Contacts of the helix formed by residues 380 - 400 (chain H) in PDB entry 2R9R
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 THR 380 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345H ALA 3.3 16.1 + - - +
346H GLU* 2.6 22.9 + - - +
349H GLU* 3.4 42.6 - - + +
379H THR* 1.3 82.4 - - - +
381H ILE* 1.3 66.0 + - - +
382H GLY* 3.5 2.8 + - - -
383H GLY 2.9 13.7 + - - -
384H LYS* 3.1 28.1 + - - +
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Residues in contact with ILE 381 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380H THR* 1.3 71.8 - - - +
382H GLY* 1.3 68.0 + - - +
384H LYS* 3.2 9.3 + - + +
385H ILE* 3.1 39.0 + - + +
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Residues in contact with GLY 382 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345H ALA* 3.9 13.5 - - - -
380H THR* 3.3 4.5 + - - -
381H ILE* 1.3 81.9 - - - +
383H GLY* 1.3 60.7 + - - +
385H ILE* 3.1 10.9 + - - +
386H VAL* 3.0 26.4 + - - +
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Residues in contact with GLY 383 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342H VAL* 4.2 8.2 - - - +
345H ALA* 3.7 12.0 - - - +
346H GLU* 3.4 20.0 - - - -
378H PRO* 3.5 18.5 - - - +
380H THR* 2.9 10.5 + - - -
382H GLY* 1.3 76.3 - - - +
384H LYS* 1.3 57.6 + - - +
386H VAL* 3.4 4.3 + - - +
387H GLY* 2.8 23.4 + - - -
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Residues in contact with LYS 384 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378H PRO* 3.7 33.0 - - + +
379H THR* 4.0 16.0 + - - +
380H THR 3.1 17.3 + - - +
381H ILE* 3.2 8.2 + - + +
383H GLY* 1.3 75.8 - - - +
385H ILE* 1.3 61.8 + - + +
387H GLY* 3.7 1.5 - - - +
388H SER* 2.8 30.5 + - - -
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Residues in contact with ILE 385 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381H ILE* 3.1 31.9 + - + +
382H GLY* 3.6 9.6 - - - +
384H LYS* 1.3 75.8 - - + +
386H VAL* 1.3 69.0 + - + +
388H SER* 3.2 7.0 + - - -
389H LEU* 3.1 42.1 + - + +
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Residues in contact with VAL 386 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338H PHE* 3.9 21.4 - - + +
341H ALA* 3.8 31.4 - - + +
342H VAL* 3.8 24.7 - - + +
345H ALA* 4.6 2.5 - - + -
363H TRP* 4.3 3.8 - - + -
382H GLY 3.0 17.4 + - - +
383H GLY* 3.5 9.6 - - - +
385H ILE* 1.3 80.0 - - + +
387H GLY* 1.3 57.6 + - - +
389H LEU* 3.3 12.1 + - + +
390H CYS* 2.8 26.3 + - - +
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Residues in contact with GLY 387 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363H TRP* 3.6 27.8 - - - -
367H SER* 5.4 1.7 - - - -
378H PRO* 5.1 2.9 - - - -
383H GLY 2.8 15.5 + - - -
384H LYS* 4.0 2.9 - - - -
385H ILE 3.2 0.2 - - - -
386H VAL* 1.3 78.9 - - - +
388H SER* 1.3 60.6 + - - +
390H CYS* 3.2 3.2 + - - +
391H ALA* 3.0 22.3 + - - +
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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
----------------------------------------------------------
384H LYS 2.8 18.8 + - - -
385H ILE* 3.2 10.8 + - - -
387H GLY* 1.3 74.9 - - - +
389H LEU* 1.3 66.5 + - - +
391H ALA* 3.1 16.0 + - - +
392H ILE* 3.2 23.8 + - - +
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Residues in contact with LEU 389 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338H PHE* 3.9 15.9 - - + -
385H ILE* 3.1 29.1 + - + +
386H VAL* 3.5 10.5 - - + +
388H SER* 1.3 80.9 - - - +
390H CYS* 1.3 58.5 + - - +
391H ALA 3.2 0.3 + - - -
392H ILE* 3.2 14.1 + - + +
393H ALA* 2.8 32.7 + - - +
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Residues in contact with CYS 390 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338H PHE* 3.7 36.3 - - + -
363H TRP* 3.9 12.6 - - + -
364H ALA* 4.1 5.4 - - - -
367H SER* 3.9 18.8 - - - -
368H MET* 3.5 27.2 - - - +
386H VAL 2.8 15.0 + - - +
387H GLY* 3.2 14.6 - - - +
