Contacts of the helix formed by residues 67 - 84 (chain A) in PDB entry 2FJX
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 SER 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A PRO 4.2 0.8 + - - -
66A MET* 1.3 79.5 - - - +
68A GLN* 1.3 64.6 + - - +
69A GLU* 3.6 10.3 + - - +
70A ALA* 3.2 23.3 + - - +
71A ARG* 3.0 20.6 + - - +
109A TYR* 5.3 0.9 + - - -
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Residues in contact with GLN 68 (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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67A SER* 1.3 74.5 - - - +
69A GLU* 1.3 58.5 + - - +
71A ARG* 3.2 14.6 + - - +
72A LEU* 2.8 67.1 + - + +
175A PRO* 4.8 14.4 - - + +
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Residues in contact with GLU 69 (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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67A SER* 3.2 9.0 + - - +
68A GLN* 1.3 80.2 - - - +
70A ALA* 1.3 62.5 + - - +
72A LEU* 3.9 7.6 - - - +
73A GLY* 3.1 18.9 + - - -
106A THR* 2.7 34.9 + - - +
109A TYR* 2.9 27.1 + - + +
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Residues in contact with ALA 70 (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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66A MET* 3.4 25.6 - - + -
67A SER* 3.2 13.3 + - - +
69A GLU* 1.3 79.0 - - - +
71A ARG* 1.3 58.2 + - - +
73A GLY* 3.1 1.7 + - - -
74A ILE* 2.9 33.4 + - - +
100A PRO* 3.4 25.8 - - + -
109A TYR* 3.7 16.2 - - + +
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Residues in contact with ARG 71 (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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66A MET* 2.5 54.9 + - - +
67A SER 3.0 11.7 + - - +
68A GLN* 3.6 16.1 - - - +
70A ALA* 1.3 76.7 - - - +
72A LEU* 1.3 56.3 + - - +
74A ILE 3.3 0.2 + - - -
75A LYS* 2.8 29.6 + - - +
172A TRP* 3.8 14.5 - - + -
173A ARG* 3.1 34.7 + - - +
174A ASP 3.7 0.9 - - - -
175A PRO* 3.3 42.2 - - + +
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Residues in contact with LEU 72 (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 GLN* 2.8 65.7 + - + +
69A GLU* 3.9 6.1 - - - +
71A ARG* 1.3 72.4 - - - +
73A GLY* 1.3 61.3 + - - +
75A LYS* 3.9 8.4 - - + +
76A PRO* 3.2 21.0 - - - +
175A PRO* 3.3 28.0 - - + -
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Residues in contact with GLY 73 (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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69A GLU 3.1 15.7 + - - -
70A ALA 3.1 4.0 + - - -
72A LEU* 1.3 78.8 - - - +
74A ILE* 1.3 56.4 + - - +
76A PRO* 3.6 5.6 - - - +
77A HIS* 3.3 24.3 + - - -
109A TYR* 3.8 25.1 + - - +
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Residues in contact with ILE 74 (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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66A MET* 3.6 35.9 - - + -
70A ALA 2.9 14.5 + - - +
71A ARG 3.9 2.7 - - - +
73A GLY* 1.3 79.4 - - - +
75A LYS* 1.3 64.7 + - - +
76A PRO 3.4 0.9 - - - -
77A HIS* 3.0 20.9 + - - +
78A ILE* 3.2 22.7 + - + -
98A LEU* 4.6 4.7 - - + -
99A LEU 4.2 6.5 - - - +
100A PRO* 4.1 18.2 - - + -
109A TYR* 4.5 6.7 - - + -
110A ARG 4.4 3.6 - - - +
111A PRO* 3.4 34.8 - - + -
172A TRP* 3.6 13.7 - - + -
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Residues in contact with LYS 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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71A ARG* 2.8 21.7 + - + +
72A LEU* 3.9 7.4 - - + +
74A ILE* 1.3 71.5 - - - +
76A PRO* 1.3 71.1 - - + +
78A ILE* 3.1 4.1 + - + +
79A GLN* 2.9 33.3 + - + +
172A TRP* 3.9 21.7 - - + +
174A ASP* 3.1 33.2 + - - +
175A PRO* 4.4 13.9 - - + +
