Contacts of the helix formed by residues 55 - 74 (chain A) in PDB entry 2JG7
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 THR 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A SER* 3.8 13.2 + - - +
34A GLY* 3.5 27.4 - - - +
54A ALA* 1.3 77.7 - - - +
56A LEU* 1.3 65.0 + - - +
57A ALA* 3.5 10.2 + - - +
58A GLU* 3.0 33.3 + - - +
59A TYR* 2.9 20.1 + - - +
228A ILE* 4.2 2.7 - - - -
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Residues in contact with LEU 56 (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 THR* 1.3 71.9 - - - +
57A ALA* 1.3 51.6 - - - +
59A TYR* 3.1 8.4 + - + +
60A GLU* 2.7 36.3 + - - +
227A ASP* 3.5 35.0 - - - +
228A ILE* 4.2 15.0 - - + +
231A ALA* 4.9 16.4 - - + -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 3.2 9.5 + - - +
56A LEU* 1.3 79.6 - - - +
58A GLU* 1.3 58.1 + - + +
60A GLU* 3.4 10.4 - - - +
61A GLU* 3.0 26.9 + - - +
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Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 4.4 9.3 - - + +
27A ASN* 4.8 0.5 + - - -
32A GLY* 3.4 16.9 + - - -
33A SER* 2.8 48.1 + - - -
54A ALA* 3.7 7.9 - - + -
55A THR* 3.0 33.5 + - - +
57A ALA* 1.3 75.0 - - + +
59A TYR* 1.3 63.9 + - - +
61A GLU* 3.5 12.3 + - - +
62A THR* 2.8 29.9 + - - -
222A THR* 5.1 0.2 - - - -
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Residues in contact with TYR 59 (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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54A ALA* 4.5 1.4 - - + +
55A THR 2.9 11.8 + - - +
56A LEU* 3.3 13.5 - - + +
58A GLU* 1.3 73.7 - - - +
60A GLU* 1.3 70.6 + - + +
62A THR* 3.0 13.5 + - - -
63A VAL* 3.0 32.6 + - + +
187A LEU* 4.1 11.0 - - + -
222A THR* 4.1 19.1 - - + -
228A ILE* 3.8 31.2 - - + -
231A ALA* 4.0 21.1 - - + -
232A MET* 3.4 34.7 - - + +
235A ASP* 2.7 41.1 + - - +
237A ARG* 4.6 4.0 - - - -
238A VAL* 3.8 4.6 - - + +
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Residues in contact with GLU 60 (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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56A LEU 2.7 19.1 + - - +
57A ALA* 3.4 11.9 - - - +
59A TYR* 1.3 81.8 - - + +
61A GLU* 1.3 63.1 + - + +
63A VAL* 3.3 10.0 + - - +
64A GLN* 2.8 38.8 + - - +
237A ARG* 2.9 35.5 + - - +
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Residues in contact with GLU 61 (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 ASN* 4.5 8.5 + - - -
57A ALA 3.0 16.5 + - - +
58A GLU* 3.9 13.7 - - - +
59A TYR 3.2 0.4 - - - -
60A GLU* 1.3 78.1 - - - +
62A THR* 1.3 61.8 + - - +
64A GLN* 3.4 13.6 + - + +
65A LYS* 3.2 47.8 + - + +
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Residues in contact with THR 62 (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 VAL* 3.6 11.6 - - - +
26A TYR 4.4 0.9 - - - +
27A ASN* 3.1 27.4 + - + +
58A GLU 2.8 17.4 + - - -
59A TYR 3.0 9.5 + - - -
61A GLU* 1.3 74.8 - - - +
63A VAL* 1.3 60.5 + - - +
65A LYS* 3.4 1.7 + - - +
66A THR* 2.9 27.9 + - - -
187A LEU* 3.8 14.8 - - + -
220A SER* 3.5 31.6 + - - +
222A THR* 3.6 14.5 - - + +
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Residues in contact with VAL 63 (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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59A TYR* 3.0 54.4 + - + +
60A GLU 3.3 7.6 + - - +
62A THR* 1.3 77.1 - - - +
64A GLN* 1.3 57.0 + - - +
66A THR* 3.4 7.0 + - - -
67A ARG* 2.9 29.4 + - + +
158A LEU* 4.1 14.1 - - + -
187A LEU* 3.8 10.8 - - + -
235A ASP* 3.9 1.8 - - - +
237A ARG* 3.4 47.6 - - + +
238A VAL* 5.4 0.4 - - + -
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Residues in contact with GLN 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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60A GLU* 2.8 40.5 + - - +
61A GLU* 3.7 13.5 - - + +
62A THR 3.3 0.8 - - - -
63A VAL* 1.3 78.5 - - - +
65A LYS* 1.3 61.7 + - - +
67A ARG* 3.4 7.2 + - - +
68A GLU* 3.1 24.9 + - - +
237A ARG* 4.1 11.9 - - - +
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Residues in contact with LYS 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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27A ASN* 3.0 53.3 + - + +
