Contacts of the helix formed by residues 357 - 367 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202D TYR* 2.7 10.9 - - - +
203D ILE* 3.4 34.4 - - - +
356D THR* 1.3 72.0 - - - +
358D PHE* 1.3 65.5 + - - +
359D ARG* 3.7 7.8 + - - +
360D HIS* 3.2 19.4 + - - +
361D GLN* 3.0 21.8 + - - +
378D ARG* 3.5 0.4 - - - -
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Residues in contact with PHE 358 (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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356D THR 3.1 6.5 + - - -
357D SER* 1.3 70.8 + - - +
359D ARG* 1.3 74.8 + - + +
361D GLN* 3.0 6.0 + - - +
362D ASN* 2.9 25.6 + - + -
378D ARG* 3.5 20.0 - - - +
381D ASP* 3.2 29.2 - - - -
382D PHE* 3.1 52.4 - + - -
385D ARG* 3.5 22.7 - - + -
387D PHE* 3.7 30.1 - + - -
7H U 5.8 5.4 - - - -
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Residues in contact with ARG 359 (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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357D SER* 3.2 7.3 + - - +
358D PHE* 1.3 86.0 - - + +
360D HIS* 1.3 62.7 + - - +
362D ASN* 2.9 39.9 + - - +
363D GLU* 3.2 29.6 + - - +
387D PHE* 5.6 1.0 - - - -
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Residues in contact with HIS 360 (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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203D ILE* 4.0 40.0 - - + +
204D PRO* 4.4 13.2 + - + +
206D GLU* 3.8 26.2 - - + +
357D SER* 3.0 26.5 + - - +
359D ARG* 1.3 80.8 - - - +
361D GLN* 1.3 68.4 + - + +
363D GLU* 3.4 11.7 + - - +
364D CYS* 3.2 47.8 + - - -
367D ARG* 4.6 2.2 - - - -
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Residues in contact with GLN 361 (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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204D PRO* 6.1 1.0 - - + +
351D ILE* 3.8 11.7 + - - +
352D VAL* 3.4 12.0 - - + +
353D TYR* 3.0 43.3 + - - +
356D THR* 2.9 26.1 + - - +
357D SER 3.0 10.2 + - - +
358D PHE 3.0 7.8 + - - +
360D HIS* 1.3 81.5 - - + +
362D ASN* 1.3 65.8 + - - +
364D CYS* 3.3 8.4 + - - +
365D ILE* 3.1 26.6 + - + +
378D ARG* 2.9 32.6 + - - +
382D PHE* 3.8 10.7 - - + -
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Residues in contact with ASN 362 (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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358D PHE* 2.9 15.0 + - + +
359D ARG* 2.9 33.8 - - - +
360D HIS 3.2 0.2 - - - -
361D GLN* 1.3 77.8 - - - +
363D GLU* 1.3 52.2 + - - +
365D ILE* 3.2 9.0 + - - +
366D THR* 2.6 41.8 + - - -
382D PHE* 3.8 23.1 - - + -
387D PHE* 4.0 30.9 - - - +
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Residues in contact with GLU 363 (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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359D ARG* 3.2 21.9 + - - +
360D HIS* 3.5 19.6 + - - +
361D GLN 3.3 0.2 - - - -
362D ASN* 1.3 79.0 - - - +
364D CYS* 1.3 63.0 + - - +
366D THR* 3.4 15.3 + - - -
367D ARG* 2.4 51.0 + - - +
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Residues in contact with CYS 364 (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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206D GLU* 4.4 4.7 - - - -
351D ILE 5.9 2.2 - - - +
360D HIS* 3.2 42.3 + - - -
361D GLN* 3.6 9.4 - - - +
362D ASN 3.2 0.4 - - - -
363D GLU* 1.3 81.1 - - - +
365D ILE* 1.3 63.8 + - + +
367D ARG* 3.4 55.7 + - - +
368D GLY 4.3 4.2 + - - +
369D CYS* 5.4 1.0 - - - +
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Residues in contact with ILE 365 (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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317D GLY* 4.7 19.1 + - - -
319D PRO* 6.3 0.9 - - + -
350D GLY* 4.9 2.0 - - - -
351D ILE 4.5 15.0 - - - +
352D VAL* 4.3 21.5 - - + -
361D GLN 3.1 18.4 + - - +
362D ASN* 3.2 11.4 + - - +
364D CYS* 1.3 75.8 - - + +
366D THR* 1.3 60.8 + - - +
367D ARG 3.2 0.7 - - - -
368D GLY* 3.0 22.0 + - - -
369D CYS* 4.1 23.5 + - - -
372D VAL* 4.7 7.9 - - + -
382D PHE* 4.7 7.0 - - + -
387D PHE 5.3 1.6 - - - +
388D ILE* 3.8 37.7 - - + -
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Residues in contact with THR 366 (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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316D LEU* 3.3 36.1 - - + +
362D ASN* 2.6 32.3 + - - -
363D GLU* 3.6 11.2 - - - -
364D CYS 3.2 0.4 - - - -
365D ILE* 1.3 73.0 - - - +
367D ARG* 1.3 57.1 + - - +
368D GLY* 2.6 12.3 + - - -
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Residues in contact with ARG 367 (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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206D GLU* 2.8 40.6 + - - -
348D LYS* 3.3 21.6 - - + +
360D HIS* 4.6 0.8 - - - -
363D GLU* 2.4 45.7 + - - +
364D CYS* 3.4 32.6 - - - +
365D ILE 3.2 0.2 - - - -
366D THR* 1.3 77.3 - - - +
368D GLY* 1.3 63.1 + - - +
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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