Contacts of the helix formed by residues 395 - 414 (chain B) in PDB entry 4R0C
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 395 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PRO* 5.4 4.5 - - - -
340B LEU* 5.2 0.9 - - - +
393B ILE* 3.4 4.5 - - - +
394B GLY* 1.3 74.5 - - - +
396B ALA* 1.3 64.0 + - - +
397B SER* 3.1 9.9 + - - -
398B ALA* 2.9 34.8 + - - +
399B LYS* 2.8 26.4 + - - +
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Residues in contact with ALA 396 (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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170B PHE* 4.0 22.4 - - + -
179B VAL* 5.3 1.3 - - + -
182B THR* 6.2 0.4 - - + -
183B LEU* 4.4 17.3 - - + -
394B GLY 3.4 4.6 + - - -
395B SER* 1.3 70.9 + - - +
397B SER* 1.3 64.2 + - - +
400B TRP* 3.0 15.0 + - - +
425B TYR* 2.5 27.1 + - + +
429B ASP* 3.4 22.4 + - - +
801B NA 4.3 0.4 - - - -
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Residues in contact with SER 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B THR* 3.3 25.3 - - - +
186B LEU* 3.8 8.9 - - - +
337B TYR* 3.7 16.3 - - - -
340B LEU* 3.8 17.9 - - - -
341B MET* 4.6 3.1 - - - -
395B SER* 3.1 7.2 + - - -
396B ALA* 1.3 77.1 - - - +
398B ALA* 1.3 65.2 + - - +
401B SER* 2.8 31.1 + - - -
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Residues in contact with ALA 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PRO* 3.6 30.1 - - + -
25B PHE* 3.4 25.7 - - + -
340B LEU* 4.0 20.3 - - + +
393B ILE* 3.9 7.6 - - + -
395B SER* 2.9 25.3 + - - +
397B SER* 1.3 77.9 - - - +
399B LYS* 1.3 62.9 + - - +
401B SER 3.6 0.2 + - - -
402B ILE* 3.7 4.0 + - - +
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Residues in contact with LYS 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B THR* 4.0 7.6 - - + +
389B ILE* 3.5 27.8 - - + -
390B ASN* 3.2 29.0 + - - +
393B ILE* 3.3 33.2 + - + +
395B SER 2.8 29.3 + - - +
397B SER 3.2 0.6 - - - -
398B ALA* 1.3 74.4 - - - +
400B TRP* 1.3 55.2 + - - +
401B SER 3.1 2.0 - - - -
402B ILE* 3.0 13.0 + - - +
403B LEU* 2.8 40.7 + - + +
425B TYR* 3.1 26.6 + - + +
429B ASP* 2.9 23.0 + - - -
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Residues in contact with TRP 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 2.9 52.9 + - + +
186B LEU* 3.5 22.5 - - + +
187B SER* 3.0 21.6 + - - +
382B PHE* 3.9 19.3 - + - -
396B ALA 3.0 19.1 + - - +
399B LYS* 1.3 77.1 - - - +
401B SER* 1.3 57.8 + - - +
403B LEU* 3.9 4.0 - - + -
404B ALA* 3.1 52.2 + - + +
408B ILE* 3.6 29.6 - - + -
421B SER 4.2 15.3 - - - -
422B GLN* 3.9 12.7 + - + -
425B TYR* 3.3 40.8 + + + -
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Residues in contact with SER 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PHE* 3.3 32.8 - - - -
80B PHE* 5.9 0.2 - - - -
186B LEU* 3.1 27.3 - - - +
340B LEU* 4.8 0.6 - - - +
341B MET* 3.8 10.2 - - - +
344B ALA* 3.9 11.9 - - - -
347B PHE* 4.6 0.9 - - - -
348B VAL* 4.6 7.4 - - - +
397B SER 2.8 22.5 + - - -
398B ALA* 4.7 0.4 - - - -
399B LYS 3.1 0.4 + - - -
400B TRP* 1.3 77.5 - - - +
402B ILE* 1.3 57.9 + - - +
405B PRO* 3.2 21.1 - - - +
