Contacts of the helix formed by residues 345 - 361 (chain R) in PDB entry 6XOX
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 ILE 345 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332R VAL* 6.4 0.7 - - + -
335R LEU* 3.7 39.7 - - + +
336R LYS* 4.6 21.5 - - + -
344R ASP* 1.3 83.6 - - + +
346R LYS* 1.3 66.0 + - + +
347R CYS 3.4 0.2 - - - -
348R ARG* 3.8 4.3 - - - +
349R LEU* 2.9 38.3 + - + +
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Residues in contact with LYS 346 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344R ASP* 3.2 22.6 - - - +
345R ILE* 1.3 81.5 - - + +
347R CYS* 1.3 60.8 + - - +
349R LEU* 3.9 4.7 - - - +
350R ALA* 2.9 30.0 + - - +
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Residues in contact with CYS 347 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344R ASP 3.7 9.4 + - - +
345R ILE 3.4 0.2 - - - -
346R LYS* 1.3 78.6 - - - +
348R ARG* 1.3 57.6 + - - +
350R ALA* 3.4 5.9 + - - +
351R LYS* 2.9 30.6 + - - +
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Residues in contact with ARG 348 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392A GLU 3.2 24.9 + - - -
393A LEU* 3.5 13.7 + - - +
394A LEU* 2.3 43.1 + - + +
331R VAL* 5.6 0.2 - - + -
335R LEU* 3.6 35.9 - - + -
344R ASP 4.1 3.3 + - - +
345R ILE* 3.4 7.4 + - - +
346R LYS 3.2 0.2 - - - -
347R CYS* 1.3 78.6 - - - +
349R LEU* 1.3 61.3 + - - +
351R LYS* 3.3 32.0 + - - +
352R SER* 2.9 34.5 + - - +
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Residues in contact with LEU 349 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328R ILE* 4.0 21.1 - - + +
331R VAL* 4.6 9.2 - - + -
332R VAL* 3.7 37.2 - - + -
335R LEU* 3.7 24.0 - - + -
345R ILE* 2.9 23.8 + - + +
346R LYS* 3.9 5.4 - - - +
348R ARG* 1.3 77.2 - - - +
350R ALA* 1.3 56.0 + - - +
352R SER* 4.3 1.6 - - - -
353R THR* 3.0 40.4 + - + +
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Residues in contact with ALA 350 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346R LYS 2.9 18.3 + - - +
347R CYS* 3.7 7.4 - - - +
348R ARG 3.3 0.2 - - - -
349R LEU* 1.3 75.5 - - - +
351R LYS* 1.3 58.4 + - - +
353R THR* 3.1 6.3 + - - -
354R LEU* 2.9 41.8 + - + +
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Residues in contact with LYS 351 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A GLU* 4.6 15.2 + - - +
347R CYS* 2.9 21.2 + - - +
348R ARG* 3.3 27.7 - - - +
349R LEU 3.3 0.2 - - - -
350R ALA* 1.3 77.3 - - - +
352R SER* 1.3 57.4 + - - +
354R LEU* 4.7 2.7 - - + -
355R THR* 2.8 59.7 + - + +
401R LEU* 5.2 3.8 - - - +
405R VAL* 5.6 5.5 - - - +
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Residues in contact with SER 352 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU* 3.6 31.0 + - - +
328R ILE* 3.5 18.4 - - - +
331R VAL* 3.8 20.9 - - - +
348R ARG* 2.9 21.2 + - - +
349R LEU* 3.7 5.2 - - - -
351R LYS* 1.3 76.2 - - - +
353R THR* 1.3 58.4 + - - +
355R THR* 3.1 7.7 + - - -
356R LEU* 2.9 30.8 + - - +
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Residues in contact with THR 353 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324R PHE* 4.4 11.7 - - + -
328R ILE* 3.7 38.6 - - + -
349R LEU* 3.0 24.4 + - + +
350R ALA* 3.1 7.6 + - - -
352R SER* 1.3 73.8 - - - +
354R LEU* 1.3 70.1 + - - +
356R LEU* 4.4 2.2 - - - +
357R ILE* 3.0 40.0 + - - +
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Residues in contact with LEU 354 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350R ALA* 2.9 33.4 + - + +
351R LYS* 4.2 3.6 - - + +
353R THR* 1.3 88.3 + - - +
