Contacts of the helix formed by residues 389 - 408 (chain R) in PDB entry 5C7L
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 GLU 389 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85R ARG* 2.7 47.5 + - + +
86R ILE* 4.4 8.9 - - + +
89R LEU* 3.6 15.7 - - + +
123R THR* 3.8 3.5 + - - +
124R HIS* 2.8 29.6 + - - +
310R PRO 4.3 7.7 - - - +
311R ASP* 3.3 21.2 + - - +
387R ASP* 3.0 6.1 + - - +
388R ASN* 1.3 86.3 - - - +
390R TYR* 1.3 63.3 + - - +
391R GLY 3.6 0.2 - - - -
392R TYR* 4.3 1.1 - - - +
393R SER* 2.9 29.8 + - - -
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Residues in contact with TYR 390 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89R LEU* 4.2 22.7 - - + -
92R ARG* 4.2 17.1 + - + +
93R ALA* 5.9 0.7 - - + -
96R GLU* 2.7 27.4 + - - -
124R HIS* 3.6 38.4 - + + -
360R GLY* 3.5 26.7 - - - -
361R ASP 3.8 5.2 - - - +
362R THR* 4.2 5.2 - - + -
387R ASP* 2.8 29.2 + - - +
389R GLU* 1.3 71.8 - - - +
391R GLY* 1.3 66.4 + - - +
393R SER* 3.4 3.0 + - - -
394R HIS* 3.1 63.2 + + - -
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Residues in contact with GLY 391 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361R ASP 3.6 8.9 + - - -
362R THR 4.1 5.8 - - - -
363R HIS 3.6 24.2 - - - -
364R SER* 5.0 3.4 - - - -
386R TYR* 6.3 0.4 - - - -
387R ASP 3.0 11.9 + - - -
390R TYR* 1.3 78.7 - - - +
392R TYR* 1.3 56.6 + - - +
394R HIS* 3.3 3.3 + - - +
395R ARG* 3.0 34.0 + - - +
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Residues in contact with TYR 392 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R ILE* 3.9 22.9 - - + -
193R SER* 2.9 39.7 - - - -
194R ALA* 3.0 1.1 + - - -
221R ASN* 3.4 31.1 + - - +
222R ALA 2.6 30.1 + - - -
223R SER* 3.6 11.2 - - - -
224R OCS 3.6 24.7 - - + -
227R ASN* 3.8 11.2 - - + -
387R ASP 4.0 3.0 + - - -
388R ASN 3.7 18.6 - - - +
389R GLU 3.9 1.9 + - - +
390R TYR 3.3 0.2 - - - -
391R GLY* 1.3 77.1 - - - +
393R SER* 1.3 56.4 + - - +
395R ARG* 3.1 7.7 + - - +
396R VAL* 2.9 42.5 + - + +
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Residues in contact with SER 393 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R ILE* 3.9 13.9 + - - +
89R LEU* 3.3 41.4 - - - +
90R VAL* 3.8 12.6 + - - +
93R ALA* 4.0 3.8 - - - +
389R GLU 2.9 21.0 + - - -
390R TYR* 3.7 6.1 - - - -
391R GLY 3.3 0.2 - - - -
392R TYR* 1.3 78.7 - - - +
394R HIS* 1.3 64.4 + - - +
396R VAL* 3.3 13.2 + - - +
397R VAL* 3.3 17.2 + - - +
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Residues in contact with HIS 394 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93R ALA* 3.8 23.8 - - + +
96R GLU* 2.9 34.0 + - + -
97R LYS* 3.1 34.1 + - + +
362R THR* 3.7 22.4 - - + +
390R TYR* 3.1 45.5 + + - +
391R GLY 3.6 7.6 - - - +
393R SER* 1.3 83.1 - - - +
395R ARG* 1.3 69.6 + - - +
397R VAL* 3.0 3.6 + - - -
398R ASP* 2.8 29.3 + - - -
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Residues in contact with ARG 395 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97R LYS* 4.1 3.8 - - - +
