Contacts of the helix formed by residues 391 - 398 (chain H) in PDB entry 1ZMD
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G LEU* 5.3 0.4 - - - -
386H PHE* 3.8 9.8 - - + -
387H PRO 3.7 1.2 + - - -
388H PHE* 3.0 31.0 + - + +
390H ALA* 1.3 77.1 - - - +
392H SER* 1.3 66.9 + - - +
393H ARG* 3.1 6.6 + - - +
394H ALA* 2.9 25.7 + - + -
395H LYS* 3.1 26.0 + - - +
454H THR 3.0 22.0 + - - -
455H LEU* 3.4 16.6 + - - +
457H GLU* 3.7 8.3 + - - +
458H ALA* 3.5 21.3 - - + +
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Residues in contact with SER 392 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G TYR* 5.7 1.0 + - - -
46G LEU* 5.3 3.8 - - - +
51G ILE* 4.2 9.9 - - - +
99G LEU* 4.2 21.7 - - - +
390H ALA 3.8 4.1 + - - -
391H ASN* 1.3 75.2 - - - +
393H ARG* 1.3 54.1 + - - +
395H LYS* 3.9 1.6 - - - +
396H THR* 2.6 37.7 + - - -
452H HIS* 3.6 31.2 + - - -
453H PRO* 3.9 9.6 - - - -
457H GLU* 4.9 2.2 - - - -
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Residues in contact with ARG 393 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G LYS* 5.5 6.1 - - + +
359G TYR* 3.8 27.6 - - - +
363G GLU* 2.8 31.9 + - - -
427G GLU* 3.0 37.9 + - - +
391H ASN* 3.1 10.3 + - - +
392H SER* 1.3 75.6 - - - +
394H ALA* 1.3 61.3 + - - +
396H THR* 3.4 5.6 + - - -
397H ASN* 3.0 56.9 + - - +
453H PRO* 3.3 25.3 + - + +
454H THR* 3.6 17.3 + - - +
455H LEU* 3.9 6.3 - - + +
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Residues in contact with ALA 394 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388H PHE* 3.4 32.5 - - + +
391H ASN* 2.9 16.3 + - + +
393H ARG* 1.3 76.1 - - - +
395H LYS* 1.3 57.8 + - - +
397H ASN* 3.3 5.4 + - - +
398H ALA 2.9 21.8 + - - -
399H ASP 2.9 31.4 + - - +
400H THR* 3.7 2.2 - - + -
423H PRO* 4.3 0.9 - - + -
455H LEU* 3.7 14.5 - - + +
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Residues in contact with LYS 395 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G GLN* 4.7 0.3 + - - -
95G ALA* 3.9 13.6 - - - +
98G ALA* 3.6 28.4 - - + +
99G LEU* 3.8 29.2 - - + -
389H ALA* 4.2 14.8 - - - +
391H ASN 3.1 16.7 + - - +
392H SER 3.9 2.9 - - - +
394H ALA* 1.3 77.4 - - - +
396H THR* 1.3 64.7 + - - +
398H ALA* 3.1 14.3 + - - +
400H THR* 3.7 22.9 + - + +
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Residues in contact with THR 396 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51G ILE* 3.2 48.4 - - + +
54G LYS* 3.9 12.9 - - + +
55G ALA* 3.3 28.3 - - + +
58G ASN* 5.2 0.5 - - - +
59G ASN* 5.6 0.2 - - - +
91G GLN* 3.1 26.7 + - - +
95G ALA* 4.0 8.2 - - + +
99G LEU* 4.1 1.4 - - - +
74H ARG* 5.0 0.5 + - - -
392H SER 2.6 24.4 + - - -
393H ARG* 3.8 7.1 - - - -
394H ALA 3.3 0.2 - - - -
395H LYS* 1.3 75.7 - - - +
397H ASN* 1.3 60.2 + - - +
453H PRO* 5.5 1.1 - - - +
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Residues in contact with ASN 397 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G LYS* 5.0 2.6 - - - +
58G ASN* 3.5 35.8 + - - +
74H ARG* 2.7 33.9 + - - -
393H ARG* 3.0 48.6 + - - +
394H ALA* 3.6 8.3 - - - +
396H THR* 1.3 76.7 - - - +
398H ALA* 1.3 58.2 + - - +
399H ASP* 4.2 11.8 - - + +
423H PRO* 6.1 2.0 - - - +
455H LEU* 4.8 9.1 - - - +
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Residues in contact with ALA 398 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G GLN* 3.7 22.2 - - + +
70H ASP* 4.7 3.6 - - - +
73H SER* 6.0 1.1 - - - +
74H ARG* 4.0 12.4 + - - +
394H ALA 2.9 5.4 + - - -
395H LYS* 3.1 14.1 + - - +
396H THR 3.1 0.2 - - - -
397H ASN* 1.3 81.8 - - - +
399H ASP* 1.3 57.7 + - - +
400H THR* 4.0 5.2 - - - -
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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