Contacts of the helix formed by residues 342 - 363 (chain B) in PDB entry 2O2C
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 GLY 342 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLU* 5.1 0.9 - - - -
185B ARG* 3.3 26.1 - - - +
338B MET* 2.7 25.0 + - - -
341B ILE* 1.3 75.8 - - - +
343B TYR* 1.3 66.5 + - - -
344B GLU 3.4 2.5 - - - -
345B ASN 3.3 1.6 + - - -
346B PHE* 3.0 21.7 + - - +
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Residues in contact with TYR 343 (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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154B ARG* 4.4 9.8 + - - -
174B LEU* 4.0 20.8 - - + +
175B ASP* 5.6 0.4 - - - -
178B ARG* 3.6 72.7 + - + +
181B SER* 4.8 2.3 + - - +
182B GLU* 4.4 15.6 + - - +
338B MET* 3.9 30.1 - - + +
342B GLY* 1.3 70.8 - - - -
344B GLU* 1.3 68.2 + - + +
346B PHE* 3.1 3.1 + - - +
347B VAL* 2.9 54.0 + - + +
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ASP* 3.8 32.9 - - + +
164A LYS* 5.7 2.8 + - - +
178B ARG* 6.0 1.6 - - - +
342B GLY 3.4 0.6 - - - -
343B TYR* 1.3 86.9 - - + +
345B ASN* 1.3 61.0 + - - +
347B VAL* 3.4 8.1 + - - +
348B GLU* 3.1 29.5 + - - +
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Residues in contact with ASN 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B PHE* 3.6 29.4 + - - +
341B ILE* 2.9 42.3 + - + +
342B GLY 3.3 1.6 + - - -
343B TYR 3.3 0.6 - - - -
344B GLU* 1.3 77.3 - - - +
346B PHE* 1.3 60.7 + - - +
348B GLU* 3.3 10.2 + - - +
349B LEU* 3.0 22.3 + - - +
536B PRO* 3.3 28.1 - - + +
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Residues in contact with PHE 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B LEU* 4.0 10.8 - - + -
177B MET* 4.2 3.1 - - + -
329B MET 3.6 23.1 - - - -
330B TRP* 4.0 14.1 - - - -
331B SER 4.1 6.5 - - - -
334B GLY* 3.4 20.9 - - - -
337B ILE* 4.0 11.0 - - + -
338B MET* 3.6 44.9 - - + -
341B ILE* 3.9 5.5 - - + +
342B GLY 3.0 13.8 + - - +
343B TYR* 3.1 8.3 + + - +
345B ASN* 1.3 72.8 - - - +
347B VAL* 1.3 62.4 + - + +
349B LEU* 3.2 22.3 + - + +
350B LEU* 3.0 53.7 + - + +
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Residues in contact with VAL 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ARG* 3.6 33.2 - - - +
174B LEU* 6.5 0.4 - - + -
343B TYR* 2.9 55.1 + - + +
344B GLU* 3.6 10.8 - - - +
346B PHE* 1.3 76.0 - - + +
348B GLU* 1.3 57.8 + - - +
350B LEU* 3.3 11.2 + - + +
351B THR* 2.8 43.7 + - - +
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Residues in contact with GLU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B SER* 4.9 3.8 - - - -
344B GLU 3.1 17.7 + - - +
345B ASN* 3.4 16.4 - - - +
347B VAL* 1.3 79.1 - - + +
349B LEU* 1.3 56.4 + - - +
351B THR* 3.3 5.7 + - - -
352B GLY 3.0 24.8 + - - -
535B THR* 6.0 0.5 - - - -
536B PRO* 4.0 13.7 - - + -
537B ARG* 2.8 65.4 + - - +
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Residues in contact with LEU 349 (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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215B ALA* 5.0 0.4 - - + -
219B LEU* 4.5 7.6 - - + -
329B MET* 4.1 19.5 - - + +
330B TRP* 3.7 16.8 - - + -
337B ILE* 4.2 15.0 - - + -
341B ILE* 5.0 0.7 - - + -
345B ASN 3.0 13.2 + - - +
346B PHE* 3.3 37.5 - - + +
348B GLU* 1.3 75.9 - - - +
350B LEU* 1.3 61.9 + - - +
352B GLY 3.4 8.7 + - - -
353B ALA 3.4 8.5 + - - -
536B PRO* 3.4 24.8 + - + +
539B LEU* 4.0 19.7 - - + -
