Contacts of the helix formed by residues 389 - 407 (chain O) in PDB entry 5C7O
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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85O ARG* 2.8 48.0 + - + +
86O ILE* 3.9 7.8 - - + +
89O LEU* 3.6 14.4 - - + -
123O THR* 3.9 2.9 + - - +
124O HIS* 2.9 22.0 + - - +
310O PRO 4.1 8.6 - - - +
311O ASP* 3.3 24.2 + - - +
387O ASP* 3.1 3.2 + - - +
388O ASN* 1.3 86.5 - - - +
390O TYR* 1.3 60.2 + - - +
391O GLY 3.7 0.2 - - - -
392O TYR 4.2 0.2 - - - -
393O SER* 2.8 34.0 + - - -
501O NAD 4.1 15.0 + - - +
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Residues in contact with TYR 390 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89O LEU* 4.0 27.8 - - + -
92O ARG* 4.4 15.6 + - + +
96O GLU* 2.6 28.2 + - - -
124O HIS* 3.7 32.8 - + + -
360O GLY* 3.5 30.1 - - - -
361O ASP 4.0 4.3 - - - +
362O THR* 4.4 3.4 - - + -
387O ASP* 2.9 28.1 + - - +
389O GLU* 1.3 71.5 - - - +
391O GLY* 1.3 67.5 + - - +
393O SER* 3.4 3.9 + - - -
394O HIS* 3.1 60.7 + + - -
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Residues in contact with GLY 391 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361O ASP 3.5 15.4 + - - -
362O THR 4.0 6.5 - - - -
363O HIS 3.8 17.7 - - - -
364O SER* 5.3 2.5 - - - -
387O ASP* 3.0 12.3 + - - -
390O TYR* 1.3 77.4 - - - +
392O TYR* 1.3 61.8 + - - +
394O HIS* 3.2 6.1 + - - +
395O ARG* 3.0 28.3 + - - +
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Residues in contact with TYR 392 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86O ILE* 4.1 8.3 - - + -
193O SER* 2.9 30.7 - - - -
194O ALA 3.2 0.9 + - - -
221O ASN* 3.4 30.9 - - - +
222O ALA 2.6 29.8 + - - -
223O SER 3.6 8.1 - - - -
224O OCS 3.6 22.0 - - + -
227O ASN* 3.6 11.2 - - + -
387O ASP 3.8 4.2 + - - -
388O ASN 3.3 21.5 - - - +
389O GLU 3.9 0.4 + - - +
390O TYR 3.3 0.2 - - - -
391O GLY* 1.3 76.6 - - - +
393O SER* 1.3 62.6 + - - +
395O ARG* 3.0 7.1 + - - +
396O VAL* 3.0 35.9 + - + +
501O NAD 3.3 27.6 - + - -
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Residues in contact with SER 393 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86O ILE* 3.7 18.7 + - - +
89O LEU* 3.4 38.9 - - - +
90O VAL* 3.8 10.8 - - - +
93O ALA* 4.5 2.9 - - - -
389O GLU 2.8 21.2 + - - -
390O TYR* 3.7 4.7 - - - -
392O TYR* 1.3 79.3 - - - +
394O HIS* 1.3 64.1 + - - +
396O VAL* 3.3 7.6 + - - +
397O VAL* 3.3 24.3 + - - +
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Residues in contact with HIS 394 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89O LEU 5.4 0.4 - - - -
93O ALA* 3.7 25.0 - - + +
96O GLU* 3.0 30.4 + - + -
97O LYS* 3.1 30.9 + - + +
362O THR* 3.7 24.0 - - + +
390O TYR* 3.1 46.5 + + - +
391O GLY 3.2 9.2 + - - +
393O SER* 1.3 79.0 - - - +
395O ARG* 1.3 73.1 + - - +
397O VAL* 3.2 4.4 + - - +
398O ASP* 2.9 31.5 + - - +