28A GLY* 4.7 1.6 - - - -
29A SER* 3.5 15.8 + - - +
61A GLU* 3.2 38.4 + - + +
62A THR 3.9 3.6 - - - +
64A GLN* 1.3 77.7 - - - +
66A THR* 1.3 57.5 + - - +
68A GLU* 3.5 6.9 + - + +
69A ALA* 3.0 22.7 + - - +
217A ALA* 3.4 11.6 - - + +
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Residues in contact with THR 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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62A THR* 2.9 17.8 + - - +
63A VAL* 3.5 6.5 - - - -
64A GLN 3.2 0.2 - - - -
65A LYS* 1.3 74.0 - - - +
67A ARG* 1.3 66.0 + - - +
69A ALA* 3.1 5.0 + - - +
70A TRP 3.0 18.5 + - - -
158A LEU* 3.6 32.1 - - + -
185A VAL* 3.4 29.7 - - + +
186A CYS 4.1 2.5 + - - +
187A LEU* 4.6 2.0 - - - +
217A ALA* 3.1 11.8 + - - +
220A SER* 3.0 29.3 + - - -
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Residues in contact with ARG 67 (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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63A VAL* 2.9 27.8 + - + +
64A GLN* 3.4 8.3 + - - +
66A THR* 1.3 75.7 - - - +
68A GLU* 1.3 62.1 + - - +
70A TRP* 3.4 36.2 + - - +
71A LYS* 3.7 13.4 + - - +
156A VAL 5.1 0.2 + - - -
157A GLY* 4.1 12.5 - - - -
158A LEU* 4.3 11.4 - - + +
236A GLU 5.1 0.8 + - - -
237A ARG* 3.5 33.9 + - + +
239A ASP* 3.1 39.4 + - - -
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Residues in contact with GLU 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 GLN 3.1 17.3 + - - +
65A LYS* 3.7 8.5 - - + +
66A THR 3.2 0.2 - - - -
67A ARG* 1.3 74.3 - - - +
69A ALA* 1.3 65.5 + - - +
71A LYS* 3.3 53.0 + - - +
72A MET* 4.2 2.9 + - - +
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Residues in contact with ALA 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 LYS 3.0 14.7 + - - +
66A THR 3.5 8.5 - - - +
68A GLU* 1.3 75.8 - - - +
70A TRP* 1.3 64.5 + - - +
71A LYS 3.2 0.7 + - - -
72A MET* 3.3 10.7 + - - +
73A TRP* 3.1 19.1 + - - +
185A VAL* 4.3 1.8 - - - -
215A PRO* 3.8 32.0 - - + +
217A ALA* 3.9 12.3 - - + +
218A ILE* 4.0 14.1 - - + +
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Residues in contact with TRP 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 THR 3.0 6.0 + - - +
67A ARG* 3.5 27.4 - - - +
68A GLU 3.2 0.4 - - - -
69A ALA* 1.3 76.3 - - - +
71A LYS* 1.3 68.0 + - + +
73A TRP* 3.1 1.7 + + - -
74A ALA* 2.8 48.6 + - + +
155A PRO* 3.8 19.6 - - + +
156A VAL 5.3 0.4 - - - -
157A GLY* 3.3 41.1 - - - -
183A GLY 2.9 26.3 + - - -
185A VAL* 3.7 28.9 - - + +
444B PRO* 3.7 24.5 - - + -
445B LYS* 3.9 17.9 - - + -
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Residues in contact with LYS 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 ARG 3.7 10.1 + - - +
68A GLU* 3.3 47.0 + - - +
69A ALA 3.2 0.6 - - - -
70A TRP* 1.3 87.9 - - + +
72A MET* 1.3 62.5 + - - +
75A ASP* 3.4 8.2 + - - +
445B LYS* 2.9 37.4 + - + +
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Residues in contact with MET 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 GLU 4.2 1.9 + - - +
69A ALA* 3.3 12.8 + - - +
71A LYS* 1.3 77.5 - - - +
73A TRP* 1.3 74.4 + - - +
75A ASP* 3.3 21.0 + - - +
76A ILE* 3.6 24.0 - - + +
213A ASN 5.1 4.3 - - - +
214A LEU* 3.7 22.2 - - + -
215A PRO* 3.8 31.6 - - + -
218A ILE* 4.4 0.9 - - - -
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Residues in contact with TRP 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 ALA 3.1 16.2 + - - +
70A TRP* 3.1 6.0 + + - +
72A MET* 1.3 79.1 - - - +
74A ALA* 1.3 56.8 + - - +
75A ASP 3.1 4.5 - - - -
76A ILE* 3.1 47.2 + - + +
81A ARG* 3.6 35.3 + - + -
84A ILE* 4.0 21.8 - - + -
180A LEU* 3.5 39.4 + - + -
183A GLY* 3.7 17.3 - - - -
184A ASN 2.9 30.6 + - - -
185A VAL* 4.0 6.1 - - + -
209A LEU* 5.5 0.2 - - + -
214A LEU* 3.8 23.3 - - + -
218A ILE* 3.6 35.9 - - + +
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Residues in contact with ALA 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 TRP* 2.8 53.9 + - + +
73A TRP* 1.3 72.1 - - - +
75A ASP* 1.3 61.6 + - - +
76A ILE 3.3 1.6 + - - +
81A ARG* 4.0 16.6 + - - +
155A PRO* 4.6 1.6 - - + -
183A GLY 4.2 8.5 - - - +
444B PRO* 3.8 23.3 - - + +
445B LYS* 4.0 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