Contacts of the helix formed by residues 45 - 59 (chain F) in PDB entry 6JBQ
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 ASP 45 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D ASP* 4.9 7.0 - - - +
270D ARG* 5.1 3.5 + - - -
271D ARG* 3.5 34.5 + - - +
275D ARG* 5.7 0.4 - - - +
41F VAL* 4.2 3.0 - - - +
42F PRO* 3.5 15.0 + - + +
43F SER 3.4 0.4 - - - -
44F GLY* 1.3 83.0 - - - +
46F VAL* 1.3 59.9 + - - +
47F PRO* 3.8 2.9 - - - -
48F ASP* 4.4 13.1 + - + +
49F VAL* 3.4 19.8 + - - +
85F TYR* 2.5 39.8 + - + +
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Residues in contact with VAL 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F ALA* 4.7 12.1 - - + +
37F VAL* 4.7 1.1 - - + -
38F SER* 3.8 28.7 - - - +
41F VAL* 3.7 13.5 - - + -
42F PRO 3.4 18.2 - - - +
43F SER* 3.4 21.5 - - - +
45F ASP* 1.3 77.7 - - - +
47F PRO* 1.4 72.9 - - + +
48F ASP 3.3 0.6 + - - -
49F VAL* 3.3 6.7 - - - +
50F VAL* 3.0 35.9 + - + +
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Residues in contact with PRO 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D ARG* 4.0 19.3 - - - +
297D ARG* 5.9 3.1 - - - +
298D MET* 3.6 34.9 - - + +
301D GLU* 6.0 2.2 - - - +
34F ALA* 6.5 0.4 - - + -
44F GLY 4.4 4.7 - - - +
45F ASP* 3.9 2.2 - - - -
46F VAL* 1.4 98.0 - - + +
48F ASP* 1.3 58.9 + - - +
50F VAL* 4.0 7.3 - - + +
51F GLN* 2.9 32.7 + - - +
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Residues in contact with ASP 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D ARG* 4.9 12.2 + - - +
274D ASN* 5.5 3.8 - - - +
275D ARG* 3.1 44.6 + - - +
278D ARG* 2.4 45.0 + - - +
295D GLU* 4.7 1.4 - - - +
298D MET* 4.8 2.7 - - - +
45F ASP* 4.7 13.8 - - + +
46F VAL 3.3 1.0 - - - -
47F PRO* 1.3 79.5 - - - +
49F VAL* 1.3 57.6 + - - +
51F GLN* 3.8 1.4 - - - -
52F GLU* 2.9 28.8 + - - +
85F TYR* 6.4 2.2 - - + -
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Residues in contact with VAL 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F VAL* 3.7 21.0 - - + +
41F VAL* 4.2 8.1 - - + -
45F ASP 3.4 15.5 - - - +
46F VAL* 3.3 15.5 - - - +
48F ASP* 1.3 76.7 - - - +
50F VAL* 1.3 60.2 + - - +
52F GLU* 3.8 7.0 - - + +
53F ALA* 2.9 28.2 + - - +
81F THR* 3.4 39.9 + - - +
82F ALA* 4.1 5.4 - - - +
85F TYR* 4.1 20.2 - - + -
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Residues in contact with VAL 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D MET* 6.5 0.7 - - + -
30F GLN* 4.7 3.4 - - + +
33F VAL* 3.9 20.9 - - + +
34F ALA* 3.8 29.8 - - + +
37F VAL* 3.9 18.4 - - + -
46F VAL* 3.0 24.2 + - + +
47F PRO* 4.0 6.3 - - + +
49F VAL* 1.3 76.8 - - - +
51F GLN* 1.3 57.4 + - + +
53F ALA* 3.3 8.4 + - - +
54F PHE* 3.0 50.0 + - + -
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Residues in contact with GLN 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D ARG* 4.7 2.5 + - - -
282D LEU* 3.9 3.9 - - - +
291D ILE* 2.6 49.6 + - + +
294D ASN* 4.1 4.7 - - + +
295D GLU* 2.9 36.6 - - - +
298D MET* 3.3 29.4 - - + +
47F PRO 2.9 18.2 + - - +
48F ASP* 4.1 2.9 - - - +
50F VAL* 1.3 76.7 - - - +
52F GLU* 1.3 57.8 + - - +
54F PHE* 3.2 15.2 + - + +
55F ILE* 2.9 38.3 + - + +
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Residues in contact with GLU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D ARG* 3.0 33.1 + - - +
281D ARG* 4.7 9.5 + - - -
48F ASP 2.9 18.5 + - - +