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Residues in contact with ARG 395 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97O LYS* 4.1 4.6 - - - +
204O MET* 4.0 17.4 - - + +
221O ASN* 3.7 16.6 + - - +
227O ASN* 3.9 15.0 - - + +
344O GLY 3.7 12.7 + - - -
345O ILE* 3.5 21.8 - - - +
362O THR* 2.8 32.3 + - - -
363O HIS 3.6 0.8 - - - -
364O SER* 2.9 46.3 + - - +
391O GLY 3.0 14.9 + - - +
392O TYR* 3.5 10.5 - - - +
394O HIS* 1.3 85.1 - - - +
396O VAL* 1.3 60.3 + - - +
398O ASP* 2.8 31.0 + - - +
399O LEU* 2.8 31.4 + - - +
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Residues in contact with VAL 396 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86O ILE* 4.8 0.2 - - + -
90O VAL* 4.0 18.6 - - + -
167O VAL* 3.8 33.7 - - + -
191O VAL* 4.4 10.6 - - + +
193O SER* 4.4 9.6 - - - -
221O ASN* 3.5 15.9 - - + +
392O TYR* 3.0 44.4 + - + +
393O SER 3.4 8.5 - - - +
394O HIS 3.3 0.4 - - - -
395O ARG* 1.3 75.9 - - - +
397O VAL* 1.3 62.7 + - - +
399O LEU* 3.4 4.0 + - - +
400O LEU* 3.0 26.0 + - + +
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Residues in contact with VAL 397 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90O VAL* 3.8 20.2 - - + +
93O ALA* 3.6 21.8 - - + +
94O CYS* 3.9 13.7 - - - -
97O LYS* 4.0 22.0 - - + -
99O VAL* 3.8 28.9 - - + -
393O SER 3.4 13.9 - - - +
394O HIS* 3.2 7.7 + - - +
395O ARG 3.2 0.4 - - - -
396O VAL* 1.3 76.8 - - - +
398O ASP* 1.3 56.4 + - - +
400O LEU* 3.2 9.4 + - + +
401O ARG* 3.0 30.5 + - - +
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Residues in contact with ASP 398 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97O LYS* 2.7 27.0 + - - +
204O MET* 4.0 17.8 - - + +
345O ILE* 4.8 3.3 - - + +
394O HIS 2.9 14.5 + - - +
395O ARG* 2.8 45.0 + - - +
397O VAL* 1.3 76.8 - - - +
399O LEU* 1.3 57.2 + - - +
401O ARG* 3.4 11.1 + - - +
402O TYR* 2.9 30.3 + - - +
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Residues in contact with LEU 399 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191O VAL* 4.0 15.5 - - + -
202O PHE* 4.2 23.1 - - + -
204O MET* 3.9 25.2 - - + +
208O GLU* 4.8 2.2 - - + -
211O TYR* 5.9 1.6 - - + -
219O VAL* 4.2 14.1 - - + -
220O SER 4.5 3.1 - - - +
221O ASN* 3.4 35.9 - - + +
395O ARG 2.8 18.2 + - - +
396O VAL 3.7 4.7 - - - +
398O ASP* 1.3 72.3 - - - +
400O LEU* 1.3 60.6 + - - +
402O TYR* 3.2 7.5 + - + +
403O MET* 2.8 53.2 + - + +
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Residues in contact with LEU 400 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76O LEU* 3.9 13.7 - - + +
78O VAL* 4.0 19.3 - - + -
90O VAL* 5.3 0.4 - - + -
94O CYS* 5.3 2.7 - - - -
99O VAL* 5.7 0.4 - - + -
165O TYR* 3.8 37.1 - - + -
166O VAL 5.0 0.7 - - - +
167O VAL* 3.6 28.7 - - + -
189O ARG* 6.2 0.2 - - + -
191O VAL* 3.6 27.6 - - + +
396O VAL* 3.0 21.2 + - + +
397O VAL* 3.5 18.2 - - + +
399O LEU* 1.3 78.4 - - - +
401O ARG* 1.3 57.5 + - - +
403O MET* 3.3 5.5 + - - +
404O PHE* 2.9 30.0 + - - +