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Residues in contact with ILE 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PHE* 3.5 7.1 - - + -
28B PHE* 3.8 36.6 - - + -
347B PHE* 3.8 32.5 - - + -
393B ILE* 6.6 0.4 - - + -
398B ALA 4.0 7.9 - - - +
399B LYS* 3.0 16.8 + - - +
401B SER* 1.3 79.8 - - - +
403B LEU* 1.3 72.6 + - + +
404B ALA 3.4 0.4 - - - -
405B PRO* 3.4 2.3 - - - +
406B VAL* 3.3 31.5 + - + +
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Residues in contact with LEU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B PHE* 4.6 7.4 - - + -
385B LEU* 4.8 5.4 - - + -
386B THR* 4.2 17.5 - - - +
389B ILE* 4.3 27.1 - - + -
399B LYS* 2.8 29.6 + - + +
400B TRP* 4.0 14.6 - - + -
402B ILE* 1.3 83.2 - - + +
404B ALA* 1.3 60.3 + - - +
406B VAL* 3.3 1.4 + - + -
407B PHE* 3.1 57.3 + - + +
425B TYR* 4.1 22.4 - - + -
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Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 4.2 10.1 - - + +
190B ALA* 3.3 14.0 - - + +
400B TRP* 3.1 57.9 + - + +
403B LEU* 1.3 75.3 - - - +
405B PRO* 1.3 67.3 - - + +
408B ILE* 3.0 28.3 + - + +
409B PRO* 3.2 5.0 - - - +
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Residues in contact with PRO 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 5.5 2.0 - - + +
190B ALA* 3.6 12.3 - - + -
193B ILE* 4.1 4.1 - - + +
347B PHE* 4.0 16.6 - - + -
348B VAL* 4.2 23.8 - - + -
351B PHE* 3.5 30.0 - - + -
357B GLY 5.1 1.0 - - - +
360B LEU* 5.1 0.7 - - - +
400B TRP 4.0 0.2 - - - +
401B SER* 3.2 27.8 - - - +
402B ILE* 3.4 9.4 - - + +
404B ALA* 1.3 93.6 - - + +
406B VAL* 1.3 56.3 + - - +
409B PRO* 3.4 18.9 - - + +
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Residues in contact with VAL 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B PHE* 5.3 0.9 - - + -
351B PHE* 4.6 9.4 - - + -
360B LEU* 4.0 30.7 - - + +
361B ALA* 6.0 0.7 - - - -
402B ILE* 3.3 37.3 + - + +
403B LEU* 3.3 2.3 + - + -
404B ALA 3.2 1.0 - - - -
405B PRO* 1.3 79.9 - - + +
407B PHE* 1.3 88.6 + - + +
409B PRO* 4.1 3.3 - - - +
410B MET* 4.1 13.5 + - - +
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Residues in contact with PHE 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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382B PHE* 3.9 26.5 - + + -
385B LEU* 4.1 20.9 - - + -
403B LEU* 3.1 48.2 + - + +
404B ALA 3.3 0.6 + - - -
405B PRO 3.5 0.2 - - - -
406B VAL* 1.3 97.8 - - + +
408B ILE* 1.3 68.2 + - - +
409B PRO* 3.2 1.8 - - - -
410B MET* 3.1 35.7 + - + +
411B LEU* 2.9 37.8 + - + +
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Residues in contact with ILE 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B SER* 3.7 19.3 - - - +
190B ALA* 3.9 1.3 - - + -
191B ALA* 4.0 23.8 - - - +
400B TRP* 3.6 38.8 - - + -
404B ALA* 3.0 16.8 + - + +
407B PHE* 1.3 76.1 - - + +
409B PRO* 1.3 64.8 - - - +
411B LEU* 4.1 7.2 - - - +
412B MET* 3.0 37.4 + - + +
416B ILE 5.1 0.2 - - - +
418B PRO* 3.8 31.0 - - + +
421B SER* 4.0 9.4 - - - -
