Contacts of the helix formed by residues 64 - 78 (chain A) in PDB entry 1JQE
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 GLY 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A GLY 3.1 12.8 + - - -
62A GLY 3.2 1.4 + - - -
63A ALA* 1.3 76.7 - - - +
65A GLU* 1.3 65.5 + - - +
66A ILE 3.4 2.2 - - - -
67A ASP* 3.5 4.0 - - - +
68A LEU* 2.9 28.6 + - - +
98A TYR* 3.6 29.4 - - - -
101A LEU* 3.8 4.7 - - - -
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Residues in contact with GLU 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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20A ARG* 2.8 35.5 + - - +
29A HIS* 3.5 32.5 - - + +
63A ALA* 3.3 22.9 + - - +
64A GLY* 1.3 73.8 + - - +
66A ILE* 1.3 65.1 + - + +
68A LEU* 3.4 4.0 + - - +
69A GLN* 3.3 24.8 + - - +
101A LEU* 3.8 17.9 - - + +
400A SAH 4.3 4.9 - - - +
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Residues in contact with ILE 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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29A HIS* 3.8 39.3 - - + +
32A MET* 3.7 37.7 - - + -
33A GLN* 4.9 3.1 - - - +
36A MET* 4.1 17.5 - - + -
61A GLY 5.9 0.2 + - - -
64A GLY 3.4 0.4 - - - -
65A GLU* 1.3 75.9 + - + +
67A ASP* 1.3 68.9 + - - +
69A GLN* 3.0 11.2 + - + +
70A ILE* 2.9 26.6 + - + +
142A ILE* 3.6 31.2 - - + -
400A SAH 4.2 11.4 + - - +
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Residues in contact with ASP 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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58A SER* 2.6 30.8 + - - -
61A GLY* 3.7 14.5 - - - +
64A GLY 3.2 7.7 + - - +
66A ILE* 1.3 79.9 - - - +
68A LEU* 1.3 56.5 + - - +
70A ILE* 3.2 11.4 + - - +
71A LEU* 2.9 33.3 + - - +
85A ASN* 4.8 3.3 - - - +
98A TYR* 2.7 41.3 + - + +
140A HIS* 3.1 22.4 + - + +
142A ILE* 5.1 1.6 - - - +
400A SAH 5.3 2.1 + - - -
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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 GLY 2.9 18.6 + - - +
65A GLU 3.7 4.7 - - - +
66A ILE 3.2 0.2 - - - -
67A ASP* 1.3 72.8 - - - +
69A GLN* 1.3 67.2 + - - +
71A LEU* 3.7 6.0 - - + +
72A SER* 3.0 26.9 + - - -
98A TYR* 4.4 4.7 - - + -
101A LEU* 3.3 37.0 - - + -
102A VAL* 4.2 11.0 - - + -
105A ILE* 4.0 21.8 - - + -
108A LEU* 3.7 17.4 - - + +
113A PHE* 3.6 36.1 - - + -
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Residues in contact with GLN 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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33A GLN* 2.8 48.6 + - - +
36A MET* 4.5 12.3 - - + -
37A ASP* 4.9 0.2 - - - +
65A GLU 3.3 14.5 + - - +
66A ILE* 3.0 14.9 + - + +
68A LEU* 1.3 81.2 + - - +
70A ILE* 1.3 64.2 + - - +
72A SER* 2.7 29.5 + - - -
73A LYS* 3.2 16.4 + - - +
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Residues in contact with ILE 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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36A MET* 3.9 23.8 - - + -
40A LEU* 3.7 13.6 - - + +
56A ILE* 4.9 6.1 - - + -
66A ILE* 2.9 18.1 + - + +
67A ASP* 3.3 8.3 - - - +
69A GLN* 1.3 77.3 - - - +
71A LEU* 1.3 64.6 + - + +
73A LYS* 3.1 6.4 + - - +
74A VAL* 3.1 26.8 + - + +
138A PHE* 3.7 29.6 - - + -
140A HIS* 3.6 32.3 - - + +
142A ILE* 3.8 24.2 - - + -
169A LEU* 4.8 2.2 - - + -
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Residues in contact with LEU 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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56A ILE* 3.4 23.6 - - + -