204R MET* 3.9 16.9 - - + +
221R ASN* 3.7 15.7 - - - +
227R ASN* 4.0 15.0 - - + +
344R GLY 3.7 17.4 + - - -
345R ILE* 3.5 17.5 - - - +
362R THR* 2.7 33.9 + - - -
363R HIS 3.6 0.4 - - - -
364R SER* 3.0 45.9 + - - +
391R GLY 3.0 15.4 + - - +
392R TYR* 3.1 10.7 + - - +
394R HIS* 1.3 90.0 - - - +
396R VAL* 1.3 56.2 + - - +
398R ASP* 2.7 30.6 + - - +
399R LEU* 2.8 30.0 + - - +
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Residues in contact with VAL 396 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86R ILE* 5.2 0.2 - - + -
90R VAL* 4.1 13.5 - - + -
167R VAL* 4.0 35.2 - - + -
191R VAL* 4.1 12.7 - - + +
193R SER* 4.2 11.4 - - - -
221R ASN* 3.5 22.2 - - + +
392R TYR* 2.9 37.0 + - + +
393R SER 3.5 8.1 - - - +
394R HIS 3.2 0.4 - - - -
395R ARG* 1.3 77.0 - - - +
397R VAL* 1.3 63.0 + - - +
399R LEU* 3.2 4.5 + - - +
400R LEU* 3.0 24.2 + - + +
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Residues in contact with VAL 397 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90R VAL* 3.8 10.1 - - + +
93R ALA* 3.6 26.9 - - + -
94R CYS* 3.7 25.6 - - - +
97R LYS* 3.9 24.7 - - + -
99R VAL* 3.7 30.3 - - + -
393R SER 3.3 4.9 + - - +
394R HIS 3.0 7.7 + - - +
396R VAL* 1.3 76.0 - - - +
398R ASP* 1.3 64.6 + - - +
400R LEU* 3.1 10.6 + - + +
401R ARG* 2.9 24.4 + - - +
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Residues in contact with ASP 398 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97R LYS* 2.8 31.5 + - - +
204R MET* 4.1 17.2 - - + +
345R ILE* 4.6 4.3 - - - +
394R HIS 2.8 8.0 + - - -
395R ARG* 2.7 43.9 + - - +
397R VAL* 1.3 77.4 - - - +
399R LEU* 1.3 55.5 + - - +
401R ARG* 3.5 11.6 + - - +
402R TYR* 2.9 29.5 + - - +
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Residues in contact with LEU 399 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191R VAL* 3.9 18.2 - - + -
202R PHE* 4.1 24.0 - - + -
204R MET* 3.7 23.5 - - + -
208R GLU* 5.0 1.8 - - + -
211R TYR* 6.2 2.0 - - + -
219R VAL* 3.8 25.8 - - + -
220R SER 4.5 2.2 - - - +
221R ASN* 3.9 24.9 - - + +
395R ARG 2.8 16.0 + - - +
396R VAL* 3.6 5.8 - - - +
397R VAL 3.2 0.4 - - - -
398R ASP* 1.3 73.3 - - - +
400R LEU* 1.3 56.2 + - - +
402R TYR* 3.1 8.7 + - + +
403R MET* 2.7 54.9 + - + +
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Residues in contact with LEU 400 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76R LEU* 4.3 13.6 - - + +
78R VAL* 3.7 22.4 - - + -
90R VAL* 5.5 0.2 - - + -
94R CYS* 5.1 2.9 - - - -
99R VAL* 5.5 0.2 - - + -
165R TYR* 3.9 33.4 - - + -
166R VAL 5.0 1.3 - - - +
167R VAL* 3.7 26.9 - - + -
191R VAL* 3.4 28.5 - - + +
396R VAL* 3.0 19.8 + - + +
397R VAL* 3.4 18.6 - - + +
399R LEU* 1.3 76.2 - - - +
401R ARG* 1.3 63.9 + - - +
403R MET* 3.1 7.7 + - - +
404R PHE* 2.9 24.8 + - - +
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Residues in contact with ARG 401 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76R LEU* 4.1 14.3 - - + +
97R LYS* 4.0 37.7 + - - +
99R VAL* 4.0 27.2 - - + +
397R VAL* 2.9 26.4 + - - +
