Contacts of the helix formed by residues 63 - 80 (chain A) in PDB entry 2J2C
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 PRO 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A SER* 4.8 6.1 - - - -
62A SER* 1.4 83.8 - - - +
64A GLU* 1.3 70.8 + - - +
65A TYR 3.3 2.9 + - - -
66A GLU* 3.4 8.8 + - - +
67A SER* 2.8 32.4 + - - -
91A TYR* 4.2 9.8 - - + -
93A SER* 3.9 29.4 - - - +
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Residues in contact with GLU 64 (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 LYS* 3.5 7.8 + - - +
62A SER 3.4 12.3 + - - +
63A PRO* 1.3 90.1 - - - +
65A TYR* 1.3 58.1 + - - +
67A SER* 3.4 6.5 + - - -
68A LEU* 3.0 23.0 + - - +
224A LYS* 4.2 33.7 - - + +
225A TYR* 3.6 22.7 + - + -
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Residues in contact with TYR 65 (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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55A TYR* 3.2 24.9 - - - -
60A TYR* 3.4 44.2 - + + -
61A LYS 2.9 19.3 + - - +
64A GLU* 1.3 75.0 - - - +
66A GLU* 1.3 68.5 + - + +
68A LEU* 3.3 3.5 + - + +
69A GLY* 3.0 20.1 + - - -
157A PHE* 3.5 32.4 - + - -
209A HIS* 3.7 14.5 + + - -
214A LEU* 3.9 19.0 - - + +
218A THR* 3.5 23.7 + - - -
225A TYR* 3.9 23.3 - + + -
255A TYR* 4.5 4.0 + - - -
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Residues in contact with GLU 66 (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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5A TRP* 3.8 10.9 + - - -
55A TYR* 4.7 8.1 + - - +
60A TYR 5.1 0.2 - - - +
61A LYS 3.6 4.0 - - - +
62A SER* 2.5 45.6 + - - -
63A PRO* 3.4 5.8 + - - +
65A TYR* 1.3 79.2 - - + +
67A SER* 1.3 56.2 + - - +
69A GLY 3.3 1.0 + - - -
70A PHE* 2.9 30.0 + - - +
91A TYR* 3.5 36.6 + - + +
93A SER* 5.5 1.2 - - - -
156A LEU 4.7 4.7 - - - +
159A LEU* 3.9 24.9 - - + +
160A PRO* 3.5 18.3 - - + +
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Residues in contact with SER 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PRO* 2.8 19.7 + - - -
64A GLU* 3.7 7.4 - - - -
66A GLU* 1.3 76.6 - - - +
68A LEU* 1.3 56.8 + - - +
70A PHE* 3.4 2.4 + - - +
71A GLU* 2.9 36.4 + - - +
91A TYR* 3.8 27.6 + - - +
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Residues in contact with LEU 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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64A GLU 3.0 17.2 + - - +
65A TYR* 3.3 5.4 + - + +
67A SER* 1.3 72.5 - - - +
69A GLY* 1.3 64.4 + - - +
71A GLU* 3.4 10.4 + - + +
72A LEU* 3.0 45.4 + - + +
214A LEU* 3.3 30.5 - - + +
217A LYS* 3.9 31.2 - - + -
218A THR* 4.2 4.3 - - - +
225A TYR* 3.8 36.8 - - + +
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Residues in contact with GLY 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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65A TYR* 3.0 15.0 + - - -
66A GLU 3.7 2.7 - - - -
68A LEU* 1.3 75.1 - - - +
70A PHE* 1.3 54.7 + - - +
72A LEU* 3.8 3.0 - - - +
73A THR* 2.7 39.2 + - - -
160A PRO* 4.3 9.9 - - - -
208A VAL* 4.6 1.0 - - - +
209A HIS* 5.9 1.8 - - - -
214A LEU* 4.3 21.4 - - - +
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Residues in contact with PHE 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 GLU 2.9 18.2 + - - +
67A SER* 3.5 4.7 - - - +
69A GLY* 1.3 72.8 - - - +
71A GLU* 1.3 64.9 + - + +
73A THR* 3.2 4.8 + - - -
74A VAL* 2.8 47.1 + - + +
89A PHE* 3.6 36.6 - - + -
90A ALA* 3.9 1.6 - - - -
91A TYR* 3.6 40.2 - + + -
160A PRO* 3.6 26.2 - - + +
163A TYR* 3.4 26.9 - + - -
164A LEU* 3.7 30.0 - - + +
167A CYS* 4.2 2.0 - - - -
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Residues in contact with GLU 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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67A SER* 2.9 25.1 + - - +
