Contacts of the helix formed by residues 380 - 389 (chain D) in PDB entry 2I3T
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 380 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C TRP* 4.2 4.0 + - - -
154C PHE* 3.7 33.3 - - - +
195C GLN* 3.4 13.2 - - - +
196C ILE 5.4 0.7 - - - -
197C ARG* 5.0 4.7 - - - -
379D PHE* 1.3 75.6 - - - +
381D LEU* 1.3 71.2 + - - +
382D GLU* 3.1 14.6 + - - +
383D GLU* 2.7 34.3 + - - +
384D VAL* 2.9 17.9 + - - +
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Residues in contact with LEU 381 (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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13C TYR* 5.2 4.0 - - - +
195C GLN* 3.9 6.5 + - - +
197C ARG* 3.6 36.2 - - - +
214C ILE* 4.9 3.1 - - + -
253C PRO* 4.9 2.9 - - + -
255C ASN* 4.4 5.4 - - - +
314C ASP* 4.6 8.7 - - + +
316C PHE* 4.2 15.3 - - + -
317C LYS* 3.5 44.4 - - + -
360D CYS* 4.0 21.1 - - - -
364D LEU* 6.4 0.4 - - + -
365D ILE* 4.2 9.2 - - + -
379D PHE 3.9 0.6 + - - -
380D SER* 1.3 69.9 - - - +
382D GLU* 1.3 71.6 + - - +
384D VAL* 2.9 13.2 + - + +
385D LEU* 2.8 22.2 + - - +
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Residues in contact with GLU 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C TYR* 4.0 22.0 + - - -
15C SER* 5.9 3.5 - - - -
31C TRP* 3.6 17.9 + - + -
60C LEU* 5.6 2.1 - - + +
105C CYS* 6.5 0.2 - - + -
106C ARG* 5.8 4.3 + - - +
120C TRP* 3.6 21.8 - - + +
154C PHE* 5.6 6.1 - - + +
197C ARG* 2.8 33.0 + - - +
298C VAL* 5.4 1.7 - - - +
316C PHE* 5.8 0.8 - - - -
380D SER* 4.0 14.1 - - - +
381D LEU* 1.3 76.2 - - - +
383D GLU* 1.3 63.0 + - - +
385D LEU* 3.0 20.2 + - - +
386D ALA 3.0 9.4 + - - -
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Residues in contact with GLU 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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120C TRP* 3.5 31.0 - - + +
152C LYS* 3.1 17.7 + - - +
154C PHE* 3.0 24.7 - - - -
379D PHE* 3.5 11.4 - - + -
380D SER* 2.7 36.6 + - - +
382D GLU* 1.3 76.4 - - - +
384D VAL* 1.3 61.0 + - - +
386D ALA* 2.8 3.6 + - - +
387D ILE* 2.8 33.8 + - - +
392D TYR* 3.1 40.3 + - + -
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Residues in contact with VAL 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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316C PHE* 5.1 9.6 - - + -
322C ILE* 4.6 8.4 - - + +
364D LEU* 4.0 45.1 - - + +
365D ILE* 4.6 2.0 - - + -
379D PHE* 3.5 28.3 - - + +
380D SER 2.9 15.3 + - - +
381D LEU* 2.9 16.2 + - + +
383D GLU* 1.3 77.2 - - - +
385D LEU* 1.3 51.7 + - - +
387D ILE* 3.4 11.6 + - + +
388D SER* 2.7 32.8 + - - -
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Residues in contact with LEU 385 (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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13C TYR* 4.3 16.6 - - + -
31C TRP* 3.8 32.1 - - + +
316C PHE* 3.8 37.9 - - + -
326C ILE* 5.5 4.7 - - + -
328C LEU* 6.0 3.8 - - + -
381D LEU 2.8 10.1 + - - +
382D GLU* 3.0 11.4 + - - +
384D VAL* 1.3 75.1 - - - +
386D ALA* 1.3 67.3 + - - +
387D ILE 3.0 1.3 - - - -
388D SER* 2.9 11.3 + - - +
389D ARG* 2.8 57.1 + - + +
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Residues in contact with ALA 386 (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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31C TRP* 3.6 14.8 - - + -
77C VAL* 3.6 28.3 - - + -
120C TRP* 4.0 2.9 - - + -
382D GLU 3.0 6.5 + - - +
383D GLU* 2.8 16.1 + - - +
385D LEU* 1.3 77.0 - - - +
387D ILE* 1.3 61.5 + - - +
389D ARG 3.2 6.1 - - - +
391D VAL* 3.0 29.4 + - - +
392D TYR* 3.9 19.1 - - - +
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Residues in contact with ILE 387 (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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322C ILE* 3.9 25.2 - - + +
379D PHE* 3.8 31.9 - - + -
383D GLU 2.8 16.4 + - - +
384D VAL* 3.4 13.9 - - + +
386D ALA* 1.3 73.1 - - - +
388D SER* 1.3 55.1 + - - +
389D ARG 2.1 25.6 - - - +
390D ASN* 4.3 4.6 + - - +
391D VAL 5.2 0.2 - - - +
392D TYR* 3.3 35.4 - - + +
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Residues in contact with SER 388 (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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316C PHE* 5.9 4.3 - - - -
322C ILE* 3.6 34.0 + - - +
323C ASP* 5.4 2.1 - - - -
324C GLN 5.1 0.3 + - - -
326C ILE* 3.2 30.5 - - - +
384D VAL* 2.7 21.3 + - - -
385D LEU* 2.9 15.6 + - - +
387D ILE* 1.3 67.9 - - - +
389D ARG* 1.3 69.9 + - - +
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Residues in contact with ARG 389 (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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12C ASP* 2.5 43.6 + - - -
13C TYR* 4.7 4.2 - - - +
31C TRP* 3.5 35.1 + - - +
58C PRO* 4.9 4.6 - - - +
326C ILE* 5.7 3.7 - - + +
328C LEU* 5.3 10.7 - - - +
385D LEU* 2.8 37.6 + - + +
386D ALA 3.3 6.5 - - - +
387D ILE 2.1 30.7 - - - +
388D SER* 1.3 78.2 - - - +
390D ASN* 1.3 64.9 + - - +
391D VAL* 4.5 9.4 - - + -
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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