355R THR* 1.3 62.8 + - + +
357R ILE* 4.3 13.5 - - + +
358R PRO* 3.5 15.6 - - - +
397R MET* 5.7 1.9 - - - +
401R LEU* 4.0 5.9 - - - +
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Residues in contact with THR 355 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A TYR 5.6 2.2 - - - -
392A GLU* 4.3 9.4 + - + +
393A LEU* 3.6 13.5 - - - +
351R LYS* 2.8 53.7 + - + +
352R SER* 3.1 7.4 + - - -
354R LEU* 1.3 79.4 - - + +
356R LEU* 1.3 56.6 + - - +
357R ILE 3.5 0.2 - - - -
358R PRO* 3.9 5.6 - - - +
359R LEU* 4.2 0.5 - - - +
401R LEU* 3.7 31.1 - - + +
402R TYR* 2.5 37.3 + - - -
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Residues in contact with LEU 356 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LEU* 4.2 23.1 - - + -
251R LEU* 4.4 13.0 - - + -
324R PHE* 3.6 27.1 - - + -
327R VAL* 3.7 28.7 - - + -
328R ILE* 3.8 16.6 - - + -
352R SER 2.9 18.0 + - - +
353R THR 3.2 2.9 + - - +
355R THR* 1.3 78.4 - - - +
357R ILE* 1.3 65.5 + - - +
358R PRO 3.6 0.2 - - - -
359R LEU* 3.4 9.8 + - + +
360R LEU* 3.3 43.9 + - + +
402R TYR* 4.0 1.6 - - - +
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Residues in contact with ILE 357 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324R PHE* 3.7 26.5 - - + -
353R THR* 3.0 26.5 + - - +
354R LEU* 4.8 14.6 - - + +
356R LEU* 1.3 76.4 - - - +
358R PRO* 1.3 65.6 - - + +
360R LEU 3.3 1.6 + - - -
361R GLY* 2.9 24.6 + - - -
362R THR* 3.3 12.9 + - + -
363R HIS* 4.0 32.0 + - + +
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Residues in contact with PRO 358 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244R LEU* 4.6 0.7 - - - +
354R LEU 3.5 16.4 - - - +
355R THR 3.9 2.2 - - - +
356R LEU 3.8 1.3 - - - -
357R ILE* 1.3 95.9 - - + +
359R LEU* 1.3 59.7 + - - +
361R GLY* 4.4 0.9 - - - +
363R HIS* 5.3 2.7 - - - +
394R GLN* 3.1 34.9 + - + +
397R MET* 3.8 28.3 - - + -
398R VAL* 3.3 18.2 - - + +
401R LEU* 3.9 24.2 - - + -
402R TYR* 5.4 0.2 - - + -
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Residues in contact with LEU 359 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A TYR* 4.5 10.1 - - + -
180R HIS* 4.4 4.3 - - + +
183R LEU* 3.9 16.4 - - + -
184R PHE* 6.0 0.4 - - + -
244R LEU* 3.3 20.4 - - - +
247R GLU* 3.6 41.5 - - + +
251R LEU* 4.5 3.1 - - + -
356R LEU* 3.4 14.5 + - + +
357R ILE 3.2 0.8 - - - -
358R PRO* 1.3 81.2 - - - +
360R LEU* 1.3 69.6 + - + +
361R GLY 3.5 0.2 - - - -
398R VAL* 3.8 8.4 - - + +
402R TYR* 3.3 55.4 - - + +
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Residues in contact with LEU 360 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244R LEU* 4.0 8.0 - - - +
247R GLU* 4.9 1.1 - - + -
248R GLY* 4.3 13.5 - - - +
251R LEU* 5.3 4.5 - - + -
320R ASN* 2.9 64.8 - - - +
323R ILE* 4.4 9.0 - - + -
324R PHE* 3.8 27.6 - - + +
327R VAL* 6.0 1.1 - - + -
356R LEU* 3.3 36.6 + - + +
359R LEU* 1.3 91.7 - - + +
361R GLY* 1.3 63.8 + - - +
362R THR* 3.3 13.2 + - - +
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Residues in contact with GLY 361 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241R TYR* 6.5 0.2 - - - -
244R LEU* 3.9 8.1 - - - -
317R ILE* 4.8 7.6 - - - +
357R ILE 2.9 7.6 + - - -
359R LEU 3.5 2.4 - - - -
360R LEU* 1.3 78.8 - - - +
362R THR* 1.3 62.1 + - - +
363R HIS* 3.1 12.7 + - - -
364R GLU* 3.3 21.1 + - - +
365R VAL 4.7 0.3 + - - -
394R GLN* 3.3 24.5 - - - +
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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
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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