Contacts of the helix formed by residues 387 - 393 (chain A) in PDB entry 1DT6
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 SER 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A SER* 4.5 2.4 + - - -
54A LEU* 5.3 7.3 - - - +
55A THR* 4.5 2.1 + - - -
76A VAL* 4.9 7.0 - - - +
77A LEU 3.0 12.7 + - - -
78A HIS* 3.6 28.0 + - - +
83A VAL* 4.5 2.7 - - - +
360A PRO 3.8 6.1 - - - -
361A THR* 4.9 4.9 - - - +
385A ILE* 4.0 1.8 + - - +
386A THR* 1.3 68.3 - - - +
388A LEU* 1.3 58.0 + - - +
389A THR* 3.1 17.1 - - - +
390A SER* 2.3 47.0 + - - -
391A VAL* 3.5 4.8 + - - +
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Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A VAL* 4.9 7.9 - - + -
87A LEU* 5.2 0.9 - - + -
357A ASP* 4.5 3.1 - - - +
359A LEU* 3.5 14.4 - - + +
360A PRO 2.8 9.4 + - - +
362A ASN* 3.5 44.2 - - + +
386A THR* 2.9 12.5 + - - +
387A SER* 1.3 67.9 - - - +
389A THR* 1.3 68.3 + - - +
390A SER 2.9 2.0 - - - -
391A VAL* 2.7 17.3 + - + +
392A LEU* 2.7 21.8 + - + +
423A MET* 3.6 45.8 - - + +
424A PRO* 4.6 3.8 - - + +
426A SER* 4.3 8.1 - - - +
501A HEM 4.4 11.7 - - + -
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Residues in contact with THR 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A SER* 2.7 32.9 + - - +
55A THR* 5.4 1.9 + - - +
357A ASP* 2.7 33.8 + - - -
360A PRO* 3.2 15.5 + - + +
387A SER* 3.1 20.6 - - - +
388A LEU* 1.3 76.4 - - - +
390A SER* 1.3 54.8 + - - +
392A LEU* 4.3 2.5 - - - -
393A HIS* 2.7 45.9 + - - +
402A LYS* 4.9 4.7 + - - -
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Residues in contact with SER 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A THR* 5.6 0.9 - - - -
78A HIS* 2.5 51.7 + - - -
80A TYR* 5.6 2.0 + - - +
387A SER* 2.3 35.1 + - - -
388A LEU 2.9 0.4 - - - -
389A THR* 1.3 83.8 - - - +
391A VAL* 1.3 60.6 + - - +
393A HIS* 4.1 1.4 - - - -
394A ASP* 3.5 21.0 + - - +
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Residues in contact with VAL 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A TYR* 3.6 32.1 - - + -
83A VAL* 4.3 15.0 - - + -
387A SER 4.0 6.1 - - - +
388A LEU* 2.7 17.5 + - - +
390A SER* 1.3 78.4 - - - +
392A LEU* 1.3 63.7 + - - +
393A HIS 3.2 1.8 - - - -
394A ASP* 3.2 17.9 + - - +
398A PHE* 3.9 0.5 - - - -
421A TYR* 3.4 42.0 - - + +
423A MET* 3.5 32.1 - - + -
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Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A GLN 4.0 6.7 - - - +
354A ARG* 2.8 61.2 + - + +
357A ASP* 3.6 30.1 - - - +
358A LEU 5.3 0.2 - - - +
388A LEU* 2.7 24.7 + - + +
389A THR* 3.9 2.9 - - - +
391A VAL* 1.3 72.7 - - - +
393A HIS* 1.3 62.9 + - + +
398A PHE* 3.4 5.5 - - - -
421A TYR 3.5 7.6 - - - +
422A PHE* 4.4 1.8 - - - -
423A MET* 3.5 34.3 - - + +
424A PRO* 3.6 25.4 - - + -
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Residues in contact with HIS 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A ARG* 3.2 28.3 + - - -
355A PHE* 3.3 21.7 + + - -
357A ASP* 3.8 15.0 - - + +
389A THR* 2.7 24.0 + - - +
390A SER* 4.1 3.8 - - - -
392A LEU* 1.3 89.3 - - + +
394A ASP* 1.3 63.8 + - - -
395A GLU* 3.2 4.9 + - - +
401A PRO* 3.1 28.2 + - + +
402A LYS* 2.8 44.3 + - + +
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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