Contacts of the helix formed by residues 74 - 88 (chain A) in PDB entry 1F9O
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 PHE 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A ALA* 4.1 9.9 - - - -
68A GLY* 3.4 39.3 - - - -
69A ARG* 3.7 2.0 - - - -
72A GLY* 3.9 12.0 + - - -
73A ASP* 1.3 76.0 + - - +
75A THR* 1.3 64.1 + - - +
76A GLY 3.2 2.7 - - - -
77A PHE* 3.2 17.7 + - + +
78A ASP* 3.2 24.8 + - - +
242A ALA* 3.6 24.2 - - + -
245A TRP* 3.9 7.0 - - + -
246A ALA* 3.6 32.5 - - + -
249A GLN* 4.3 7.9 - - - -
251A LYS* 4.5 13.1 - - + +
252A SER 5.4 2.2 - - - +
253A VAL* 3.7 28.7 - - + -
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Residues in contact with THR 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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73A ASP* 2.7 28.1 + - - +
74A PHE* 1.3 79.4 - - - +
76A GLY* 1.3 58.2 + - - +
78A ASP* 3.4 11.6 + - - +
79A LYS* 3.0 26.3 + - - +
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Residues in contact with GLY 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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17A TYR* 5.3 1.1 - - - -
21A LYS* 5.7 2.0 - - - -
60A TYR* 4.4 2.8 + - - -
64A GLU* 3.4 31.2 - - - +
67A HIS* 5.9 2.6 - - - -
73A ASP* 4.7 3.8 + - - -
74A PHE* 3.2 1.0 - - - +
75A THR* 1.3 78.9 + - - +
77A PHE* 1.3 60.5 + - - +
79A LYS* 3.5 7.0 + - - +
80A SER* 3.0 20.8 + - - -
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Residues in contact with PHE 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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61A MET* 3.2 43.7 - - + -
64A GLU* 3.5 20.5 + - + +
65A ALA* 3.8 11.9 - - + -
73A ASP 5.6 0.2 + - - -
74A PHE* 3.2 15.8 + - + +
76A GLY* 1.3 75.1 - - - +
78A ASP* 1.3 66.4 + - - +
80A SER* 3.0 19.7 + - - -
81A TRP* 3.2 14.3 + + - +
238A ALA 4.2 4.0 - - - -
239A THR* 3.6 28.3 - - + -
242A ALA* 3.6 29.4 - - + -
253A VAL* 4.1 15.5 - - + -
256A SER* 3.6 28.7 - - - -
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Residues in contact with ASP 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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74A PHE* 3.2 16.4 + - - +
75A THR* 3.6 15.1 - - - +
76A GLY 3.3 0.2 - - - -
77A PHE* 1.3 75.7 - - - +
79A LYS* 1.3 63.3 - - - +
81A TRP* 3.2 4.9 + - - +
82A SER* 3.1 24.3 + - - -
252A SER 5.0 2.4 - - - +
253A VAL* 3.8 23.3 - - - +
255A THR* 6.1 4.3 - - - -
256A SER* 2.8 25.7 + - - +
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Residues in contact with LYS 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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31A GLN 4.3 11.7 + - - -
32A GLY* 4.3 9.1 + - - -
60A TYR* 4.8 10.3 + - - +
75A THR 3.0 17.1 + - - +
76A GLY* 3.5 8.3 + - - +
77A PHE 3.3 0.2 - - - -
78A ASP* 1.3 73.0 - - - +
80A SER* 1.3 66.9 + - - +
82A SER* 3.1 10.0 + - - -
83A VAL* 3.1 45.9 + - + +
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Residues in contact with SER 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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57A MET* 3.9 6.4 - - - +
60A TYR* 3.9 36.3 + - - -
61A MET* 3.3 29.8 - - - +
64A GLU* 4.2 4.7 - - - -
76A GLY 3.0 14.1 + - - -
77A PHE* 3.0 16.7 + - - -
78A ASP 3.1 0.4 - - - -
79A LYS* 1.3 79.7 - - - +
81A TRP* 1.3 57.2 + - - +
83A VAL 3.8 0.3 + - - -
84A THR* 3.0 25.3 + - - -
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Residues in contact with TRP 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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61A MET* 3.4 30.6 - - + +
77A PHE* 3.2 20.0 + + - +
