Contacts of the helix formed by residues 391 - 398 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99C LEU* 5.3 0.2 - - - -
386D PHE* 4.2 8.7 - - + -
387D PRO 3.7 0.6 + - - -
388D PHE* 2.8 25.5 + - + +
390D ALA* 1.3 78.8 - - - +
392D SER* 1.3 60.2 + - - +
393D ARG* 3.0 13.0 + - - +
394D ALA* 2.7 30.8 + - + -
395D LYS* 3.0 28.3 + - - +
454D THR 3.0 23.8 + - - -
455D LEU* 3.5 11.5 + - - +
457D GLU* 3.6 9.9 + - - +
458D ALA* 3.6 19.3 - - + +
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Residues in contact with SER 392 (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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19C TYR* 5.6 1.7 + - - -
51C ILE* 4.0 9.4 - - - +
99C LEU* 3.5 30.1 - - - +
390D ALA 3.8 4.0 + - - -
391D ASN* 1.3 71.7 - - - +
393D ARG* 1.3 64.9 + - - +
395D LYS* 3.3 2.0 + - - +
396D THR* 2.8 31.4 + - - -
452D HIS* 3.7 31.1 - - - -
453D PRO* 4.1 2.5 - - - -
457D GLU* 4.9 1.3 + - - -
473D ASN* 6.1 0.7 - - - -
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Residues in contact with ARG 393 (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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54C LYS* 4.8 9.7 + - - +
58C ASN* 5.6 4.4 - - - +
359C TYR* 3.7 27.1 - - - +
363C GLU* 3.2 28.7 + - - -
424C GLY* 6.3 0.2 - - - -
426C GLY* 5.2 3.0 - - - -
427C GLU* 3.3 24.0 + - - +
391D ASN* 3.0 9.8 + - - +
392D SER* 1.3 77.1 - - - +
394D ALA* 1.3 63.1 + - - +
396D THR* 4.0 4.6 - - - -
397D ASN* 3.1 51.6 + - - +
453D PRO* 3.6 24.1 + - - +
454D THR* 3.7 19.7 - - - +
455D LEU* 3.6 25.9 - - + +
457D GLU* 5.2 0.2 + - - -
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Residues in contact with ALA 394 (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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388D PHE* 3.3 31.6 - - + +
391D ASN* 2.7 18.5 + - + +
393D ARG* 1.3 72.6 - - - +
395D LYS* 1.3 57.1 + - - +
397D ASN* 3.3 5.2 + - - +
398D ALA 2.8 23.0 + - - -
399D ASP* 3.0 29.8 + - - +
400D THR* 3.7 3.8 - - + -
423D PRO* 4.4 0.4 - - + -
455D LEU* 3.6 16.5 - - + +
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Residues in contact with LYS 395 (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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91C GLN* 4.6 0.3 + - - -
94C THR* 6.1 2.9 - - - +
95C ALA* 4.2 15.4 - - - +
98C ALA* 3.5 28.0 - - - +
99C LEU* 3.5 33.9 - - + -
389D ALA* 4.6 13.3 + - - +
391D ASN 3.0 16.6 + - - +
392D SER 3.6 4.3 - - - +
394D ALA* 1.3 74.9 - - - +
396D THR* 1.3 61.8 + - - +
398D ALA* 2.8 22.0 + - - +
400D THR* 3.7 21.2 + - + +
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Residues in contact with THR 396 (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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51C ILE* 3.1 53.0 - - + +
54C LYS* 3.9 10.5 - - + -
55C ALA* 3.2 29.5 - - + +
58C ASN* 5.1 0.5 - - - +
91C GLN* 3.3 23.9 + - - +
95C ALA* 4.0 9.9 - - + -
99C LEU* 4.3 1.4 - - - +
74D ARG* 5.0 0.9 + - - -
392D SER 2.8 18.3 + - - -
393D ARG* 4.0 5.8 - - - -
395D LYS* 1.3 76.4 - - - +
397D ASN* 1.3 58.6 + - - +
453D PRO* 5.6 0.7 - - - +
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Residues in contact with ASN 397 (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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54C LYS* 4.7 4.3 - - - +
58C ASN* 3.3 37.8 + - - +
74D ARG* 2.8 28.9 + - - +
393D ARG* 3.1 51.7 + - - +
394D ALA* 3.6 6.1 - - - +
396D THR* 1.3 78.1 - - - +
398D ALA* 1.3 62.4 + - - +
399D ASP* 3.4 12.6 + - + +
455D LEU* 5.3 5.3 - - - +
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Residues in contact with ALA 398 (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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91C GLN* 3.8 22.0 - - + +
70D ASP* 4.7 5.5 - - - +
74D ARG* 4.0 12.0 + - - +
394D ALA 2.8 2.0 + - - -
395D LYS* 2.8 17.3 + - - +
397D ASN* 1.3 81.8 - - - +
399D ASP* 1.3 58.7 + - - +
400D THR* 3.8 6.0 + - - +
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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