Contacts of the helix formed by residues 57 - 73 (chain A) in PDB entry 2JNU
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 ASP 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ILE* 3.8 3.7 - - + +
54A PRO* 2.9 19.9 + - + +
56A SER* 1.3 74.6 - - - +
58A THR* 1.3 64.1 + - - +
59A GLN* 3.1 13.0 + - - +
60A GLN* 2.8 47.4 + - + +
61A LEU* 3.3 13.5 + - - +
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Residues in contact with THR 58 (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 ALA 3.3 13.9 + - - -
56A SER 3.1 7.0 + - - -
57A ASP* 1.3 74.0 - - - +
59A GLN* 1.3 56.1 + - - +
60A GLN 3.4 0.2 - - - -
61A LEU* 3.3 10.1 + - + +
62A ALA* 2.9 28.1 + - - +
97A PRO* 3.7 34.1 - - + +
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Residues in contact with GLN 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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57A ASP* 3.1 9.1 - - - +
58A THR* 1.3 79.4 - - - +
60A GLN* 1.3 62.5 + - - +
62A ALA* 3.2 9.1 + - + +
63A GLN* 3.1 39.6 + - + +
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Residues in contact with GLN 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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49A ARG* 5.8 4.0 - - - +
53A ILE* 3.7 32.3 - - + -
57A ASP* 2.8 23.5 + - + +
59A GLN* 1.3 72.7 - - - +
61A LEU* 1.3 60.9 + - - +
63A GLN* 3.1 18.7 + - - +
64A GLU* 2.9 29.5 + - + +
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Residues in contact with LEU 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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50A PHE* 3.1 38.9 - - + +
53A ILE* 3.6 28.0 - - + +
55A ALA* 3.9 17.3 - - + +
57A ASP 3.6 7.0 - - - +
58A THR* 3.3 20.6 + - - +
60A GLN* 1.3 79.3 - - - +
62A ALA* 1.3 56.1 + - - +
64A GLU 3.3 0.2 + - - -
65A ALA* 2.8 28.4 + - - +
97A PRO* 3.5 31.4 - - + +
99A PRO* 3.6 29.2 - - + -
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Residues in contact with ALA 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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58A THR* 2.9 14.5 + - + +
59A GLN* 3.4 13.0 - - - +
60A GLN 3.2 0.2 - - - -
61A LEU* 1.3 75.8 - - - +
63A GLN* 1.3 64.9 + - + +
65A ALA* 3.5 3.5 + - - +
66A ARG* 3.3 24.3 + - - +
94A LEU* 5.2 5.6 - - - +
97A PRO* 3.6 17.7 - - + +
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Residues in contact with GLN 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 GLN* 3.2 29.5 + - + +
60A GLN* 3.1 21.7 + - - +
62A ALA* 1.3 78.3 - - - +
64A GLU* 1.3 59.2 + - - +
66A ARG* 3.0 42.4 - - - +
67A ASN* 3.0 17.3 + - - +
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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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46A ALA* 5.7 1.3 - - - +
49A ARG* 3.3 47.8 + - + +
50A PHE* 3.7 23.8 - - + -
53A ILE* 3.7 14.6 - - + +
60A GLN* 2.9 16.0 + - - +
63A GLN* 1.3 74.2 - - - +
65A ALA* 1.3 66.6 + - - +
67A ASN* 3.1 32.6 + - - +
68A ILE* 3.0 44.0 + - + +
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Residues in contact with ALA 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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50A PHE* 3.6 17.4 - - + -
61A LEU 2.8 19.7 + - - +
62A ALA* 3.7 6.7 - - - +
63A GLN 3.3 0.2 - - - -
64A GLU* 1.3 77.5 - - - +
66A ARG* 1.3 57.1 + - - +
68A ILE* 3.5 1.7 + - - +
69A TYR* 2.9 30.0 + - - +
