Contacts of the helix formed by residues 346 - 356 (chain D) in PDB entry 5MG3
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 346 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324D ASP 4.8 7.4 - - - +
325D HIS* 2.9 26.6 + - - +
327D THR* 3.9 25.1 - - + +
345D LEU* 1.3 70.1 - - - +
347D SER* 1.3 73.1 + - - +
348D ALA* 3.9 10.5 + - - +
349D GLY 4.4 5.2 - - - +
350D GLY 2.7 29.5 + - - -
404D ASN* 2.9 7.8 + - - -
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Residues in contact with SER 347 (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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346D ASP* 1.3 82.5 + - - +
348D ALA* 1.4 56.4 + - - -
350D GLY* 3.2 1.0 + - - -
351D ASN* 2.8 52.5 + - - +
404D ASN* 3.5 11.4 - - - +
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Residues in contact with ALA 348 (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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325D HIS* 4.2 10.3 - - + +
346D ASP* 3.9 8.7 + - - +
347D SER* 1.4 76.0 - - - +
349D GLY* 1.3 61.2 - - - +
351D ASN* 3.5 9.3 + - - +
352D ILE* 3.2 28.4 + - + +
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Residues in contact with GLY 349 (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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321D LEU* 3.7 10.2 - - - +
325D HIS* 3.2 35.8 + - - -
345D LEU* 5.0 3.6 - - - -
346D ASP* 3.5 7.0 + - - +
347D SER 3.3 0.4 - - - -
348D ALA* 1.3 77.3 - - - +
350D GLY* 1.4 62.3 + - - +
352D ILE* 3.0 5.6 + - - +
353D MET* 3.0 28.5 + - - +
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Residues in contact with GLY 350 (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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345D LEU* 4.5 2.2 - - - +
346D ASP 2.7 21.5 + - - -
347D SER 3.5 1.8 - - - -
349D GLY* 1.4 71.7 - - - +
351D ASN* 1.3 51.6 + - - +
353D MET* 3.4 3.9 + - - +
354D SER* 2.9 33.8 + - - -
403D GLY* 3.5 28.6 + - - -
404D ASN* 3.7 9.2 - - - -
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Residues in contact with ASN 351 (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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347D SER* 2.8 40.5 + - - +
348D ALA* 3.8 8.5 - - - +
350D GLY* 1.3 68.3 - - - -
352D ILE* 1.4 61.3 + - + +
354D SER* 3.4 9.2 + - - -
355D ASN* 3.0 39.9 + - - +
404D ASN* 5.7 0.9 + - - -
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Residues in contact with ILE 352 (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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320D ILE* 3.6 25.8 - - + +
321D LEU* 4.3 4.3 - - + -
325D HIS* 4.2 22.9 - - + +
348D ALA* 3.2 17.1 + - + +
349D GLY 3.0 8.2 + - - +
351D ASN* 1.4 72.9 - - + +
353D MET* 1.4 62.8 + - - +
355D ASN* 3.2 6.7 + - - +
356D PHE* 3.1 45.4 + - + -
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Residues in contact with MET 353 (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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320D ILE* 3.8 19.7 - - - -
321D LEU* 3.5 33.9 - - + -
345D LEU* 3.9 14.6 - - + -
349D GLY 3.0 14.6 + - - +
350D GLY 3.6 7.9 - - - +
352D ILE* 1.4 74.8 - - - +
354D SER* 1.4 49.9 + - - +
356D PHE* 3.4 2.8 + - - -
357D THR* 2.8 39.7 + - - -
360D ASN* 5.8 0.9 - - - -
365D MET* 4.3 5.8 - - + -
398D ILE* 4.8 17.3 - - + -
403D GLY* 4.2 12.3 - - - +
405D SER 6.1 0.4 - - - +
406D PHE* 3.6 36.8 - - + -
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Residues in contact with SER 354 (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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350D GLY 2.9 18.9 + - - -
351D ASN* 3.4 16.2 - - - -
353D MET* 1.4 73.2 - - - +
355D ASN* 1.3 67.4 + - - +
357D THR* 3.2 22.7 + - - -
358D LYS* 5.1 5.2 + - - -
403D GLY* 4.7 10.1 - - - +
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Residues in contact with ASN 355 (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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351D ASN* 3.0 25.0 + - - +
352D ILE* 3.2 6.8 + - - +
354D SER* 1.3 85.5 + - - +
356D PHE* 1.3 69.3 + - + +
357D THR 3.6 0.5 + - - -
358D LYS* 4.9 8.7 + - - -
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Residues in contact with PHE 356 (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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318D ARG* 3.5 24.0 - - - +
320D ILE* 5.0 8.5 - - + -
352D ILE* 3.1 44.8 + - + +
353D MET* 3.5 3.8 - - - +
355D ASN* 1.3 84.8 - - + +
357D THR* 1.4 59.9 + - - +
358D LYS 3.5 2.4 + - - -
359D ASP* 3.8 11.3 + - + +
360D ASN* 3.4 38.1 + - - +
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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