Contacts of the helix formed by residues 391 - 398 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E LEU* 5.3 0.2 - - - -
386F PHE* 4.1 9.8 - - + -
387F PRO 3.7 0.8 + - - -
388F PHE* 3.0 23.3 + - + +
390F ALA* 1.3 79.3 - - - +
392F SER* 1.3 60.6 + - - +
393F ARG* 2.9 9.6 + - - +
394F ALA* 2.7 32.9 + - + +
395F LYS* 2.9 30.2 + - - +
454F THR 3.0 25.2 + - - -
455F LEU* 3.6 14.0 + - - +
457F GLU* 3.8 6.5 + - - +
458F ALA* 3.6 18.0 - - + +
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Residues in contact with SER 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E TYR* 5.6 1.6 + - - -
51E ILE* 4.9 4.2 - - - +
99E LEU* 4.1 25.2 - - - +
390F ALA 3.9 3.0 + - - -
391F ASN* 1.3 72.3 + - - +
393F ARG* 1.3 65.6 + - - +
395F LYS* 3.9 1.3 - - - +
396F THR* 2.9 30.8 + - - -
452F HIS* 3.5 33.1 + - - -
453F PRO* 3.8 8.7 - - - -
457F GLU* 4.5 2.9 + - - -
473F ASN* 5.8 1.9 + - - -
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Residues in contact with ARG 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E LYS* 5.5 4.8 - - + +
58E ASN* 6.1 1.0 - - - +
359E TYR* 3.7 29.4 - - - +
363E GLU* 2.7 30.1 + - - -
426E GLY* 4.6 2.4 - - - -
427E GLU* 3.0 44.6 + - - +
391F ASN* 2.9 11.1 + - - +
392F SER* 1.3 74.5 - - - +
394F ALA* 1.3 65.6 + - - +
396F THR* 3.3 5.7 + - - -
397F ASN* 2.8 47.0 + - - +
453F PRO* 3.7 23.5 - - + +
454F THR* 3.9 16.4 - - - +
455F LEU* 4.0 12.5 - - + +
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Residues in contact with ALA 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388F PHE* 3.3 30.7 - - + +
391F ASN* 2.7 19.7 + - + +
393F ARG* 1.3 72.8 - - - +
395F LYS* 1.3 57.3 + - - +
397F ASN* 3.1 6.1 + - - +
398F ALA 2.9 23.7 + - - -
399F ASP* 3.1 29.2 + - - +
400F THR* 3.8 2.7 - - + -
455F LEU* 3.6 17.5 - - + +
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Residues in contact with LYS 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E GLN* 4.8 0.5 + - - -
94E THR* 6.5 0.7 - - - -
95E ALA* 4.2 11.4 - - - +
98E ALA* 3.9 25.5 - - + +
99E LEU* 3.9 29.8 - - + -
389F ALA* 4.1 17.8 + - - +
391F ASN 2.9 18.3 + - - +
392F SER 3.9 2.9 - - - +
394F ALA* 1.3 73.8 - - - +
396F THR* 1.3 65.8 + - - +
398F ALA* 3.0 14.7 + - - +
400F THR* 3.7 25.3 + - + +
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Residues in contact with THR 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E ILE* 3.6 35.5 - - + +
54E LYS* 4.1 9.6 - - + +
55E ALA* 3.4 42.8 - - + +
58E ASN* 5.2 0.2 - - - +
91E GLN* 3.1 23.9 + - - -
95E ALA* 4.0 10.0 - - + +
99E LEU* 4.0 2.5 - - - +
74F ARG* 5.1 0.7 + - - -
392F SER 2.9 19.2 + - - -
393F ARG* 3.7 5.8 - - - -
395F LYS* 1.3 76.4 - - - +
397F ASN* 1.3 60.1 + - - +
453F PRO* 5.8 1.8 - - - +
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Residues in contact with ASN 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E LYS* 4.8 3.1 - - - +
58E ASN* 3.1 40.0 + - - +
74F ARG* 2.8 32.6 + - - +
393F ARG* 2.8 50.7 + - - +
394F ALA* 3.7 5.1 - - - +
396F THR* 1.3 79.2 - - - +
398F ALA* 1.3 60.2 + - - +
399F ASP* 4.4 11.1 - - + +
455F LEU* 5.3 4.2 - - - +
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Residues in contact with ALA 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E GLN* 4.1 17.3 - - + +
70F ASP* 4.6 5.7 - - - +
73F SER* 6.2 0.4 - - - +
74F ARG* 4.0 12.0 + - - +
394F ALA 2.9 4.2 + - - -
395F LYS* 3.0 14.2 + - - +
396F THR 3.3 0.2 - - - -
397F ASN* 1.3 82.3 - - - +
399F ASP* 1.3 59.3 + - - +
400F THR* 3.9 6.1 - - - -
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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