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Residues in contact with ARG 401 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76O LEU* 3.9 11.9 - - + -
97O LYS* 3.9 37.4 + - - +
99O VAL* 3.8 27.8 - - + +
397O VAL* 3.0 26.4 + - - +
398O ASP* 3.8 11.7 + - - +
400O LEU* 1.3 76.0 - - - +
402O TYR* 1.3 61.7 + - - +
404O PHE* 3.4 4.8 + - - +
405O SER* 3.0 23.0 + - - -
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Residues in contact with TYR 402 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204O MET* 3.9 13.9 - - + -
208O GLU* 3.2 48.9 - - + -
209O ASN* 3.4 16.1 + - - +
211O TYR* 4.4 5.4 - + + -
398O ASP 2.9 17.9 + - - +
399O LEU* 3.6 10.8 - - + +
401O ARG* 1.3 74.5 - - - +
403O MET* 1.3 70.8 + - + +
405O SER* 2.6 29.1 + - - -
406O ARG* 2.9 53.8 + - + +
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Residues in contact with MET 403 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165O TYR* 4.0 8.1 - - + -
189O ARG* 4.0 25.6 - - + -
190O VAL 4.7 1.3 - - - +
191O VAL* 3.5 28.0 - - + -
211O TYR* 3.5 52.9 - - + +
217O ASN 5.3 1.1 - - - +
219O VAL* 3.8 19.1 - - + -
399O LEU* 2.8 41.1 + - + +
400O LEU* 3.6 6.1 - - - +
402O TYR* 1.3 72.8 - - + +
404O PHE* 1.3 62.4 + - - +
406O ARG* 3.0 6.4 + - - +
407O ASP* 2.5 27.4 - - - +
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Residues in contact with PHE 404 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74O ARG 4.0 11.7 - - - -
75O GLU* 3.2 38.6 - - - -
76O LEU* 3.4 35.2 - - + -
77O THR 5.3 0.2 - - - -
165O TYR* 3.7 31.8 - + - +
400O LEU 2.9 16.7 + - - +
401O ARG* 3.7 5.8 - - - +
402O TYR 3.2 0.2 - - - -
403O MET* 1.3 76.4 - - - +
405O SER* 1.3 63.5 + - - +
407O ASP* 3.2 12.3 + - + +
408O LYS* 3.8 14.0 + - + +
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Residues in contact with SER 405 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401O ARG 3.0 14.0 + - - -
402O TYR* 2.6 29.5 + - - -
404O PHE* 1.3 78.9 - - - +
406O ARG* 1.3 64.8 + - - +
408O LYS* 4.3 10.4 + - - +
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Residues in contact with ARG 406 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208O GLU 4.2 0.2 + - - -
209O ASN* 3.8 11.3 + - - +
211O TYR* 2.9 33.3 + - + -
212O ASN* 4.6 2.4 + - - +
213O PRO* 3.5 25.4 - - + +
402O TYR* 2.9 59.3 + - + +
403O MET 3.0 8.3 + - - +
405O SER* 1.3 79.8 + - - +
407O ASP* 1.3 63.9 + - - +
408O LYS 3.2 11.7 + - - -
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Residues in contact with ASP 407 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165O TYR* 2.6 29.4 + - - +
189O ARG* 3.2 17.6 + - - +
211O TYR* 2.9 22.3 + - - -
213O PRO* 3.0 33.2 - - - +
403O MET 2.5 25.0 + - - +
404O PHE* 3.2 7.4 + - + +
406O ARG* 1.3 75.4 - - - +
408O LYS* 1.3 58.1 + - - +
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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