Contacts of the helix formed by residues 74 - 90 (chain A) in PDB entry 3FIA
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 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PHE* 3.6 4.7 - - - -
37A GLY 3.4 16.2 - - - +
38A PHE* 3.8 20.8 - - + -
73A MSE 1.3 74.2 - - - +
75A GLN* 1.3 60.2 + - - +
76A VAL* 3.3 12.0 + - - +
77A GLU* 3.0 36.6 + - - +
78A PHE* 2.9 29.8 + - - +
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Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ARG* 2.9 21.5 + - - +
26A ASP* 3.0 47.2 + - - +
29A PHE* 3.6 35.8 - - + -
37A GLY 4.1 1.0 + - - +
74A ASP* 1.3 77.5 - - - +
76A VAL* 1.3 64.3 + - + +
78A PHE* 3.4 4.9 + - - +
79A SER* 3.0 22.3 + - - -
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ARG* 3.7 31.2 - - - +
67A MSE 3.6 26.2 - - + -
74A ASP* 3.3 11.8 + - - +
75A GLN* 1.3 76.8 - - + +
77A GLU* 1.3 63.3 + - - +
79A SER* 3.1 5.9 + - - -
80A ILE* 3.1 27.5 + - + +
102A MSE 5.9 0.4 - - - +
103A LYS* 5.3 8.3 - - - +
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A PHE* 6.0 0.2 - - - -
65A ALA* 3.2 30.6 - - - +
66A ASP* 3.7 2.4 - - - +
67A MSE 3.2 29.0 + - + +
68A ASN* 3.0 16.3 + - - +
72A ARG 3.1 9.4 - - - +
73A MSE 3.2 20.4 - - + +
74A ASP* 3.0 26.1 + - - +
76A VAL* 1.3 75.6 - - - +
78A PHE* 1.3 63.0 + - - +
80A ILE* 3.3 9.2 + - - +
81A ALA* 3.0 18.9 + - - +
201A CA 2.4 30.8 - - - -
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Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A HIS* 3.5 22.4 - - + -
28A GLN* 3.9 6.1 - - + -
29A PHE* 3.4 39.7 - + + -
32A LEU* 3.6 25.4 - - + -
39A ILE* 4.1 4.9 - - + -
47A PHE* 3.7 22.9 - + + -
48A PHE* 3.8 28.3 - + - -
73A MSE 3.6 14.7 - - + +
74A ASP 2.9 18.4 + - - +
75A GLN* 3.5 5.2 - - + +
76A VAL 3.2 0.2 - - - -
77A GLU* 1.3 77.6 - - - +
79A SER* 1.3 58.0 + - - +
81A ALA* 3.2 2.6 + - - +
82A MSE 2.9 52.4 + - + +
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Residues in contact with SER 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ILE* 3.6 17.5 - - - +
22A ARG* 3.4 29.6 + - - -
25A HIS* 2.8 40.5 + - - -
75A GLN 3.0 13.8 + - - -
76A VAL 3.1 9.2 + - - -
78A PHE* 1.3 76.0 - - - +
80A ILE* 1.3 62.5 + - - +
82A MSE 3.2 0.9 + - - -
83A LYS* 2.9 21.3 + - - +
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Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ILE* 4.0 11.4 - - + -
65A ALA* 4.0 14.6 - - + -
67A MSE 3.6 41.1 - - + -
76A VAL* 3.1 17.4 + - + +
77A GLU* 3.5 8.3 - - - +
79A SER* 1.3 77.5 - - - +
81A ALA* 1.3 62.5 + - - +
83A LYS* 3.2 3.6 + - - +
84A LEU* 3.0 28.3 + - + +
98A LEU* 3.6 34.3 - - + -
102A MSE 3.7 29.6 - - + +
103A LYS* 4.7 0.9 - - - -
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 3.4 36.3 - - + -
61A ILE* 3.9 11.8 - - + +
65A ALA* 3.7 21.3 - - + -
73A MSE 4.2 1.3 - - + -
77A GLU 3.0 9.7 + - - +
78A PHE 3.5 5.2 - - - +
80A ILE* 1.3 75.1 - - - +
82A MSE 1.3 58.2 + - - +
84A LEU* 3.2 3.7 + - - +
85A ILE* 2.9 35.2 + - - +
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Residues in contact with MSE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A HIS* 3.4 34.4 + - + +
28A GLN* 4.2 25.8 - - + -
47A PHE* 3.9 18.4 - - + -
48A PHE* 4.2 10.1 - - - -