398R ASP* 3.8 9.2 + - - +
400R LEU* 1.3 75.2 - - - +
402R TYR* 1.3 63.8 + - - +
404R PHE* 3.2 3.9 + - - +
405R SER* 3.1 22.3 + - - -
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Residues in contact with TYR 402 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204R MET* 4.0 11.9 - - + -
208R GLU* 3.2 50.9 + - + -
209R ASN* 3.3 14.4 - - + +
211R TYR* 4.3 7.2 - + + -
398R ASP 2.9 18.9 + - - +
399R LEU* 3.5 8.5 - - + +
401R ARG* 1.3 76.4 - - - +
403R MET* 1.3 72.2 + - + +
405R SER* 2.6 28.2 + - - -
406R ARG* 2.8 50.9 + - + +
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Residues in contact with MET 403 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165R TYR* 4.2 4.9 - - + -
189R ARG* 3.8 26.9 - - + -
190R VAL 4.7 2.0 - - - +
191R VAL* 3.8 26.9 - - + -
211R TYR* 3.5 47.8 - - + +
216R MET 5.4 0.4 - - - +
217R ASN 5.8 1.1 - - - +
219R VAL* 3.8 22.7 - - + -
399R LEU* 2.7 37.0 + - + +
400R LEU* 3.6 5.8 - - - +
402R TYR* 1.3 75.3 - - + +
404R PHE* 1.3 63.1 + - - +
406R ARG* 2.9 10.6 + - - +
407R ASP* 2.9 27.9 + - - +
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Residues in contact with PHE 404 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74R ARG 3.2 28.5 - - - -
75R GLU* 3.4 19.7 - - - -
76R LEU* 3.6 33.0 - - + -
165R TYR* 3.4 36.5 - + - +
400R LEU 2.9 16.1 + - - +
401R ARG* 3.6 7.0 - - - +
402R TYR 3.2 0.4 - - - -
403R MET* 1.3 76.0 - - - +
405R SER* 1.3 60.0 + - - +
406R ARG 3.1 4.2 + - - -
407R ASP* 3.5 8.1 + - + +
408R ALA* 3.8 16.0 + - + +
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Residues in contact with SER 405 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401R ARG 3.1 11.2 + - - -
402R TYR* 2.6 27.9 + - - -
404R PHE* 1.3 77.9 - - - +
406R ARG* 1.3 65.5 + - - +
408R ALA* 4.8 6.7 - - - +
409R GLU* 4.8 2.4 - - - +
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Residues in contact with ARG 406 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208R GLU 4.0 4.0 + - - -
209R ASN* 4.3 7.9 + - - +
211R TYR* 2.9 33.9 + - + +
212R ASN* 4.8 0.2 - - - +
213R PRO* 3.3 29.6 - - + +
402R TYR* 2.8 64.3 + - + +
403R MET 2.9 8.0 + - - +
405R SER* 1.3 83.0 - - - +
407R ASP* 1.3 63.6 + - - +
408R ALA 3.2 2.9 - - - -
409R GLU* 3.1 49.5 + - - +
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Residues in contact with ASP 407 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165R TYR* 2.4 43.6 + - - +
189R ARG* 3.5 22.0 + - - +
211R TYR* 2.8 35.4 + - - -
213R PRO* 3.6 13.1 - - - +
403R MET 2.9 17.9 + - - +
404R PHE* 3.5 2.8 + - + +
406R ARG* 1.3 76.8 - - - +
408R ALA* 1.3 59.1 + - - +
409R GLU* 3.3 6.3 + - - +
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Residues in contact with ALA 408 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404R PHE* 3.8 16.8 + - + +
405R SER 5.3 5.0 - - - +
406R ARG 3.2 1.2 - - - -
407R ASP* 1.3 75.2 - - - +
409R GLU* 1.3 64.4 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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