67A ASP 2.9 21.9 + - - +
68A LEU* 3.7 13.5 - - + +
70A ILE* 1.3 75.6 - - + +
72A SER* 1.3 59.9 + - - +
74A VAL* 3.2 4.4 + - - +
75A GLN* 2.8 32.7 + - - +
83A ILE* 3.7 18.2 - - + +
85A ASN* 3.3 28.9 - - + +
108A LEU* 4.2 13.0 - - + -
111A VAL* 4.2 7.6 - - + -
113A PHE* 3.5 39.3 - - + -
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Residues in contact with SER 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 14.9 + - - -
69A GLN* 2.7 30.2 + - - -
71A LEU* 1.3 77.2 - - - +
73A LYS* 1.3 69.2 + - - +
75A GLN* 3.4 4.4 + - - +
76A ALA* 2.9 29.3 + - - +
107A ASN* 5.4 8.1 - - - -
108A LEU* 4.1 13.9 - - - +
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Residues in contact with LYS 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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33A GLN* 4.7 4.0 - - - +
36A MET* 3.5 27.8 - - - +
37A ASP* 2.8 34.7 + - - +
40A LEU* 3.9 19.3 - - + -
41A PRO* 4.4 17.4 - - + +
44A ILE* 3.9 7.6 - - + +
69A GLN* 3.2 14.9 + - - +
70A ILE 3.1 6.0 + - - +
72A SER* 1.3 92.3 + - - +
74A VAL* 1.3 64.4 + - - +
76A ALA* 3.4 8.1 + - + +
77A GLN* 3.1 23.4 + - - +
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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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40A LEU* 5.7 0.2 - - + -
44A ILE* 4.3 20.2 - - + -
47A ILE* 4.3 16.6 - - + -
54A ILE* 3.9 31.2 - - + -
56A ILE* 3.9 20.0 - - + -
70A ILE* 3.1 19.8 + - + +
71A LEU 3.8 5.2 - - - +
73A LYS* 1.3 74.5 - - - +
75A GLN* 1.3 60.7 + - - +
77A GLN 3.2 1.4 + - - -
78A TYR* 2.9 33.4 + - + +
83A ILE* 3.8 19.5 - - + +
138A PHE* 5.5 0.7 - - + -
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Residues in contact with GLN 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 LEU 2.8 14.1 + - - +
72A SER* 3.7 5.4 - - - +
74A VAL* 1.3 76.6 - - - +
76A ALA* 1.3 63.1 + - - +
78A TYR 3.3 3.4 - - - +
79A PRO* 3.2 27.2 - - - +
81A VAL 5.3 0.4 - - - +
83A ILE* 3.6 22.9 - - + -
107A ASN 3.0 25.5 + - - -
108A LEU* 3.2 25.6 - - - +
109A GLU 3.4 1.2 + - - +
110A ASN* 3.1 44.9 + - + +
111A VAL* 3.4 5.7 - - + +
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Residues in contact with ALA 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 SER 2.9 17.9 + - - +
73A LYS* 3.6 10.3 - - + +
75A GLN* 1.3 78.5 - - - +
77A GLN* 1.3 60.0 + - - +
79A PRO* 3.6 10.8 - - - +
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Residues in contact with GLN 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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41A PRO* 4.6 8.3 - - - +
44A ILE* 3.9 18.3 - - + +
45A GLY* 3.5 24.0 + - - -
49A ASP* 5.6 0.2 + - - -
73A LYS 3.1 16.7 + - - +
74A VAL 3.2 4.2 + - - +
76A ALA* 1.3 77.0 - - - +
78A TYR* 1.3 88.0 + - + +
79A PRO* 3.5 6.8 - - - +
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Residues in contact with TYR 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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44A ILE 3.6 9.6 - - - -
45A GLY 2.8 15.7 + - - -
46A ARG* 3.0 4.0 - - - -
47A ILE* 4.4 2.9 - - + -
48A GLY* 3.0 46.4 + - - -
49A ASP* 2.7 25.3 + - - -
54A ILE* 3.5 28.3 - - + -
74A VAL* 2.9 18.3 + - + +
75A GLN* 3.3 9.4 - - - +
77A GLN* 1.3 107.1 - - + +
79A PRO* 1.3 67.2 - - - +
80A GLY 3.4 0.3 + - - -
81A VAL* 3.2 29.5 + - + +
83A ILE* 5.6 1.0 - - + +
110A ASN* 5.0 0.7 + - - -
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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