49F VAL* 3.8 9.9 - - + +
50F VAL 3.3 0.2 - - - -
51F GLN* 1.3 72.4 - - - +
53F ALA* 1.3 62.4 + - - +
55F ILE* 3.3 16.0 + - - +
56F LYS* 2.9 48.3 + - + +
81F THR* 4.8 4.3 - - + -
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Residues in contact with ALA 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F VAL* 5.2 4.0 - - + -
37F VAL* 6.0 0.4 - - + -
49F VAL 2.9 14.8 + - - +
50F VAL* 3.5 7.4 - - - +
52F GLU* 1.3 74.8 - - - +
54F PHE* 1.3 60.5 + - + +
56F LYS* 3.4 1.5 + - - +
57F ALA* 2.9 29.5 + - - +
74F LEU* 5.7 1.3 - - + -
77F ILE* 3.5 18.7 - - + +
78F ALA* 4.3 9.4 - - + -
81F THR* 3.4 35.5 - - + +
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Residues in contact with PHE 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291D ILE* 5.3 9.4 - - + -
294D ASN* 6.4 0.4 - - - -
22F PHE* 4.3 16.5 - + + -
26F VAL* 3.7 29.8 - - + -
29F TYR* 4.3 1.1 - - + -
30F GLN* 3.7 33.0 - - + -
33F VAL* 3.7 21.5 - - + -
50F VAL* 3.0 34.4 + - + -
51F GLN* 3.2 16.6 + - + +
53F ALA* 1.3 75.9 - - + +
55F ILE* 1.3 59.4 + - + +
57F ALA* 3.4 3.6 + - - +
58F TYR* 2.9 29.7 + - - +
74F LEU* 3.7 38.1 - - + -
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Residues in contact with ILE 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D ARG* 3.9 29.4 - - + -
282D LEU* 3.7 39.0 - - + -
285D LEU* 5.9 0.9 - - + -
291D ILE* 4.7 11.2 - - + -
51F GLN* 2.9 25.9 + - + +
52F GLU* 3.3 16.4 + - - +
54F PHE* 1.3 77.5 - - + +
56F LYS* 1.3 58.8 + - + +
58F TYR* 3.2 6.8 + - + +
59F ARG* 2.9 51.0 + - + +
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Residues in contact with LYS 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F GLU* 2.9 32.0 + - - +
53F ALA* 4.0 4.0 - - - +
55F ILE* 1.3 76.9 - - + +
57F ALA* 1.3 60.1 + - - +
59F ARG* 4.0 15.5 - - - +
60F ALA* 3.5 23.9 + - - +
77F ILE* 4.7 6.8 - - + +
80F ASN* 6.1 1.2 - - - +
81F THR* 3.7 27.7 - - - +
84F ASN* 4.3 11.5 - - - +
23H T 4.3 23.5 - - + +
24H G 5.2 5.5 + - - -
25H T 4.3 21.8 + - - +
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Residues in contact with ALA 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F PHE* 4.8 9.6 - - + -
53F ALA 2.9 18.2 + - - +
54F PHE* 3.7 5.2 - - - +
55F ILE 3.2 0.2 - - - -
56F LYS* 1.3 77.3 - - - +
58F TYR* 1.3 63.3 + - - +
61F LEU* 3.6 10.9 + - - +
70F PHE* 4.9 0.2 - - + -
73F TRP* 3.2 35.1 - - + -
74F LEU* 4.0 18.2 - - + -
77F ILE* 3.8 18.3 - - + +
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Residues in contact with TYR 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D LEU* 5.2 6.0 + - + -
286D ALA 4.1 6.9 + - - -
287D ALA* 5.0 4.7 - - + -
288D PRO* 4.2 22.2 - - + -
291D ILE* 5.1 8.1 - - + -
14F VAL* 4.5 20.2 - - + -
19F GLN* 2.8 36.4 + - - -
22F PHE* 4.4 34.3 - + + -
54F PHE 2.9 16.8 + - - +
55F ILE* 3.8 7.4 - - + +
57F ALA* 1.3 77.5 - - - +
59F ARG* 1.3 70.7 + - + +
60F ALA 3.2 1.1 + - - -
61F LEU* 3.8 15.2 + - + +
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Residues in contact with ARG 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285D LEU* 3.6 30.1 - - + +
55F ILE* 2.9 39.4 + - + +
56F LYS* 4.6 14.0 - - - +
57F ALA 3.4 0.2 - - - -
58F TYR* 1.3 87.1 - - + +
60F ALA* 1.3 58.8 + - - +
61F LEU 3.8 0.7 - - - -
62F ASP* 4.4 5.0 - - - +
23H T 5.5 7.1 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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