Contacts of the helix formed by residues 391 - 398 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386C PHE* 4.4 4.8 - - + -
387C PRO 3.7 0.6 + - - -
388C PHE* 3.0 26.9 + - + +
390C ALA* 1.3 79.2 - - - +
392C SER* 1.3 63.0 + - - +
393C ARG 3.2 5.4 + - - -
394C ALA* 2.9 26.5 + - + +
395C LYS* 2.9 30.8 + - - +
454C THR 3.1 22.4 + - - +
455C LEU* 3.4 17.6 + - - +
457C GLU* 3.7 9.3 + - - +
458C ALA* 3.6 24.3 - - + +
99D LEU* 5.2 0.9 - - - -
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Residues in contact with SER 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390C ALA 3.8 2.6 + - - -
391C ASN* 1.3 74.3 - - - +
393C ARG* 1.3 67.7 + - - +
395C LYS* 3.9 1.0 - - - +
396C THR* 2.9 29.4 + - - -
452C HIS* 3.5 21.7 - - - -
453C PRO* 3.7 20.6 - - - -
457C GLU* 4.6 2.4 + - - -
51D ILE* 3.8 12.7 - - - +
99D LEU* 4.2 19.8 - - - +
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Residues in contact with ARG 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C ASN* 3.2 8.8 + - - +
392C SER* 1.3 78.5 - - - +
394C ALA* 1.3 57.6 + - - +
396C THR* 3.7 5.9 - - - -
397C ASN* 2.9 56.1 + - - +
453C PRO* 3.7 30.0 - - + +
454C THR* 3.8 8.9 - - - +
455C LEU* 3.9 11.1 - - + +
54D LYS* 5.2 6.0 - - + +
359D TYR* 3.5 32.4 - - - +
363D GLU* 2.9 32.5 + - - -
426D GLY* 4.7 1.0 - - - -
427D GLU* 3.0 42.5 + - - +
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Residues in contact with ALA 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388C PHE* 3.0 33.0 - - + +
391C ASN* 2.9 20.0 + - + +
392C SER 3.1 0.2 - - - -
393C ARG* 1.3 76.9 - - - +
395C LYS* 1.3 56.8 + - - +
397C ASN* 3.1 5.3 + - - +
398C ALA 2.9 22.3 + - - -
399C ASP 3.1 27.0 + - - +
400C THR* 3.6 3.8 - - + -
455C LEU* 3.7 13.0 - - + +
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Residues in contact with LYS 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389C ALA* 4.3 17.1 + - - +
391C ASN 2.9 16.8 + - - +
392C SER 3.9 2.5 - - - +
394C ALA* 1.3 73.7 - - - +
396C THR* 1.3 65.8 - - - +
398C ALA* 3.0 15.3 + - - +
400C THR* 3.6 20.9 + - + +
91D GLN* 4.4 0.3 + - - -
95D ALA* 3.9 15.1 - - - +
98D ALA* 3.5 28.1 - - + +
99D LEU* 4.0 31.2 - - + -
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Residues in contact with THR 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ARG* 4.9 0.9 + - - -
392C SER 2.9 19.3 + - - -
393C ARG* 3.7 7.4 - - + -
395C LYS* 1.3 76.9 - - - +
397C ASN* 1.3 66.2 + - - +
453C PRO* 6.0 0.2 - - - -
51D ILE* 3.3 35.0 - - + +
54D LYS* 3.7 13.7 - - + +
55D ALA* 3.2 41.0 - - + +
58D ASN* 5.2 0.9 - - - +
91D GLN* 3.4 20.6 + - - +
95D ALA* 4.0 8.3 - - - -
99D LEU* 4.4 0.9 - - - +
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Residues in contact with ASN 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ARG* 2.5 33.6 + - - +
393C ARG* 2.9 46.0 + - - +
394C ALA* 3.1 5.4 + - - +
396C THR* 1.3 81.6 - - - +
398C ALA* 1.3 58.4 + - - +
399C ASP* 4.0 13.9 + - + +
455C LEU* 5.0 9.1 - - - +
54D LYS* 4.9 1.7 - - - +
58D ASN* 3.5 36.0 + - - +
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Residues in contact with ALA 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C MET* 5.8 1.4 - - - +
70C ASP* 4.5 3.8 - - - +
73C SER* 6.0 0.9 - - - +
74C ARG* 3.5 17.0 + - - +
394C ALA 2.9 4.6 + - - -
395C LYS* 3.0 14.3 + - - +
397C ASN* 1.3 81.7 - - - +
399C ASP* 1.3 59.3 + - - +
400C THR* 4.0 3.8 - - - -
91D GLN* 3.7 21.3 - - + +
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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