Contacts of the helix formed by residues 380 - 389 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G TRP* 4.1 2.8 + - - -
154G PHE* 3.7 33.5 - - - -
195G GLN* 3.6 11.2 - - - +
196G ILE 5.7 0.4 - - - -
197G ARG* 5.2 4.3 - - - -
379H PHE* 1.3 74.7 - - - +
381H LEU* 1.3 65.8 + - - +
382H GLU* 3.4 16.7 + - - +
383H GLU* 3.1 30.3 + - - +
384H VAL* 2.9 24.5 + - - +
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Residues in contact with LEU 381 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G TYR* 5.5 4.3 - - - +
195G GLN* 4.0 6.2 + - - +
197G ARG* 3.6 39.4 - - - +
214G ILE* 4.6 4.3 - - + -
253G PRO* 4.9 2.2 - - + -
255G ASN* 4.7 3.4 - - - +
314G ASP* 5.1 5.2 - - + +
316G PHE* 3.9 17.6 - - + -
317G LYS* 4.3 31.2 - - + -
360H CYS* 4.3 15.5 - - - -
365H ILE* 3.7 23.6 - - + -
380H SER* 1.3 73.4 - - - +
382H GLU* 1.3 59.5 + - - +
384H VAL* 3.1 9.9 - - + +
385H LEU* 2.8 35.1 + - - +
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Residues in contact with GLU 382 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G TYR* 4.4 20.5 + - - -
15G SER* 6.0 1.6 - - - -
31G TRP* 3.9 16.8 + - + -
60G LEU* 5.4 2.5 - - + +
105G CYS* 6.4 0.4 - - + -
120G TRP* 3.2 28.5 - - + +
154G PHE 5.7 4.3 - - - +
197G ARG* 2.9 34.2 + - - +
380H SER* 3.4 14.1 - - - +
381H LEU* 1.3 77.3 - - - +
383H GLU* 1.3 60.7 + - - +
385H LEU* 3.2 7.5 + - - +
386H ALA* 2.8 28.9 + - - +
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Residues in contact with GLU 383 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G TRP* 3.7 33.4 - - + +
152G LYS* 2.4 28.9 + - - +
154G PHE* 2.9 31.9 - - - -
379H PHE* 3.4 9.6 - - + -
380H SER* 3.1 25.6 + - - +
382H GLU* 1.3 77.0 - - - +
384H VAL* 1.3 64.1 + - - +
386H ALA* 2.8 14.5 + - - +
387H ILE* 3.0 19.7 + - - +
392H TYR* 2.4 37.1 + - + -
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Residues in contact with VAL 384 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316G PHE* 5.0 9.9 - - + -
317G LYS* 6.0 0.2 - - - -
322G ILE* 4.4 9.7 - - + +
364H LEU* 4.0 50.0 - - + +
365H ILE* 4.2 9.6 - - + -
379H PHE* 4.1 9.0 - - + -
380H SER 2.9 24.8 + - - +
381H LEU* 3.1 12.6 - - + +
383H GLU* 1.3 76.9 - - - +
385H LEU* 1.3 58.0 + - - +
387H ILE* 3.3 11.8 + - - +
388H SER* 3.0 25.3 + - - -
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Residues in contact with LEU 385 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G TYR* 4.8 11.0 - - + -
31G TRP* 3.6 42.6 - - + +
316G PHE* 3.7 34.5 - - + -
326G ILE* 5.0 9.0 - - + -
328G LEU* 5.8 2.2 - - + -
381H LEU 2.8 19.2 + - - +
382H GLU* 3.2 5.4 + - - +
384H VAL* 1.3 71.9 - - - +
386H ALA* 1.3 64.3 + - - +
387H ILE 3.3 0.2 - - - -
388H SER* 3.7 17.5 - - - +
389H ARG* 3.5 43.3 + - + +
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Residues in contact with ALA 386 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G TRP* 4.1 9.2 - - - -
77G VAL* 4.1 11.4 - - + -
120G TRP* 4.0 10.3 - - + -
382H GLU 2.8 12.7 + - - +
383H GLU 2.8 9.8 + - - +
385H LEU* 1.3 77.9 - - - +
387H ILE* 1.3 52.9 + - - +
389H ARG* 2.5 23.8 - - - +
391H VAL* 3.0 19.6 + - - -
392H TYR* 3.2 30.8 + - + +
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Residues in contact with ILE 387 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322G ILE* 3.8 24.8 - - + +
379H PHE* 4.2 20.6 - - + -
383H GLU 3.1 19.1 - - - +
384H VAL* 3.6 9.9 - - - +
386H ALA* 1.3 74.0 - - - +
388H SER* 1.3 57.1 + - - +
389H ARG 2.4 19.2 - - - +
390H ASN* 4.5 6.5 - - - +
392H TYR* 3.5 37.7 - - + -
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Residues in contact with SER 388 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316G PHE* 6.2 1.8 - - - -
322G ILE* 3.5 32.3 + - - +
323G ASP* 5.5 1.9 - - - -
324G GLN 4.8 0.9 + - - -
326G ILE* 3.3 27.4 - - - +
384H VAL* 3.0 18.1 + - - -
385H LEU* 3.6 20.4 - - - -
387H ILE* 1.3 76.3 - - - +
389H ARG* 1.3 59.6 + - - +
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Residues in contact with ARG 389 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ASP* 3.2 36.4 + - - -
13G TYR* 5.2 2.2 - - - +
31G TRP* 3.7 39.4 + - - +
58G PRO* 4.8 4.4 - - - +
326G ILE* 5.9 4.1 - - + +
328G LEU* 5.0 12.5 - - - +
385H LEU* 3.5 33.4 + - + +
386H ALA* 2.5 20.6 + - - +
387H ILE* 2.4 18.2 - - - +
388H SER* 1.3 79.1 - - - +
390H ASN* 1.3 58.9 + - - +
391H VAL* 3.3 13.0 - - + -
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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