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Residues in contact with PRO 409 (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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190B ALA* 4.0 17.5 - - + +
193B ILE* 4.1 13.0 - - + -
194B ILE* 3.5 31.9 - - + +
357B GLY 4.7 1.8 - - - +
361B ALA* 3.6 12.1 - - + -
404B ALA 3.2 14.4 - - - +
405B PRO* 3.4 20.4 - - + +
406B VAL 4.1 1.6 - - - +
407B PHE 3.4 5.4 - - - +
408B ILE* 1.3 93.5 - - + +
410B MET* 1.3 62.2 + - - +
412B MET* 3.1 19.5 + - + +
413B LEU* 3.2 5.0 + - - +
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Residues in contact with MET 410 (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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360B LEU* 5.2 6.5 - - - +
361B ALA* 3.5 30.7 - - - +
364B GLY* 4.0 21.1 - - - -
365B ALA* 3.9 9.1 - - + +
368B LEU* 3.4 31.6 - - + -
406B VAL 4.1 14.0 + - - +
407B PHE* 3.1 43.3 + - + +
409B PRO* 1.3 80.2 - - - +
411B LEU* 1.3 73.2 + - + +
413B LEU* 3.1 6.8 + - - +
414B LEU* 3.0 24.5 + - + +
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Residues in contact with LEU 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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368B LEU* 4.8 9.9 - - + -
378B LEU* 4.1 20.2 - - + -
379B LEU* 5.3 3.4 - - + -
382B PHE* 4.8 17.7 - - + -
407B PHE* 2.9 37.7 + - + +
408B ILE 4.1 2.5 - - - +
410B MET* 1.3 83.1 - - + +
412B MET* 1.3 59.8 + - - +
414B LEU* 3.1 10.9 + - + +
415B GLY 3.1 4.5 + - - -
416B ILE* 2.8 56.7 + - + +
421B SER* 3.3 29.6 - - - +
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Residues in contact with MET 412 (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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191B ALA* 3.8 38.1 - - + +
194B ILE* 4.1 28.0 - - + -
195B ASP* 4.6 5.6 - - + -
198B ARG* 4.4 16.4 - - + +
408B ILE* 3.0 26.2 + - + +
409B PRO* 3.2 9.4 - - - +
411B LEU* 1.3 77.8 - - - +
413B LEU* 1.3 58.7 + - - +
415B GLY* 3.0 18.9 + - - -
416B ILE 3.6 8.5 + - - +
417B SER* 5.2 0.2 - - - -
418B PRO* 4.0 30.3 - - + -
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Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS* 5.3 2.2 - - + -
49B PRO* 4.3 19.5 - - + -
50B LEU* 3.8 31.5 - - + +
194B ILE* 3.7 31.6 - - + -
358B LEU* 5.6 0.7 - - + -
361B ALA* 3.7 29.2 - - + +
362B VAL* 4.1 11.4 - - + +
365B ALA* 3.6 13.2 - - + -
409B PRO 3.2 8.7 + - - +
410B MET 3.1 8.6 + - - +
412B MET* 1.3 78.7 - - - +
414B LEU* 1.3 62.1 + - - +
415B GLY 3.4 1.0 + - - -
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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
----------------------------------------------------------
365B ALA* 3.3 33.4 - - + +
368B LEU* 3.7 29.6 - - + +
369B GLY* 3.7 14.8 - - - +
375B LYS* 3.4 20.3 - - + +
378B LEU* 3.6 31.9 - - + -
410B MET* 3.0 17.1 + - + +
411B LEU* 3.1 13.2 + - + +
412B MET 3.1 0.6 - - - -
413B LEU* 1.3 77.6 - - - +
415B GLY* 1.3 60.1 + - - +
416B ILE* 3.4 3.4 + - + +
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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
------------------------------------------------------------
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