68A LEU* 3.8 10.7 - - + +
70A PHE* 1.3 79.1 - - + +
72A LEU* 1.3 61.9 + - + +
74A VAL* 3.5 5.2 + - - +
75A GLU* 3.0 54.4 + - + +
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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 LEU* 3.0 38.9 + - + +
69A GLY 4.0 0.2 - - - +
71A GLU* 1.3 77.7 - - + +
73A THR* 1.3 61.2 + - - +
75A GLU* 3.4 20.8 + - - +
76A ARG* 3.0 23.0 + - - +
207A TRP* 5.4 0.3 - - - -
208A VAL* 3.3 26.1 - - + +
213A SER* 3.6 17.5 - - - +
214A LEU* 3.6 42.2 - - + +
217A LYS* 4.1 14.6 - - + -
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Residues in contact with THR 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 GLY* 2.7 24.5 + - - -
70A PHE* 3.6 5.4 - - - -
72A LEU* 1.3 74.1 - - - +
74A VAL* 1.3 66.0 + - - +
76A ARG* 3.3 4.4 + - - +
77A LEU* 3.0 24.4 + - + +
160A PRO* 5.6 2.2 - - - +
161A GLU* 6.1 0.2 - - - -
164A LEU* 3.6 24.5 - - + -
201A VAL 4.3 2.5 - - - +
204A ALA* 3.9 15.9 - - + -
205A VAL* 3.8 36.8 - - + +
208A VAL* 4.0 12.2 - - - +
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Residues in contact with VAL 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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70A PHE* 2.8 37.7 + - + +
71A GLU* 3.7 7.2 - - + +
73A THR* 1.3 76.7 - - - +
75A GLU* 1.3 58.3 + - + +
77A LEU* 3.1 9.1 + - - +
78A VAL* 2.9 28.2 + - - +
86A LEU* 3.4 38.6 - - + +
87A LEU* 4.1 15.5 - - + +
89A PHE* 4.5 2.2 - - + +
164A LEU* 3.7 29.2 - - + -
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Residues in contact with GLU 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 GLU* 3.0 42.5 + - + +
72A LEU* 3.7 24.5 - - - +
74A VAL* 1.3 76.8 - - + +
76A ARG* 1.3 57.9 + - - +
78A VAL* 3.5 6.8 + - - +
79A SER* 2.9 29.6 + - - -
87A LEU* 4.4 18.0 - - + +
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Residues in contact with ARG 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 3.0 17.2 + - - +
73A THR 3.6 5.4 - - - +
74A VAL 3.3 0.2 - - - -
75A GLU* 1.3 77.0 - - - +
77A LEU* 1.3 61.4 + - - +
79A SER* 3.2 16.6 + - - -
80A ILE* 3.1 45.4 + - + +
204A ALA* 3.7 24.8 - - + +
207A TRP* 3.5 63.2 - - + +
208A VAL* 4.2 2.9 - - + -
1495A SO4 3.0 40.2 + - - -
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A THR* 3.0 16.6 + - + +
74A VAL* 3.6 7.0 - - - +
76A ARG* 1.3 76.1 - - - +
78A VAL* 1.3 61.1 + - - +
80A ILE* 3.2 13.9 - - + +
81A GLY 3.2 5.9 + - - -
82A TYR* 3.0 47.9 + - + +
86A LEU* 3.9 22.4 - - + -
164A LEU* 3.8 28.9 - - + -
168A LEU* 4.3 7.0 - - + -
200A ASP* 3.6 32.8 - - + +
201A VAL* 4.3 13.0 - - + +
204A ALA* 3.9 8.3 - - + -
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Residues in contact with VAL 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 VAL 2.9 20.0 + - - +
75A GLU 3.9 4.0 - - - +
77A LEU* 1.3 76.1 - - - +
79A SER* 1.3 64.1 + - - +
81A GLY* 3.0 14.4 + - - -
82A TYR 3.6 9.7 - - - +
83A PRO 3.7 19.5 - - - +
84A GLN* 3.5 34.2 + - - +
86A LEU* 3.8 14.1 - - + -
87A LEU* 3.7 30.5 - - + -
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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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75A GLU 2.9 18.4 + - - -
76A ARG* 3.2 25.1 + - - -
78A VAL* 1.3 79.3 - - - +
80A ILE* 1.3 58.7 + - - +
81A GLY* 3.6 0.5 + - - -
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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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76A ARG* 3.1 49.4 + - + +
77A LEU* 3.2 24.5 - - + +
79A SER* 1.3 77.5 - - - +
81A GLY* 1.3 57.2 + - - +
82A TYR* 4.1 21.9 - - + -
200A ASP* 4.6 13.9 - - + +
204A ALA* 6.3 0.2 - - + -
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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