78A PHE* 2.9 49.8 + - + +
79A SER 3.2 1.8 + - - +
81A ALA* 1.3 75.0 - - - +
83A LYS* 1.3 64.1 + - - +
85A ILE* 3.4 14.3 + - + +
86A LYS* 3.1 23.2 + - - +
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Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ASP 3.7 6.5 + - - -
14A THR 3.2 25.1 + - - -
15A TRP 4.5 0.7 - - - +
16A ALA 2.6 26.1 + - - -
17A ILE* 3.8 13.5 - - + -
18A THR* 5.5 0.6 - - - +
21A GLU* 3.0 36.4 + - - +
25A HIS* 4.0 6.7 - - + -
79A SER 2.9 12.3 + - - +
80A ILE 3.2 2.7 + - - +
82A MSE 1.3 77.9 - - - +
84A LEU* 1.3 56.9 + - - +
86A LYS* 3.3 12.7 + - - +
87A LEU* 3.0 43.4 + - + +
102A MSE 3.2 30.7 - - + -
301A SO4 4.4 5.8 + - - -
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TRP* 5.6 1.1 - - + -
61A ILE* 4.0 26.5 - - + +
64A LEU* 3.8 33.2 - - + -
80A ILE* 3.0 32.2 + - + +
81A ALA* 3.7 5.6 - - - +
83A LYS* 1.3 76.3 - - - +
85A ILE* 1.3 58.6 + - - +
87A LEU* 3.4 15.0 + - + +
88A LYS* 2.9 30.3 + - - +
94A LEU* 4.1 17.0 - - + +
95A PRO* 4.2 18.2 - - + -
98A LEU* 4.5 2.7 - - + -
102A MSE 3.8 23.1 - - + -
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 3.5 48.9 - - + +
51A SER* 3.8 24.2 - - - -
53A LEU* 3.9 4.7 - - + +
58A LEU* 4.1 8.5 - - + -
61A ILE* 3.8 21.5 - - + -
81A ALA 2.9 22.3 + - - +
82A MSE 3.7 15.0 - - + +
84A LEU* 1.3 76.6 - - - +
86A LYS* 1.3 56.8 + - - +
88A LYS* 3.2 2.4 + - - +
89A LEU* 2.9 41.0 + - + +
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Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU* 2.7 36.7 + - - +
24A LYS* 6.2 1.6 - - - +
25A HIS* 6.0 2.7 - - - -
82A MSE 3.1 13.5 + - - +
83A LYS* 3.7 16.4 - - - +
85A ILE* 1.3 78.1 - - - +
87A LEU* 1.3 64.7 + - - +
89A LEU* 3.3 10.8 + - + +
90A GLN* 3.0 41.5 + - + +
301A SO4 3.0 29.8 + - - -
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A THR* 3.5 35.2 - - + +
15A TRP* 4.0 22.7 - - + +
83A LYS* 3.0 39.1 + - + +
84A LEU* 3.7 16.2 - - + +
86A LYS* 1.3 78.8 - - + +
88A LYS* 1.3 62.5 + - - +
90A GLN* 3.1 14.1 + - - +
91A GLY 3.2 0.2 + - - -
92A TYR* 3.0 60.0 + - + -
94A LEU* 5.8 2.0 - - + -
102A MSE 5.4 0.4 - - + -
301A SO4 6.1 0.7 - - - +
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Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.7 20.4 - - + +
54A PRO* 6.1 0.2 - - - -
57A VAL* 3.6 43.1 - - + +
61A ILE* 4.6 0.7 - - + -
84A LEU 2.9 17.2 + - - +
85A ILE 3.2 3.6 + - - +
87A LEU* 1.3 76.9 - - - +
89A LEU* 1.3 59.1 + - - +
91A GLY* 2.9 20.1 + - - -
92A TYR 3.2 19.5 + - - +
93A GLN* 3.8 25.1 + - - +
94A LEU* 4.4 23.5 - - + +
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A SER* 3.8 23.8 - - - +
52A GLY 5.4 1.3 - - - -
53A LEU* 3.7 24.5 - - + +
85A ILE* 2.9 36.7 + - + +
86A LYS* 3.6 8.7 - - + +
88A LYS* 1.3 77.5 - - - +
90A GLN* 1.3 61.3 + - + +
91A GLY* 3.1 1.1 + - - -
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Residues in contact with GLN 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A LYS* 3.0 35.2 + - + +
87A LEU* 3.1 16.0 + - - +
89A LEU* 1.3 77.0 - - + +
91A GLY* 1.3 58.8 - - - +
92A TYR* 3.5 28.0 + - + -
301A SO4 2.9 29.6 + - - -
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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