Contacts of the helix formed by residues 391 - 397 (chain B) in PDB entry 1ZMC
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 391 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A LEU* 5.1 0.4 - - - -
386B PHE* 4.2 10.0 - - + -
387B PRO 3.9 1.2 + - - -
388B PHE* 3.4 24.3 + - + +
390B ALA* 1.3 78.4 - - - +
392B SER* 1.3 66.8 + - - +
393B ARG* 2.9 13.1 + - - +
394B ALA* 2.8 30.4 + - + +
395B LYS* 3.0 25.7 + - - +
454B THR 2.9 22.2 + - - -
455B LEU* 3.6 11.0 + - - +
457B GLU* 3.6 18.2 + - - +
458B ALA* 3.6 11.1 - - + +
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Residues in contact with SER 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TYR* 5.7 0.7 + - - -
51A ILE* 4.0 11.8 - - - +
99A LEU* 4.3 20.0 - - - +
390B ALA 3.8 3.3 + - - -
391B ASN* 1.3 76.9 - - - +
393B ARG* 1.3 53.7 + - - +
395B LYS* 3.9 1.0 - - - +
396B THR* 2.5 39.1 + - - -
452B HIS* 3.4 32.2 - - - -
453B PRO* 3.8 9.2 - - - -
457B GLU* 4.7 2.2 + - - -
473B ASN* 6.1 1.0 - - - -
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Residues in contact with ARG 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LYS* 5.3 5.8 - - + +
359A TYR* 3.7 27.5 + - - +
363A GLU* 2.8 29.1 + - - -
426A GLY 4.6 2.8 - - - -
427A GLU* 2.8 54.9 + - - +
391B ASN* 2.9 9.8 + - - +
392B SER* 1.3 76.3 - - - +
394B ALA* 1.3 61.7 + - - +
396B THR* 3.3 5.7 + - - -
397B ASN* 2.9 56.5 + - - +
453B PRO* 3.6 23.5 - - + +
454B THR* 3.7 14.5 - - - +
455B LEU* 3.9 9.1 - - + +
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Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B PHE* 3.1 33.0 - - + +
391B ASN* 2.8 17.0 + - + +
393B ARG* 1.3 77.7 - - - +
395B LYS* 1.3 58.1 + - - +
397B ASN* 3.3 5.1 + - - -
398B ALA 3.0 21.3 + - - -
399B ASP 3.1 29.1 + - - +
400B THR* 3.4 3.4 - - + -
423B PRO* 4.6 0.4 - - + -
455B LEU* 3.8 15.0 - - + +
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Residues in contact with LYS 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ALA* 3.9 18.8 - - - +
98A ALA* 4.2 22.2 - - + +
99A LEU* 3.7 33.2 - - + -
389B ALA* 3.9 20.6 + - - +
391B ASN 3.0 16.5 + - - +
392B SER 4.0 2.7 - - - +
394B ALA* 1.3 75.4 - - - +
396B THR* 1.3 63.7 - - - +
398B ALA* 3.0 14.3 + - - +
400B THR* 3.5 20.1 + - + +
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Residues in contact with THR 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ILE* 3.4 35.7 - - + +
54A LYS* 3.9 11.8 - - + +
55A ALA* 3.3 40.2 - - + +
58A ASN* 5.0 1.0 + - - -
91A GLN* 3.3 23.9 + - - +
95A ALA* 4.2 8.7 - - + -
99A LEU* 4.4 0.9 - - - +
74B ARG* 5.0 0.7 + - - -
392B SER 2.5 25.4 + - - -
393B ARG* 3.3 7.1 + - - -
395B LYS* 1.3 76.1 - - - +
397B ASN* 1.3 60.5 + - - +
398B ALA 3.1 0.4 - - - -
453B PRO* 5.4 0.6 - - - +
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Residues in contact with ASN 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LYS* 4.9 3.6 - - - +
58A ASN* 3.4 37.2 + - - +
74B ARG* 2.7 31.0 + - - -
393B ARG* 2.9 48.2 + - - +
394B ALA* 3.7 5.9 - - - +
395B LYS 3.2 0.2 - - - -
396B THR* 1.3 77.9 - - - +
398B ALA* 1.3 58.7 + - - +
399B ASP* 3.3 12.9 + - + +
455B LEU* 5.1 7.5 - - - +
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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