Contacts of the helix formed by residues 84 - 98 (chain A) in PDB entry 2FPO
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 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A SER* 5.1 4.0 + - - -
82A GLU* 3.0 18.3 + - - +
83A MSE 1.3 76.5 - - - +
85A ARG* 1.3 55.1 + - - +
86A ALA* 2.9 19.9 + - - +
87A VAL* 3.0 24.9 + - + +
88A SER* 2.7 37.5 + - - -
55B GLN* 2.7 42.1 + - - +
76B ALA* 3.3 18.6 - - - +
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Residues in contact with ARG 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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83A MSE 3.4 2.8 + - - -
84A ASP* 1.3 70.8 - - - +
86A ALA* 1.3 61.6 + - - +
88A SER* 3.4 1.4 + - - -
89A GLN* 3.0 55.7 + - + +
107A ASN* 3.4 28.9 - - - +
18B GLN* 5.1 4.8 - - - +
52B VAL* 4.9 1.6 - - - +
53B ASP* 2.8 28.1 + - - +
71B LEU 5.2 0.2 + - - -
74B TYR* 2.9 41.3 + - - +
75B ALA 3.0 22.4 + - - -
76B ALA* 2.8 26.5 + - - +
102B ASN* 4.0 11.0 - - - +
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Residues in contact with ALA 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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27A PRO* 4.6 8.3 - - + +
84A ASP* 2.9 10.1 + - - +
85A ARG* 1.3 78.7 - - - +
87A VAL* 1.3 62.8 + - + +
89A GLN* 3.5 13.7 + - - +
90A GLN* 3.2 22.3 + - - +
53B ASP* 3.9 29.8 - - + +
76B ALA* 4.0 10.1 - - + +
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Residues in contact with VAL 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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27A PRO* 4.8 11.9 - - + -
29A SER* 3.6 24.9 - - - +
62A GLY* 2.9 38.1 - - - +
63A SER* 5.0 1.3 - - - -
82A GLU* 3.7 14.8 - - + +
84A ASP* 3.0 30.5 + - + +
86A ALA* 1.3 74.2 - - + +
88A SER* 1.3 64.7 + - - +
90A GLN* 3.2 6.7 + - - +
91A LEU* 3.0 22.9 + - - +
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Residues in contact with SER 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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82A GLU* 2.9 29.5 + - - +
84A ASP 2.7 28.2 + - - -
85A ARG* 3.7 4.9 - - - -
87A VAL* 1.3 71.7 - - - +
89A GLN* 1.3 62.4 + - - +
91A LEU* 3.4 5.9 - - - +
92A ILE* 3.1 31.1 + - - +
105A VAL* 3.7 21.7 - - - +
107A ASN* 3.3 18.8 + - - -
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Residues in contact with GLN 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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85A ARG* 3.0 50.1 + - + +
86A ALA* 3.6 11.2 - - - +
87A VAL 3.2 0.2 - - - -
88A SER* 1.3 77.5 - - - +
90A GLN* 1.3 55.5 + - - +
92A ILE* 3.3 15.5 + - + +
93A LYS* 3.1 40.6 + - - +
53B ASP* 5.3 2.4 - - - +
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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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25A PRO* 3.4 29.0 + - - +
26A VAL* 4.3 1.3 - - + -
27A PRO* 3.3 39.7 - - + +
86A ALA 3.2 12.7 + - - +
87A VAL 3.2 6.2 + - - +
89A GLN* 1.3 72.6 - - - +
91A LEU* 1.3 60.6 + - - +
93A LYS* 3.2 29.8 + - - +
94A ASN* 2.8 55.8 + - - +
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Residues in contact with LEU 91 (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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61A ALA* 3.9 27.4 - - + -
62A GLY 4.1 12.6 - - - +
63A SER 4.1 7.4 - - - +
64A GLY* 3.8 23.1 - - - -
68A LEU* 4.1 17.9 - - + -
80A LEU* 4.2 22.0 - - + -
82A GLU* 5.0 5.8 - - + -
87A VAL 3.0 12.2 + - - +
88A SER 3.4 10.3 - - - +
90A GLN* 1.3 77.1 - - - +
92A ILE* 1.3 55.3 + - - +
94A ASN* 3.1 6.7 + - + +
95A LEU* 2.9 32.8 + - + +
105A VAL* 3.9 19.5 - - + -
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Residues in contact with ILE 92 (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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88A SER* 3.1 20.7 + - - +
89A GLN* 3.5 14.6 - - + +
90A GLN 3.3 0.2 - - - -
91A LEU* 1.3 75.8 - - - +
93A LYS* 1.3 65.4 + - + +
95A LEU* 3.4 11.1 + - + +
96A ALA* 3.1 23.3 + - + +
105A VAL* 3.7 31.0 - - + +
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Residues in contact with LYS 93 (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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89A GLN* 3.1 28.2 + - - +
90A GLN* 3.4 32.1 + - - +
92A ILE* 1.3 78.8 - - + +
94A ASN* 1.3 63.3 + - - +
96A ALA* 3.1 9.2 + - - +
97A THR* 3.0 25.7 + - - -
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Residues in contact with ASN 94 (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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24A LEU* 4.0 31.7 - - + +
25A PRO* 3.0 36.0 + - - +
26A VAL* 4.1 9.1 - - - +
63A SER 4.9 4.8 + - - -
68A LEU* 4.6 8.1 - - + +
90A GLN* 2.8 43.1 + - - +
91A LEU* 3.7 7.5 - - - +
93A LYS* 1.3 72.5 - - - +
95A LEU* 1.3 62.8 + - - +
97A THR* 3.4 9.0 + - - -
98A LEU* 3.2 28.9 + - - +
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Residues in contact with LEU 95 (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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68A LEU* 3.7 26.5 - - + -
71A LEU* 3.7 21.5 - - + -
80A LEU* 4.3 7.6 - - + -
91A LEU* 2.9 15.4 + - + +
92A ILE* 3.7 9.0 - - + +
93A LYS 3.3 0.2 - - - -
94A ASN* 1.3 77.5 - - - +
96A ALA* 1.3 56.6 + - - +
98A LEU* 3.5 3.1 + - - +
99A LYS 3.0 6.4 + - - -
100A ALA* 2.9 48.2 + - + +
103A ALA* 3.8 24.2 - - + +
104A ARG* 5.2 0.4 - - - -
105A VAL* 3.5 32.3 - - + -
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Residues in contact with ALA 96 (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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92A ILE* 3.1 15.0 + - + +
93A LYS* 3.1 11.8 + - - +
95A LEU* 1.3 74.9 - - - +
97A THR* 1.3 66.0 + - - +
99A LYS* 3.0 19.4 + - - +
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Residues in contact with THR 97 (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 24.9 + - - +
24A LEU* 4.0 17.0 - - + -
93A LYS 3.0 13.6 + - - -
94A ASN* 3.5 14.9 + - - -
96A ALA* 1.3 76.5 - - - +
98A LEU* 1.3 59.4 + - - +
99A LYS* 3.4 6.8 + - - +
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Residues in contact with LEU 98 (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 ILE* 4.0 3.4 - - + -
19A TRP* 3.5 69.9 + - + +
22A ARG* 3.9 29.4 - - + +
24A LEU* 3.6 35.7 - - + -
68A LEU* 3.8 22.0 - - + -
94A ASN 3.2 16.8 + - - +
95A LEU* 3.9 4.5 - - - +
97A THR* 1.3 74.4 - - - +
99A LYS* 1.3 69.1 + - - +
100A ALA* 3.4 2.4 + - + +
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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
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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