Contacts of the helix formed by residues 405 - 418 (chain B) in PDB entry 3H11
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 TRP 405 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397B TYR* 3.2 47.2 + + + +
399B ASN* 4.7 15.6 - - + +
402B GLU* 6.2 0.2 - - - -
403B GLY 4.8 4.5 - - - -
404B THR* 1.3 71.6 - - - +
406B TYR* 1.3 59.3 + - - +
408B GLN* 4.1 2.3 - - - +
409B SER* 3.0 32.6 + - - -
435B VAL* 3.8 21.7 - - + +
438B LYS* 4.1 47.5 + - + +
445B GLY 4.3 8.5 - - - -
446B LYS* 4.6 1.6 - - - -
447B GLN* 3.5 30.3 - - + +
701C ILE* 3.4 28.5 - - + +
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Residues in contact with TYR 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B PHE* 3.8 5.8 - + - -
342B ILE 4.2 4.7 - - - -
343B GLN* 3.3 13.9 + - - +
387B GLY* 3.2 38.4 - - - -
388B MET 3.8 13.1 + - - -
389B ALA* 3.5 31.0 - - + -
397B TYR 4.9 0.2 + - - -
404B THR* 3.3 1.8 + - - -
405B TRP* 1.3 80.6 - - - +
407B ILE* 1.3 78.9 + - + +
409B SER* 3.7 0.9 - - - -
410B LEU* 2.8 43.4 + - + +
428B LEU* 3.8 17.0 - - + +
431B VAL* 3.7 25.4 - - + -
435B VAL* 4.0 6.3 - - - +
447B GLN* 4.0 7.9 - - - +
449B PRO* 4.0 15.3 - - + -
451B PRO* 6.2 0.2 - - - +
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Residues in contact with ILE 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B ASP* 3.6 29.2 - - + +
255B LEU* 3.8 32.8 - - + -
298B CYS* 6.3 0.2 - - + -
300B LEU* 4.1 13.7 - - + -
341B PHE* 5.0 7.0 - - + -
343B GLN* 3.7 21.5 - - + +
404B THR* 3.1 18.9 + - - +
406B TYR* 1.3 98.0 - - + +
408B GLN* 1.3 65.0 + - - +
410B LEU* 3.3 13.1 + - + +
411B CYS* 2.9 27.2 + - - -
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Residues in contact with GLN 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B LEU* 3.7 24.7 + - - +
251B ASP* 3.0 24.0 + - - +
254B ALA* 4.0 14.4 - - - +
402B GLU* 3.1 28.7 + - + +
403B GLY* 4.0 1.8 - - - -
404B THR 3.0 22.2 + - - +
405B TRP* 4.1 2.0 - - - +
407B ILE* 1.3 77.5 - - - +
409B SER* 1.3 62.5 + - - +
411B CYS* 4.0 3.3 - - - +
412B GLN* 3.1 24.6 + - - +
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Residues in contact with SER 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B TRP 3.0 19.7 + - - -
406B TYR 3.7 2.5 - - - -
408B GLN* 1.3 77.9 - - - +
410B LEU* 1.3 64.2 + - - +
412B GLN* 3.3 4.9 + - - +
413B SER* 3.0 25.8 + - - -
431B VAL* 3.8 14.3 - - - +
434B GLU* 3.1 33.6 + - - +
435B VAL* 3.8 13.9 - - - -
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Residues in contact with LEU 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 4.7 9.4 - - + -
259B PHE* 5.6 0.2 - - + -
341B PHE* 3.6 45.1 - - + -
406B TYR* 2.8 24.9 + - + +
407B ILE* 3.6 17.5 - - + +
409B SER* 1.3 77.5 + - - +
411B CYS* 1.3 58.5 + - - +
413B SER* 3.8 1.4 - - - -
414B LEU* 2.9 56.0 + - + +
424B ILE* 6.1 0.4 - - + -
427B ILE* 5.0 2.0 - - + -
428B LEU* 3.8 29.2 - - + -
431B VAL* 3.8 15.9 - - + +
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Residues in contact with CYS 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B ALA* 3.7 14.6 - - + -