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Residues in contact with PRO 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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72A LEU 3.2 19.1 - - - +
73A GLY 3.6 8.1 - - - +
74A ILE 3.4 4.9 - - - -
75A LYS* 1.3 92.3 - - + +
77A HIS* 1.3 66.5 + - + +
79A GLN* 3.8 6.1 - - + +
80A ARG* 3.0 25.5 + - - +
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Residues in contact with HIS 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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73A GLY 3.3 21.2 + - - -
74A ILE* 3.0 9.6 + - - +
76A PRO* 1.3 82.1 - - + +
78A ILE* 1.3 63.0 + - - +
80A ARG* 3.0 34.8 + - - +
81A LEU* 3.1 33.0 + - + +
109A TYR 3.2 27.7 + - - -
110A ARG* 4.5 6.0 - - + +
111A PRO* 3.8 24.6 - - + +
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Residues in contact with ILE 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 ILE* 3.2 25.5 + - + +
75A LYS 3.1 6.6 + - - +
77A HIS* 1.3 77.5 - - - +
79A GLN* 1.3 62.4 + - - +
81A LEU* 3.3 6.1 + - + +
82A LEU* 2.9 32.1 + - + +
87A LEU* 3.9 19.3 - - + -
98A LEU* 4.6 1.8 - - + -
111A PRO* 3.9 24.0 - - + -
170A PHE* 4.5 16.8 - - + -
172A TRP* 4.0 25.6 - - + +
183A LEU* 3.7 26.2 - - + -
185A TRP* 5.9 1.1 - - + -
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Residues in contact with GLN 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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75A LYS* 2.9 26.9 + - + +
76A PRO* 3.8 6.7 - - + +
78A ILE* 1.3 75.6 - - - +
80A ARG* 1.3 58.5 + - - +
82A LEU* 3.2 20.8 + - - +
83A ASP* 2.9 64.4 + - - +
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Residues in contact with ARG 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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76A PRO 3.0 15.1 + - - +
77A HIS* 3.0 54.4 + - - +
78A ILE 3.3 0.2 - - - -
79A GLN* 1.3 77.8 - - - +
81A LEU* 1.3 77.7 + - - +
83A ASP* 3.2 9.7 + - - +
84A GLN* 2.9 55.8 + - + +
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Residues in contact with LEU 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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39A MET* 5.8 0.4 - - + -
77A HIS* 3.1 28.0 + - + +
78A ILE* 4.7 4.3 - - + -
79A GLN 3.3 0.2 - - - -
80A ARG* 1.3 92.9 - - - +
82A LEU* 1.3 61.2 + - - +
84A GLN* 3.3 15.1 + - - +
85A GLY 3.0 2.9 + - - -
86A ILE* 2.9 50.5 + - + -
87A LEU* 3.2 27.6 + - + +
111A PRO* 5.8 2.7 - - + -
156A PHE* 4.0 19.1 - - + -
185A TRP* 3.7 27.1 - - + -
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Residues in contact with LEU 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 ILE* 2.9 32.0 + - + +
79A GLN* 3.5 28.3 - - - +
81A LEU* 1.3 77.0 - - - +
83A ASP* 1.3 64.9 + - - +
85A GLY* 3.1 13.5 + - - -
87A LEU* 3.5 33.1 - - + +
88A VAL* 4.2 3.6 - - - +
89A PRO* 4.6 6.1 - - + -
172A TRP* 5.7 0.4 - - + -
179A ILE* 3.5 25.8 - - + -
183A LEU* 4.0 19.1 - - + -
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Residues in contact with ASP 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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79A GLN* 2.9 48.3 + - - +
80A ARG* 3.6 8.4 - - - +
82A LEU* 1.3 78.0 - - - +
84A GLN* 1.3 60.7 + - + +
85A GLY 3.2 0.7 + - - -
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Residues in contact with GLN 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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39A MET* 3.7 35.7 - - + +
80A ARG* 2.9 41.4 + - + +
81A LEU* 3.3 18.0 + - - +
82A LEU 3.1 0.2 - - - -
83A ASP* 1.3 78.1 - - + +
85A GLY* 1.3 60.1 + - - +
86A ILE* 3.1 31.7 + - + +
187A ARG* 4.8 7.8 + - - -
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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