Contacts of the helix formed by residues 357 - 366 (chain A) in PDB entry 2DB3
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 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A TYR 3.5 14.1 - - - +
203A ILE* 3.1 36.1 + - - +
356A THR* 1.3 72.3 - - - +
358A PHE* 1.3 64.8 + - - +
359A ARG* 3.1 6.9 + - - -
360A HIS* 3.1 20.8 + - - +
361A GLN* 3.5 14.6 + - - +
378A ARG* 4.3 0.2 - - - -
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Residues in contact with PHE 358 (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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356A THR 3.2 4.9 + - - -
357A SER* 1.3 71.0 - - - +
359A ARG* 1.3 56.6 + - - +
361A GLN* 5.0 0.9 - - - -
362A ASN* 3.0 25.8 + - + +
378A ARG* 3.9 26.0 - - - +
381A ASP* 2.9 34.8 - - + -
382A PHE* 3.4 53.2 - + - -
385A ARG* 3.2 31.2 - - - +
387A PHE* 3.8 19.7 - + - -
6E U 4.8 0.2 - - - -
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Residues in contact with ARG 359 (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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357A SER* 3.0 6.2 - - - +
358A PHE* 1.3 78.7 - - - +
360A HIS* 1.3 61.4 + - - +
362A ASN* 3.8 6.1 + - - +
363A GLU* 2.9 43.1 + - + +
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Residues in contact with HIS 360 (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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203A ILE* 4.0 23.1 - - + +
204A PRO* 3.8 40.3 + - + +
206A GLU* 3.3 37.0 + - - -
357A SER* 3.1 22.2 + - - +
359A ARG* 1.3 80.4 - - - +
361A GLN* 1.3 66.7 + - + +
363A GLU* 3.5 17.0 + - - +
364A CYS* 3.0 36.5 + - - -
367A ARG* 5.2 0.7 - - - -
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Residues in contact with GLN 361 (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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204A PRO* 5.2 2.6 - - + +
351A ILE* 3.9 13.8 + - - +
352A VAL* 3.6 7.4 - - + +
353A TYR* 3.1 52.3 + - - +
356A THR* 2.9 27.8 + - - +
357A SER 3.5 9.0 + - - +
358A PHE 4.2 0.9 - - - +
359A ARG 3.2 0.4 - - - -
360A HIS* 1.3 86.3 - - + +
362A ASN* 1.3 66.4 + - - +
363A GLU 3.0 1.5 + - - -
364A CYS* 3.3 5.5 + - - +
365A ILE* 3.0 28.5 + - - +
378A ARG* 2.7 24.5 + - - +
382A PHE* 3.8 11.9 - - + -
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Residues in contact with ASN 362 (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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358A PHE* 3.0 26.2 + - + +
359A ARG* 3.8 6.0 + - - +
361A GLN* 1.3 75.9 - - - +
363A GLU* 1.3 68.8 + - - +
365A ILE* 3.7 0.7 - - - +
366A THR* 2.9 41.5 + - - +
382A PHE* 3.3 28.0 - - + -
387A PHE* 3.7 25.4 - - - +
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Residues in contact with GLU 363 (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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359A ARG* 2.9 30.4 + - + +
360A HIS* 3.5 20.4 + - - +
361A GLN 3.0 0.2 - - - -
362A ASN* 1.3 80.9 - - - +
364A CYS* 1.3 56.6 + - - +
365A ILE 2.7 12.0 + - - -
366A THR* 2.9 19.4 + - - +
367A ARG* 3.3 32.8 + - - +
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Residues in contact with CYS 364 (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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206A GLU* 3.5 20.4 - - - -
350A GLY* 5.8 4.6 - - - -
351A ILE 6.0 0.9 - - - +
360A HIS* 3.0 36.6 - - - +
361A GLN* 3.3 6.5 + - - +
363A GLU* 1.3 78.3 - - - +
365A ILE* 1.3 67.2 + - + +
367A ARG* 3.3 49.2 + - - +
368A GLY 4.8 0.3 - - - +
369A CYS* 3.7 9.7 - - - -
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Residues in contact with ILE 365 (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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316A LEU* 4.6 1.6 - - - +
317A GLY* 5.2 7.3 + - - -
350A GLY* 4.5 2.7 - - - -
351A ILE* 3.9 31.4 - - - +
352A VAL* 3.9 16.6 - - + -
361A GLN 3.0 19.5 + - - +
362A ASN* 3.7 7.2 - - - +
363A GLU 2.7 5.1 + - - -
364A CYS* 1.3 76.7 - - + +
366A THR* 1.3 59.8 + - + +
367A ARG 2.9 5.4 - - - -
368A GLY* 2.7 29.3 + - - -
369A CYS* 3.5 22.7 + - - -
372A VAL* 5.0 9.0 - - + -
382A PHE* 4.6 7.4 - - + -
387A PHE* 4.9 4.9 - - + +
388A ILE* 4.6 24.5 - - + -
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Residues in contact with THR 366 (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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316A LEU* 3.4 34.8 - - + +
362A ASN* 2.9 40.0 + - - +
363A GLU* 2.9 21.2 + - - +
365A ILE* 1.3 72.2 - - + +
367A ARG* 1.3 56.2 + - - +
368A GLY 3.1 5.4 - - - -
387A PHE* 5.5 6.3 - - + +
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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