255B LEU* 3.5 45.1 - - - -
258B THR* 3.3 29.2 - - - +
407B ILE* 2.9 20.5 + - - +
408B GLN* 4.0 3.4 - - - +
410B LEU* 1.3 74.9 - - - +
412B GLN* 1.3 67.1 + - - +
414B LEU* 3.3 2.1 + - - +
415B ARG* 2.9 33.3 + - - +
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Residues in contact with GLN 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B GLN 3.1 18.8 + - - +
409B SER* 3.8 5.8 - - - +
411B CYS* 1.3 77.4 - - - +
413B SER* 1.3 58.2 + - - +
415B ARG* 3.5 10.6 + - - +
416B GLU* 2.4 78.4 + - - +
434B GLU* 5.6 2.9 - - - +
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Residues in contact with SER 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B SER 3.0 17.9 + - - -
410B LEU 3.8 1.8 - - - -
412B GLN* 1.3 74.9 - - - +
414B LEU* 1.3 57.5 + - - +
416B GLU* 4.7 4.0 - - - -
417B ARG* 2.7 50.7 + - - +
427B ILE* 3.8 22.7 - - - -
430B GLU* 4.4 7.4 - - - +
431B VAL* 3.9 11.6 - - - +
434B GLU* 3.8 20.4 + - - -
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Residues in contact with LEU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B THR* 3.8 20.9 - - + -
259B PHE* 3.5 34.5 - - + -
262B LEU* 4.6 4.2 - - + +
341B PHE* 5.1 2.5 - - + -
410B LEU* 2.9 43.4 + - + +
411B CYS* 4.6 0.9 - - - -
413B SER* 1.3 75.0 - - - +
415B ARG* 1.3 63.7 + - - +
418B CYS* 2.9 52.2 + - - +
419B PRO* 3.6 0.2 - - - +
424B ILE* 3.9 23.6 - - + -
427B ILE* 4.0 15.3 - - + -
461B PHE* 4.7 4.5 - - + -
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Residues in contact with ARG 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B THR* 3.3 37.4 + - - +
258B THR* 3.4 25.8 - - + +
261B GLU* 2.7 49.6 + - - +
262B LEU* 6.2 1.1 - - - -
411B CYS* 2.9 22.0 + - - +
412B GLN* 3.8 12.9 + - - +
414B LEU* 1.3 77.0 - - - +
416B GLU* 1.3 59.9 + - + +
419B PRO* 3.1 24.7 - - - +
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Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412B GLN* 2.4 54.3 + - - +
413B SER* 4.2 3.1 - - - +
415B ARG* 1.3 80.3 - - + +
417B ARG* 1.3 70.1 + - + +
419B PRO* 3.7 5.6 - - - +
420B ARG* 3.3 23.8 - - - +
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Residues in contact with ARG 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A GLN* 2.9 31.3 + - - +
238A SER* 3.7 12.7 + - - +
239A ILE* 4.0 33.6 - - + +
413B SER* 2.7 34.7 + - - +
416B GLU* 1.3 83.4 - - + +
418B CYS* 1.3 64.2 + - - +
419B PRO 3.3 2.2 - - - -
420B ARG* 3.0 42.3 + - - +
422B ASP* 2.6 51.5 + - - +
427B ILE* 3.8 15.9 - - + -
430B GLU* 5.8 0.9 - - + -
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Residues in contact with CYS 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B LEU* 4.0 21.1 - - + -
414B LEU* 2.9 50.6 + - - +
417B ARG* 1.3 73.9 - - - +
419B PRO* 1.3 62.6 - - + +
421B GLY* 2.9 21.1 + - - -
422B ASP 4.4 8.0 - - - +
424B ILE* 3.9 18.2 - - - -
427B ILE* 3.9 3.1 - - - -
461B PHE* 3.7 27.0 - - - +
462B PRO* 5.3 1.4 - - - +
463B SER* 4.2 5.4 + - - -
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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