS* 1.3 63.9 + - - +
337D THR 3.0 2.2 - - - -
338D LEU* 3.0 32.6 + - - +
339D ILE* 3.8 3.8 + - - +
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Residues in contact with HIS 336 (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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605B HEM 2.1 77.4 + + + -
333D ARG* 2.9 25.9 + - + +
335D GLY* 1.3 77.9 - - - +
337D THR* 1.3 61.1 + - - +
338D LEU 3.2 0.9 + - - -
339D ILE* 3.4 22.2 + - + +
390D LYS* 5.6 0.2 - - - +
398D ALA* 4.5 4.9 - - + +
399D VAL* 6.0 0.2 - - - +
402D ILE* 3.8 21.5 - - + +
417D LEU* 3.7 17.0 - - + +
418D PRO* 5.9 0.9 - - + -
421D ASN* 3.0 31.8 + - - +
477D TRP* 4.4 11.4 - - + -
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Residues in contact with THR 337 (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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334D TYR* 2.8 23.0 + - - +
336D HIS* 1.3 77.7 - - - +
338D LEU* 1.3 62.6 + - - +
339D ILE 3.5 0.4 - - - -
390D LYS* 3.0 34.9 + - - +
392D ASN* 3.5 34.4 + - - +
397D ILE* 3.3 26.5 - - + +
398D ALA* 4.9 0.7 - - + +
477D TRP* 4.1 11.9 - - + -
481D VAL* 3.9 25.5 - - + +
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Residues in contact with LEU 338 (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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79B ASP* 5.8 1.6 - - - +
84B LEU* 4.2 1.4 - - - +
86B PHE* 3.7 38.4 - - + +
87B MET* 3.9 27.8 - - + +
605B HEM 5.3 2.2 - - + -
334D TYR* 4.0 22.2 - - + +
335D GLY* 3.0 23.7 + - - +
337D THR* 1.3 89.1 - - - +
339D ILE* 1.3 61.4 + - - +
340D GLN 3.5 1.2 + - - -
389D ALA* 4.0 9.5 - - + +
390D LYS* 3.1 36.9 + - - +
391D LEU* 5.6 0.2 - - - -
392D ASN* 5.1 7.2 - - + +
490D ARG* 5.1 11.2 - - + +
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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