Contacts of the helix formed by residues 392 - 414 (chain C) in PDB entry 4Q5U
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 ARG 392 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU* 3.1 35.6 + - - -
113A GLY 5.9 0.2 + - - -
114A GLU* 3.1 33.2 + - - +
116A LEU* 5.2 8.7 - - + -
391C ALA* 1.3 84.3 - - + +
393C LYS* 1.3 64.7 + - - +
394C GLU 3.3 2.7 - - - -
395C VAL* 3.1 22.4 - - - +
396C ILE* 2.9 42.5 + - + +
399C LYS* 4.8 1.0 - - - +
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Residues in contact with LYS 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU* 4.5 17.2 + - - +
144A MET* 4.8 6.5 - - - -
147A ALA 3.5 17.6 + - - -
391C ALA 3.3 10.9 - - - +
392C ARG* 1.3 78.2 - - - +
394C GLU* 1.3 63.7 + - + +
396C ILE* 3.4 6.0 + - - +
397C ARG* 2.9 70.1 + - + +
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Residues in contact with GLU 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 3.4 27.8 - - - +
391C ALA 5.2 1.0 + - - -
392C ARG 3.3 0.4 - - - -
393C LYS* 1.3 83.1 - - + +
395C VAL* 1.3 63.3 + - - +
397C ARG* 3.3 33.4 + - - +
398C ASN* 3.0 32.6 + - - -
401C ARG* 5.0 6.1 + - - -
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Residues in contact with VAL 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 4.1 29.2 + - + +
14A GLU* 3.8 37.2 - - + +
391C ALA 5.5 0.2 - - - +
392C ARG* 3.1 50.9 - - + +
394C GLU* 1.3 78.3 - - - +
396C ILE* 1.3 59.6 + - + +
398C ASN* 3.4 1.3 + - - +
399C LYS* 2.9 40.4 + - - +
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Residues in contact with ILE 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A MET* 4.0 20.4 - - + -
112A LEU* 5.5 1.8 - - + -
114A GLU* 3.8 32.3 - - + +
116A LEU* 4.5 17.0 - - + -
124A MET* 4.6 17.5 - - + -
144A MET* 6.3 0.2 - - - -
392C ARG* 2.9 40.3 + - + +
393C LYS* 3.7 5.6 - - - +
395C VAL* 1.3 75.1 - - - +
397C ARG* 1.3 68.9 + - + +
398C ASN 3.2 0.2 + - - -
399C LYS* 3.2 7.5 + - + +
400C ILE* 3.0 40.0 + - + +
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Residues in contact with ARG 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A MET* 3.0 34.3 + - + -
145A MET* 3.4 32.3 - - + +
146A THR 3.9 0.2 - - - -
147A ALA* 3.1 46.4 + - - +
393C LYS* 2.9 44.4 + - + +
394C GLU* 3.3 33.4 + - - +
396C ILE* 1.3 78.8 - - + +
398C ASN* 1.3 57.4 + - - +
400C ILE* 3.4 1.4 + - + -
401C ARG* 3.0 49.9 + - - +
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Residues in contact with ASN 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A GLN* 5.3 3.8 + - - +
11A GLU* 2.6 40.2 + - + +
12A PHE* 3.5 36.2 - - + -
15A ALA* 4.3 3.0 - - - +
72A MET* 3.6 10.6 - - - +
394C GLU* 3.0 20.1 + - - +
395C VAL* 4.0 4.9 - - - +
397C ARG* 1.3 75.6 - - - +
399C LYS* 1.3 64.1 + - - +
400C ILE 3.2 0.2 - - - -
401C ARG* 3.3 29.4 + - - +
402C ALA* 3.0 19.4 + - - +
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Residues in contact with LYS 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 3.9 23.2 + - - +
15A ALA* 4.0 22.4 - - + +
18A LEU* 4.8 12.2 - - + +
112A LEU* 2.8 41.8 + - + +
113A GLY* 3.7 12.7 + - - -
114A GLU* 3.0 31.0 + - + +
392C ARG* 4.8 1.8 - - - +
395C VAL* 2.9 34.2 + - + +
396C ILE* 3.2 6.5 + - + +
398C ASN* 1.3 75.5 - - - +
400C ILE* 1.3 57.5 + - - +
402C ALA* 3.2 4.4 + - - +