540B GLY* 3.4 31.7 - - - +
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Residues in contact with LEU 350 (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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151B LEU 3.9 13.2 - - - +
152B ARG* 3.3 27.0 - - + +
154B ARG* 3.8 29.4 - - - +
174B LEU* 4.0 17.3 - - + -
330B TRP* 3.6 41.1 - - + +
346B PHE* 3.0 40.1 + - + +
347B VAL* 3.6 11.4 - - + +
349B LEU* 1.3 75.0 - - + +
351B THR* 1.3 58.8 + - - +
353B ALA* 3.2 2.4 + - - +
354B HIS* 3.0 23.8 + - - +
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Residues in contact with THR 351 (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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154B ARG* 3.7 24.9 + - + +
347B VAL* 2.8 32.4 + - - +
348B GLU* 3.3 6.7 + - - -
350B LEU* 1.3 74.3 - - - +
352B GLY* 1.3 60.2 + - - +
354B HIS* 3.2 3.1 + - + +
355B VAL* 2.9 34.7 + - + +
537B ARG* 3.6 38.6 + - - +
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Residues in contact with GLY 352 (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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91B LEU* 5.4 0.9 - - - -
348B GLU 3.0 10.3 + - - -
349B LEU 3.4 1.8 + - - -
350B LEU 3.3 0.2 - - - -
351B THR* 1.3 76.4 - - - +
353B ALA* 1.3 61.2 + - - +
355B VAL* 3.5 6.5 + - - +
356B ILE* 3.3 17.5 + - - +
537B ARG* 3.2 35.8 - - - +
541B ALA* 3.5 20.2 - - - +
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Residues in contact with ALA 353 (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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152B ARG* 3.7 24.9 - - - +
330B TRP* 3.7 20.6 - - + -
349B LEU 3.4 3.8 + - - -
350B LEU 3.2 9.5 + - - +
352B GLY* 1.3 75.4 - - - +
354B HIS* 1.3 56.5 + - - +
356B ILE* 3.2 4.7 + - - +
357B ASP* 2.9 34.7 + - - +
540B GLY 3.5 19.4 - - - +
544B ALA* 3.7 6.9 - - + +
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Residues in contact with HIS 354 (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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149B ILE 5.2 0.6 + - - -
152B ARG* 3.2 25.6 + - - +
153B ASN* 3.5 27.4 - - + -
154B ARG* 3.8 21.3 - - + -
155B SER* 3.6 20.4 + - - -
157B ARG* 4.6 0.7 - - - -
350B LEU 3.0 8.5 + - - +
351B THR* 3.2 11.6 + - + +
353B ALA* 1.3 76.2 - - - +
355B VAL* 1.3 60.5 + - + +
357B ASP* 3.1 15.2 + - + +
358B GLU* 3.0 59.2 + - + +
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Residues in contact with VAL 355 (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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89B VAL* 5.0 6.1 - - + -
90B SER 3.5 24.7 - - - +
91B LEU* 3.5 32.1 - - + +
92B GLY* 5.4 1.3 - - - -
351B THR* 2.9 31.8 + - + +
352B GLY* 3.8 7.0 - - - +
353B ALA 3.3 0.2 - - - -
354B HIS* 1.3 78.7 - - + +
356B ILE* 1.3 59.7 + - - +
358B GLU* 3.5 7.9 + - - +
359B HIS* 3.0 25.7 + - + +
537B ARG* 4.5 1.1 - - - +
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Residues in contact with ILE 356 (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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89B VAL* 3.9 29.8 - - + -
91B LEU* 4.5 8.5 - - + -
99B LEU* 4.1 17.5 - - + -
352B GLY 3.3 3.5 + - - +
353B ALA 3.2 7.8 + - - +
355B VAL* 1.3 76.4 - - - +
357B ASP* 1.3 60.3 + - - +
359B HIS* 3.6 9.4 - - + +
360B PHE* 2.8 28.8 + - - +
369B VAL* 6.0 1.8 - - + -
370B PRO* 4.4 11.9 - - + -
541B ALA* 3.6 29.2 - - + +
