Contacts of the helix formed by residues 379 - 384 (chain D) in PDB entry 2IB8
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 GLY 379 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218D SER* 3.4 7.5 + - - -
351D GLU* 5.6 1.1 - - - -
354D GLU* 3.1 17.5 + - - -
375D ASN* 5.3 1.1 - - - -
378D GLY* 1.3 73.7 - - - -
380D ALA* 1.3 54.3 + - - -
382D SER* 3.0 7.0 + - - -
383D LEU* 2.7 38.6 + - - +
393D ARG* 3.8 16.6 - - - -
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Residues in contact with ALA 380 (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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284D SER* 3.6 10.1 - - - -
285D THR 4.2 0.2 + - - -
353D ASN* 3.8 19.5 - - - +
354D GLU* 3.4 29.4 + - - +
379D GLY* 1.3 70.3 - - - -
381D VAL* 1.3 59.7 + - - +
384D GLY* 3.0 42.8 + - - +
385D HIS* 4.1 16.2 - - + +
390D SER* 5.1 0.9 - - - +
393D ARG* 3.7 7.5 - - - +
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Residues in contact with VAL 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D TYR* 5.3 0.2 - - + -
215D ALA* 4.0 16.2 - - - -
218D SER* 4.3 4.7 - - - +
219D TYR* 3.5 8.5 + - + -
255D GLU* 5.2 0.9 - - - +
281D ALA 3.7 20.4 - - - +
282D ASN 3.4 20.9 - - - +
283D ALA 3.8 8.7 - - - +
284D SER* 4.1 4.8 - - - +
285D THR* 5.1 2.9 + - - +
354D GLU* 3.1 34.4 + - + +
357D SER* 3.7 25.6 - - - +
380D ALA* 1.3 79.8 - - - +
382D SER* 1.3 58.7 + - - +
384D GLY 4.9 0.2 + - - -
3004D K 2.8 24.8 - - - -
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Residues in contact with SER 382 (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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218D SER* 2.7 22.9 + - - -
219D TYR* 3.5 41.1 - - - -
222D SER* 2.6 27.4 + - - -
255D GLU* 3.3 9.5 - - - +
256D TYR* 3.1 28.9 + - - -
379D GLY 3.0 1.8 + - - -
381D VAL* 1.3 80.0 - - - +
383D LEU* 1.3 60.2 + - - +
384D GLY 3.4 1.6 - - - -
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Residues in contact with LEU 383 (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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49D ARG* 4.5 6.7 - - - +
52D ILE* 3.2 35.6 - - + +
222D SER* 3.4 30.1 - - - +
226D TRP* 4.1 12.3 - - + +
231D PHE* 4.8 5.8 - - + -
253D ASP* 3.7 29.9 - - + +
255D GLU* 3.7 11.9 + - - +
256D TYR* 4.4 4.5 - - + +
377D ASN 4.3 6.7 - - - +
378D GLY 4.2 4.7 - - - -
379D GLY 2.7 33.3 + - - +
382D SER* 1.3 74.1 - - - +
384D GLY* 1.3 59.2 + - - +
393D ARG* 3.8 26.5 - - - +
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Residues in contact with GLY 384 (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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52D ILE* 4.1 6.2 - - - +
255D GLU* 4.2 1.2 - - - +
285D THR* 3.4 8.7 - - - -
287D ASN* 3.0 20.6 - - - -
380D ALA* 3.0 28.8 + - - +
382D SER 3.4 2.2 - - - -
383D LEU* 1.3 82.0 - - - +
385D HIS* 1.3 60.3 + - - -
386D PRO* 3.7 9.8 - - - +
390D SER* 4.4 2.1 + - - -
393D ARG* 5.0 2.6 + - - -
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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