403C ILE* 3.0 32.8 + - - +
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Residues in contact with ILE 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 6.3 0.7 - - - -
88A ALA* 3.9 14.4 - - + +
92A PHE* 3.8 30.7 - - + -
109A MET* 4.6 9.4 - - + -
112A LEU* 3.9 12.8 - - + -
124A MET* 6.0 0.2 - - + -
141A PHE* 4.0 11.0 - - + -
144A MET* 5.0 7.9 - - - -
145A MET* 3.7 33.2 - - + -
396C ILE* 3.0 37.4 + - + +
397C ARG* 3.7 4.7 - - + +
399C LYS* 1.3 72.5 - - - +
401C ARG* 1.3 62.1 + - - +
403C ILE* 3.3 8.0 + - - +
404C GLY* 2.9 25.3 + - - -
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Residues in contact with ARG 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A MET* 4.2 11.4 - - + -
84A GLU* 4.6 11.2 - - + +
85A ILE* 5.6 9.0 - - + +
145A MET* 3.0 39.3 + - + +
147A ALA 5.0 2.2 - - - +
394C GLU* 5.0 5.5 + - - -
397C ARG* 3.0 45.7 + - - +
398C ASN* 3.3 31.6 + - - +
399C LYS 3.3 0.2 - - - -
400C ILE* 1.3 75.9 - - - +
402C ALA* 1.3 62.3 + - - +
404C GLY* 3.4 2.5 + - - +
405C LYS* 3.1 31.0 + - - +
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Residues in contact with ALA 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA* 4.4 4.9 - - + -
19A PHE* 4.2 13.2 - - + -
68A PHE* 4.0 19.3 - - + -
71A MET* 5.1 1.9 - - + +
72A MET* 3.8 23.1 - - + +
398C ASN 3.0 14.3 + - - +
399C LYS* 3.5 9.4 - - - +
400C ILE 3.2 0.2 - - - -
401C ARG* 1.3 75.2 - - - +
403C ILE* 1.3 64.6 + - - +
405C LYS* 3.4 5.5 + - - +
406C MET* 3.2 25.6 + - - +
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Residues in contact with ILE 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.1 9.6 - - + -
19A PHE* 3.7 24.2 - - + -
35A VAL* 4.3 4.5 - - + -
36A MET* 4.8 5.3 - - + +
39A LEU* 3.9 25.4 - - + -
88A ALA* 4.8 2.5 - - - -
91A VAL* 4.5 15.5 - - + -
92A PHE* 4.1 17.3 - - + -
112A LEU* 3.6 31.6 - - + -
399C LYS 3.0 13.7 + - - +
400C ILE* 3.6 9.2 - - - +
402C ALA* 1.3 77.8 - - - +
404C GLY* 1.3 53.2 + - - +
406C MET* 3.3 6.0 + - - +
407C ALA* 2.7 33.2 + - + +
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Residues in contact with GLY 404 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLU* 3.2 34.2 - - - +
87A GLU* 4.2 0.5 - - - +
88A ALA* 4.0 10.7 - - - +
400C ILE 2.9 15.8 + - - -
401C ARG* 3.8 2.5 - - - -
402C ALA 3.3 0.2 - - - -
403C ILE* 1.3 75.8 - - - +
405C LYS* 1.3 56.3 + - - +
407C ALA* 3.8 1.8 - - - +
408C ARG* 2.9 31.9 + - - +
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Residues in contact with LYS 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A MET* 3.6 44.5 + - + -
72A MET* 4.0 30.9 + - - +
74A ARG* 5.7 1.2 - - - +
76A MET* 3.3 28.5 - - - +
84A GLU* 2.8 45.3 + - - +
401C ARG* 3.1 17.7 + - - +
402C ALA* 3.5 8.7 - - - +
404C GLY* 1.3 77.2 - - - +
406C MET* 1.3 62.5 + - - +
408C ARG* 3.4 3.1 + - - +
409C VAL* 3.1 29.0 + - + +
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Residues in contact with MET 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 4.2 14.6 - - + -
32A LEU* 4.1 30.5 - - + -
36A MET* 3.7 17.5 - - + -
51A MET* 3.6 22.6 - - + +
55A VAL* 3.8 19.5 - - + -
63A ILE* 5.4 5.8 - - + -
68A PHE* 6.2 0.4 - - + -
71A MET* 3.5 36.1 - - + -
402C ALA 3.2 10.5 + - - +
403C ILE 3.7 6.3 - - - +
405C LYS* 1.3 79.3 - - + +