78A ASP 3.2 8.4 + - - +
79A LYS 3.2 0.4 - - - -
80A SER* 1.3 80.9 + - - +
82A SER* 1.3 62.1 + - - +
84A THR* 3.9 9.2 - - + -
85A GLU* 3.3 24.0 + - - +
89A ILE* 4.6 0.9 - - + -
150A TYR* 4.0 9.4 - - - -
235A ALA* 4.3 5.8 - - + -
239A THR* 3.0 29.4 + - - -
256A SER* 3.6 36.0 + - - +
259A LYS* 3.8 37.8 - - + -
260A ALA* 3.7 27.6 - - + -
263A MET* 3.9 31.6 - - + -
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Residues in contact with SER 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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78A ASP 3.1 14.1 + - - -
79A LYS* 3.1 15.8 + - - -
81A TRP* 1.3 76.3 - - - +
83A VAL* 1.3 66.9 - - - +
85A GLU* 3.4 5.0 + - - +
86A GLN* 3.0 33.2 + - - +
259A LYS* 5.3 5.0 - - - +
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Residues in contact with VAL 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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31A GLN 4.4 5.2 - - - +
32A GLY 4.0 15.0 - - - +
33A ILE* 3.9 17.5 - - + -
57A MET* 3.8 17.9 - - + -
60A TYR* 4.9 4.0 - - + -
79A LYS* 3.1 42.1 + - + +
80A SER* 4.0 5.4 - - - +
82A SER* 1.3 75.6 - - - +
84A THR* 1.3 58.4 + - - +
86A GLN* 4.4 4.5 - - - +
87A TYR* 2.8 52.1 + - + +
88A LEU* 5.7 0.2 - - - +
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Residues in contact with THR 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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57A MET* 3.2 19.6 - - + +
61A MET* 3.5 22.8 - - + +
80A SER 3.0 17.4 + - - -
81A TRP* 3.8 10.1 - - + -
82A SER 3.2 0.4 - - - -
83A VAL* 1.3 78.0 - - - +
85A GLU* 1.3 61.3 + - - +
88A LEU* 2.7 33.7 + - + +
89A ILE* 3.2 14.6 + - + -
152A MET* 3.4 39.7 - - + -
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Residues in contact with GLU 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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81A TRP* 3.3 15.6 + - + +
82A SER* 3.9 3.6 - - - +
84A THR* 1.3 78.6 - - - +
86A GLN* 1.3 60.1 + - - +
89A ILE* 3.4 33.4 - - + +
91A THR* 4.6 4.7 - - - +
150A TYR* 2.6 39.7 + - + +
259A LYS* 3.4 26.0 + - - +
262A LYS* 5.3 1.0 + - - -
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Residues in contact with GLN 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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82A SER* 3.0 25.2 + - - +
83A VAL* 3.7 5.6 - - - +
85A GLU* 1.3 81.2 - - - +
87A TYR* 1.3 95.2 + - + +
89A ILE 4.7 1.2 - - - +
91A THR* 4.0 18.0 - - - +
176A TYR* 5.0 1.2 + - - -
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Residues in contact with TYR 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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31A GLN* 3.8 39.7 + - + +
33A ILE* 3.7 14.8 - - + -
83A VAL* 2.8 38.5 + - + +
86A GLN* 1.3 114.3 + - + +
88A LEU* 1.3 59.0 + - + +
156A LEU* 3.8 18.8 - - + +
174A PRO* 3.4 38.1 - - + +
176A TYR* 2.9 27.7 + - - -
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Residues in contact with LEU 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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33A ILE* 6.2 0.9 - - + -
52A THR* 4.8 4.7 - - + -
53A THR 3.9 4.3 - - - +
54A SER* 3.6 25.1 - - - -
57A MET* 3.1 37.9 - - + -
83A VAL 5.7 0.2 - - - +
84A THR* 2.7 20.3 + - + +
87A TYR* 1.3 74.9 - - + +
89A ILE* 1.3 55.4 + - - +
90A PRO* 3.4 2.8 - - - +
152A MET* 3.9 16.6 - - + -
153A HIS* 2.9 44.2 + - - +
155A ILE 5.1 0.4 - - - -
156A LEU* 3.7 40.2 - - + +
176A TYR* 3.1 12.8 + - + -
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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