544B ALA* 4.0 8.7 - - + -
545B MET* 3.8 32.1 - - + +
548B HIS* 4.4 2.7 - - + -
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Residues in contact with ASP 357 (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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133B PHE* 3.6 18.3 - - + -
149B ILE* 3.8 15.0 - - + +
152B ARG* 2.8 44.3 + - - +
353B ALA 2.9 21.4 + - - +
354B HIS* 3.1 15.1 + - - +
356B ILE* 1.3 76.6 - - - +
358B GLU* 1.3 61.2 + - - +
360B PHE* 3.7 1.4 - - - +
361B ALA* 3.0 30.1 + - - +
544B ALA* 4.1 0.5 - - - +
548B HIS* 2.7 33.4 + - - -
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Residues in contact with GLU 358 (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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133B PHE* 5.2 6.1 - - - -
155B SER* 6.0 0.4 - - - -
157B ARG* 3.4 34.3 + - - -
354B HIS* 3.0 42.9 + - + +
355B VAL* 3.7 6.3 - - - +
357B ASP* 1.3 78.3 - - - +
359B HIS* 1.3 62.4 + - - +
361B ALA* 3.5 3.1 + - - +
362B ASN* 3.0 48.1 + - - +
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Residues in contact with HIS 359 (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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87B VAL* 4.7 1.3 - - + -
89B VAL* 3.4 40.9 - - + +
355B VAL* 3.0 17.7 + - + +
356B ILE* 3.6 13.9 - - + +
358B GLU* 1.3 75.9 - - - +
360B PHE* 1.3 60.5 + - - +
362B ASN* 5.4 0.2 - - - -
363B ALA* 2.8 51.6 + - + +
367B GLN 3.2 23.1 - - - -
368B ASN* 3.7 1.8 - - - -
369B VAL* 3.0 28.2 + - + +
370B PRO* 3.8 17.7 - - + -
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Residues in contact with PHE 360 (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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125B ILE* 5.2 0.9 - - + -
129B VAL* 3.6 40.9 - - + +
133B PHE* 4.1 6.1 - + - -
356B ILE 2.8 17.5 + - - +
357B ASP 3.7 2.9 - - - +
359B HIS* 1.3 80.1 - - - +
361B ALA* 1.3 58.6 + - - +
368B ASN* 2.9 42.4 + - - +
370B PRO* 3.7 21.8 - - + -
371B LEU* 4.4 5.8 - - + -
548B HIS* 3.5 40.6 - + + -
551B LEU* 4.1 11.7 - - + -
552B VAL* 3.6 33.4 - - + -
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Residues in contact with ALA 361 (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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126B ARG* 5.9 2.8 - - - +
129B VAL* 4.4 11.4 - - + -
130B GLN* 3.7 24.5 + - - +
133B PHE* 4.0 21.5 - - + -
357B ASP 3.0 18.6 + - - +
358B GLU* 4.1 4.3 - - - +
360B PHE* 1.3 76.3 - - - +
362B ASN* 1.3 71.9 + - - +
363B ALA 5.3 0.4 - - - -
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Residues in contact with ASN 362 (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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130B GLN* 5.0 2.4 + - - -
358B GLU* 3.0 43.3 + - - +
359B HIS* 5.4 0.2 - - - -
361B ALA* 1.3 91.0 - - - +
363B ALA* 1.3 65.6 + - - +
364B PRO* 3.7 4.0 - - - +
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Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B HIS* 2.8 51.7 + - + +
361B ALA 3.9 0.5 - - - -
362B ASN* 1.3 74.6 - - - +
364B PRO* 1.4 75.1 - - + +
365B PRO* 3.5 2.1 - - - +
367B GLN 4.0 7.6 - - - +
368B ASN* 3.3 17.3 + - - +
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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
------------------------------------------------------------
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