407C ALA* 1.3 66.2 + - - +
409C VAL* 3.3 10.5 + - + +
410C PHE* 3.0 23.4 + - - +
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Residues in contact with ALA 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A MET* 5.2 5.8 - - - +
41A GLN* 5.3 3.0 + - - +
87A GLU* 3.8 23.1 - - + +
91A VAL* 3.8 27.4 - - + -
403C ILE* 2.7 23.1 + - + +
404C GLY 3.8 1.1 - - - +
406C MET* 1.3 74.4 - - - +
408C ARG* 1.3 58.8 + - - +
410C PHE* 3.4 11.2 + - - +
411C SER* 2.9 30.0 + - - -
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Residues in contact with ARG 408 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A MET* 6.4 0.2 - - - -
80A ASP* 3.4 35.3 + - - +
83A GLU* 4.0 34.7 - - + +
84A GLU* 4.0 20.5 + - + +
87A GLU* 3.9 15.7 - - + -
404C GLY 2.9 18.2 + - - +
405C LYS 3.8 4.7 - - - +
407C ALA* 1.3 75.4 - - - +
409C VAL* 1.3 67.1 + - + +
411C SER* 3.3 3.6 + - - -
412C VAL* 3.0 41.5 + - + +
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Residues in contact with VAL 409 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ASP 5.0 0.9 - - - +
51A MET* 4.1 30.5 - - + +
54A GLU* 3.2 37.9 - - + +
55A VAL* 6.2 1.1 - - + -
405C LYS 3.1 17.7 + - - +
406C MET* 3.7 16.6 - - + +
408C ARG* 1.3 77.6 - - + +
410C PHE* 1.3 62.9 + - - +
412C VAL* 3.4 8.3 + - + +
413C LEU* 3.2 29.0 + - + +
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Residues in contact with PHE 410 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A MET* 5.6 4.0 - - - -
41A GLN* 3.5 39.7 - - + -
42A ASN 4.3 3.6 - - - -
43A PRO* 3.7 22.4 - - + -
47A GLU* 3.5 27.4 - - + -
51A MET* 4.1 24.0 - - + +
406C MET 3.0 17.1 + - - +
407C ALA* 3.5 8.3 - - - +
409C VAL* 1.3 74.6 - - - +
411C SER* 1.3 66.7 + - - +
413C LEU* 3.3 10.6 + - + +
414C ARG* 3.1 63.3 + - + +
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Residues in contact with SER 411 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLU* 2.7 35.5 + - - -
90A ARG* 4.5 3.3 + - - -
407C ALA 2.9 13.2 + - - -
408C ARG* 3.3 10.1 + - - -
410C PHE* 1.3 80.2 - - - +
412C VAL* 1.3 63.0 + - - +
414C ARG* 3.1 23.7 + - - +
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Residues in contact with VAL 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C ARG* 3.0 42.9 + - + +
409C VAL* 3.7 9.0 - - - +
410C PHE 3.3 0.4 - - - -
411C SER* 1.3 74.5 - - - +
413C LEU* 1.3 69.0 + - + +
414C ARG 3.3 7.6 - - - +
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Residues in contact with LEU 413 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A GLU* 3.8 40.6 - - + +
50A ASP* 3.9 26.2 - - + +
51A MET* 3.8 16.8 - - + +
54A GLU* 6.0 0.4 - - - +
409C VAL* 3.2 21.2 + - + +
410C PHE* 3.3 9.2 + - + +
412C VAL* 1.3 82.2 - - + +
414C ARG* 1.3 63.7 + - + +
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Residues in contact with ARG 414 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ASN* 3.2 23.6 + - - +
44A THR* 4.3 4.8 - - - +
47A GLU* 2.6 41.5 + - - +
410C PHE* 3.1 50.2 + - + +
411C SER* 3.1 19.8 - - - +
412C VAL 3.2 8.5 - - - +
413C LEU* 1.3 78.3 - - - +
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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
------------------------------------------------------------
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