388H SER 3.1 0.2 - - - -
389H LEU* 1.3 77.8 - - - +
391H ALA* 1.3 56.9 + - - +
393H ALA* 3.8 1.2 - - - +
394H GLY 3.0 22.0 + - - -
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Residues in contact with ALA 391 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367H SER* 4.2 19.4 - - - +
368H MET 4.7 1.2 - - - +
370H THR* 4.9 5.1 - - + +
387H GLY 3.0 10.6 + - - +
388H SER* 3.1 10.9 + - - +
390H CYS* 1.3 74.1 - - - +
392H ILE* 1.3 68.0 + - + +
394H GLY* 3.0 10.9 + - - -
395H VAL* 3.2 19.3 + - + +
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Residues in contact with ILE 392 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388H SER* 3.2 21.1 + - - +
389H LEU* 3.7 16.2 - - + +
391H ALA* 1.3 77.2 - - + +
393H ALA* 1.3 64.0 + - - +
394H GLY 3.2 0.5 + - - -
395H VAL* 3.2 17.3 + - + +
396H LEU* 3.3 30.4 + - + +
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Residues in contact with ALA 393 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338H PHE* 3.7 30.1 - - + -
368H MET* 4.2 3.6 - - + -
389H LEU 2.8 22.1 + - - +
390H CYS 3.8 0.7 - - - +
392H ILE* 1.3 73.5 - - - +
394H GLY* 1.3 57.1 + - - +
396H LEU* 4.1 8.2 - - - +
397H THR* 2.7 34.9 + - - +
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Residues in contact with GLY 394 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331H LEU* 5.7 0.2 - - - -
368H MET* 3.3 43.9 - - - +
390H CYS 3.0 10.1 + - - -
391H ALA 3.0 3.2 + - - -
393H ALA* 1.3 75.8 - - - +
395H VAL* 1.3 66.4 + - - +
397H THR* 3.1 2.8 + - - -
398H ILE* 3.0 27.6 + - - +
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Residues in contact with VAL 395 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368H MET 3.9 1.5 + - - -
370H THR* 4.1 20.0 - - + -
391H ALA 3.2 16.3 + - - +
392H ILE* 3.2 9.4 + - + +
394H GLY* 1.3 75.2 - - - +
396H LEU* 1.3 65.1 + - + +
398H ILE* 4.1 4.1 - - - +
399H ALA* 3.0 35.8 + - + +
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Residues in contact with LEU 396 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392H ILE* 3.3 30.0 + - + +
393H ALA* 4.1 7.0 - - - +
394H GLY 3.3 0.2 - - - -
395H VAL* 1.3 84.1 - - + +
397H THR* 1.3 64.0 + - - +
399H ALA* 3.4 5.7 + - + +
400H LEU* 3.1 37.4 + - + +
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Residues in contact with THR 397 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327H LEU* 4.3 4.6 - - + +
330H PHE* 3.8 32.1 + - + +
331H LEU* 3.8 28.9 - - + +
334H GLY* 5.9 0.2 - - - -
368H MET* 3.9 7.9 - - + +
393H ALA* 2.7 24.5 + - - +
394H GLY* 3.1 7.2 + - - -
396H LEU* 1.3 77.2 - - - +
398H ILE* 1.3 63.8 + - - +
400H LEU* 4.0 5.9 - - - +
401H PRO* 3.1 21.8 - - - +
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Residues in contact with ILE 398 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327H LEU* 3.9 17.7 - - + -
331H LEU* 4.4 13.5 - - + -
368H MET 3.8 22.0 - - - +
369H THR* 3.9 25.8 - - + +
394H GLY 3.0 11.1 + - - +
395H VAL* 4.1 3.4 - - - +
397H THR* 1.3 77.7 - - - +
399H ALA* 1.3 65.3 + - - +
400H LEU 3.1 1.6 + - - -
401H PRO* 3.3 7.4 - - - +
402H VAL* 3.0 40.4 - - + +
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Residues in contact with ALA 399 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395H VAL* 3.0 25.0 + - + +
396H LEU* 3.8 7.6 - - + +
397H THR 3.4 0.2 - - - -
398H ILE* 1.3 80.3 - - - +
400H LEU* 1.3 60.1 + - + +
402H VAL* 4.9 2.0 - - - -
403H PRO* 2.9 29.6 - - - +
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Residues in contact with LEU 400 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330H PHE* 5.0 14.6 - - + -
396H LEU* 3.1 27.1 + - + +
397H THR* 4.0 4.3 - - - +
398H ILE 3.1 1.6 + - - -
399H ALA* 1.3 85.2 - - + +
401H PRO* 1.3 71.1 - - + +
403H PRO* 3.6 6.6 - - - +
404H VAL* 4.5 7.8 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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