93A VAL* 4.1 19.9 - - - +
94A LEU* 4.1 10.0 - - + +
97A PRO* 4.3 2.9 - - + -
102A PHE* 4.6 15.1 - - + -
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Residues in contact with ARG 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 ALA 3.3 9.3 + - - +
63A GLN* 3.0 43.0 - - - +
65A ALA* 1.3 76.0 - - - +
67A ASN* 1.3 74.8 + - - +
69A TYR* 3.9 2.9 - - + -
70A GLN* 3.0 65.2 + - - +
94A LEU* 3.9 17.9 - - + +
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Residues in contact with ASN 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 GLN* 3.0 27.1 + - - +
64A GLU* 3.1 33.8 + - - +
66A ARG* 1.3 92.0 + - - +
68A ILE* 1.3 64.2 + - + +
70A GLN* 4.0 5.7 + - - +
71A GLU* 3.1 25.6 + - - +
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Residues in contact with ILE 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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43A PHE* 3.8 23.1 - - + -
46A ALA* 3.3 43.1 - - + +
47A CYS* 4.2 2.2 - - - +
50A PHE* 4.1 15.0 - - + -
64A GLU* 3.0 32.9 + - + +
65A ALA 4.0 2.9 - - - +
67A ASN* 1.3 75.6 - - + +
69A TYR* 1.3 62.8 + - - +
72A PHE* 2.9 43.9 + - + -
73A LEU* 3.5 11.7 + - + -
102A PHE* 4.2 13.9 - - + -
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Residues in contact with TYR 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 ALA 2.9 20.6 + - - +
66A ARG* 3.6 8.5 - - + +
67A ASN 3.2 0.2 - - - -
68A ILE* 1.3 75.1 - - - +
70A GLN* 1.3 72.1 + - + +
73A LEU* 2.7 28.0 + - + +
74A SER* 2.6 48.9 + - - -
75A SER* 5.3 2.4 + - - -
88A TRP* 4.0 31.9 - + - -
90A GLY* 4.5 7.4 - - - -
91A GLU* 5.5 0.7 + - - -
93A VAL* 4.5 1.6 - - + -
94A LEU* 3.8 32.5 - - + -
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Residues in contact with GLN 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 ARG* 3.0 66.4 + - + +
67A ASN* 4.1 5.0 + - - +
69A TYR* 1.3 92.0 - - + +
71A GLU* 1.3 59.7 + - - +
74A SER* 3.4 23.0 - - - +
76A GLN 4.5 0.3 - - - +
77A ALA* 3.4 9.5 - - - -
78A LEU* 3.9 10.8 - - + +
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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 ASN 3.1 17.9 + - - +
70A GLN* 1.3 78.0 - - - +
72A PHE* 1.3 93.0 + - + +
77A ALA* 3.2 1.6 - - - +
78A LEU* 3.1 38.1 + - - +
79A SER* 2.9 49.8 + - - -
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Residues in contact with PHE 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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39A GLU 3.7 4.7 - - - -
42A THR* 3.4 43.1 - - + -
43A PHE* 3.7 22.4 - + + -
46A ALA* 4.0 20.2 - - + -
68A ILE* 2.9 30.7 + - + +
71A GLU* 1.3 97.7 - - + +
73A LEU* 1.3 56.4 + - - +
74A SER 3.6 1.1 - - - -
77A ALA* 3.5 4.0 - - - +
79A SER* 3.1 36.8 - - - +
80A PRO* 3.5 4.3 - - - +
81A VAL* 3.5 23.0 + - + +
85A ARG* 2.7 29.6 + - - -
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Residues in contact with LEU 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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43A PHE* 3.6 19.3 - - + -
68A ILE* 3.7 17.7 - - + +
69A TYR* 2.7 38.0 + - + +
72A PHE* 1.3 74.6 - - - +
74A SER* 1.3 66.5 + - - +
75A SER 3.9 0.2 + - - -
81A VAL* 4.1 3.1 - - + -
83A ILE* 3.6 31.2 - - + -
85A ARG* 3.2 18.2 + - - +
88A TRP* 3.4 41.4 - - + -
102A PHE* 3.5 20.2 - - + -
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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