Contacts of the helix formed by residues 72 - 87 (chain A) in PDB entry 2JRF
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 TYR 72 (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 5.7 1.7 + - - -
6A ASP* 5.3 9.3 + - - +
7A ILE* 5.8 2.3 + - - +
10A LEU* 4.9 9.0 - - + +
11A GLU* 3.5 44.1 - - + +
14A PHE* 4.2 21.9 - + + -
27A GLY 5.0 3.8 - - - +
28A GLN* 3.1 14.5 + - - +
71A ASN* 1.3 71.2 - - - +
73A GLU* 1.3 77.6 + - + +
75A PHE* 2.9 29.2 + + - +
76A LYS* 2.9 52.7 + - + +
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Residues in contact with GLU 73 (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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71A ASN* 3.0 16.3 + - - +
72A TYR* 1.3 90.8 - - + +
74A GLU* 1.3 59.9 + - + +
76A LYS* 2.8 47.2 + - - +
77A LYS* 3.0 25.6 + - - +
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Residues in contact with GLU 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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62A VAL* 3.0 37.6 - - + +
63A LYS* 3.2 12.4 - - - +
65A LYS* 2.6 36.2 + - - +
70A ILE* 3.9 14.6 - - + +
71A ASN* 2.7 35.5 + - - +
73A GLU* 1.3 72.3 - - + +
75A PHE* 1.3 59.7 + - - +
77A LYS* 3.6 9.7 - - + +
78A ALA* 2.9 27.9 + - - +
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Residues in contact with PHE 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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10A LEU* 4.1 21.1 - - + -
14A PHE* 3.5 48.5 - + + -
30A MET* 4.4 3.1 - - - -
35A TRP* 3.4 34.3 - + - -
38A LEU* 3.6 27.4 - - + -
70A ILE* 3.9 15.2 - - + +
71A ASN 3.0 6.5 + - - +
72A TYR* 2.9 22.4 + + - +
74A GLU* 1.3 78.2 - - - +
76A LYS* 1.3 60.2 + - - +
78A ALA* 3.1 5.1 + - - +
79A LEU* 2.9 58.6 + - + +
103A VAL* 5.6 0.2 - - + -
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Residues in contact with LYS 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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10A LEU* 5.5 2.0 - - + -
72A TYR* 2.9 41.2 + - + +
73A GLU* 2.8 59.5 + - - +
75A PHE* 1.3 77.3 - - + +
77A LYS* 1.3 60.5 + - - +
79A LEU* 3.8 14.4 - - + -
80A GLU* 3.2 17.7 + - - +
96A PHE* 3.3 28.7 - - + -
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Residues in contact with LYS 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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62A VAL* 4.3 15.4 - - + +
73A GLU 3.0 17.5 + - - +
74A GLU* 3.6 11.0 - - + +
76A LYS* 1.3 76.0 - - - +
78A ALA* 1.3 65.2 + - - +
80A GLU* 2.7 34.1 + - - +
81A GLU* 3.2 17.7 + - - +
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Residues in contact with ALA 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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35A TRP* 3.9 17.7 - - + -
58A VAL* 3.7 25.6 - - + -
59A PHE 5.6 0.2 - - - +
62A VAL* 4.1 11.6 - - + +
70A ILE* 4.7 3.4 - - + -
74A GLU 2.9 18.5 + - - +
75A PHE* 3.4 8.5 - - - +
77A LYS* 1.3 74.9 - - - +
79A LEU* 1.3 64.2 + - - +
81A GLU* 3.1 3.8 - - - +
82A LEU* 3.0 29.2 + - - +
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Residues in contact with LEU 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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10A LEU* 3.5 39.5 - - + -
35A TRP* 4.2 16.2 - - + -
38A LEU* 5.5 1.8 - - + -
44A VAL* 6.5 0.2 - - + -
75A PHE* 2.9 46.9 + - + +
76A LYS* 3.6 14.8 - - + +
78A ALA* 1.3 75.7 - - - +
80A GLU* 1.3 52.3 + - - +
82A LEU* 3.4 2.0 + - + -
83A ALA* 2.7 37.3 + - - +
96A PHE* 4.0 8.7 - - + -
99A ILE* 3.4 27.2 - - + +
100A CYS* 4.0 7.0 - - - -
103A VAL* 5.4 7.9 - - + -
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Residues in contact with GLU 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 LYS 3.2 11.1 + - - +
77A LYS* 2.7 45.7 + - - +
79A LEU* 1.3 77.0 - - - +
81A GLU* 1.3 58.7 + - - +
83A ALA* 3.3 6.8 + - - +
84A THR* 2.9 46.6 + - + +
92A LYS* 2.6 34.8 + - + +
96A PHE* 4.0 14.2 - - + -
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Residues in contact with GLU 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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58A VAL* 3.6 31.1 - - + +
61A LYS* 2.6 32.7 + - - -
62A VAL* 5.7 2.7 - - + +
77A LYS 3.2 6.4 + - - +
78A ALA* 3.1 14.3 + - - +
80A GLU* 1.3 76.9 - - - +
82A LEU* 1.3 63.7 + - - +
84A THR* 2.7 28.5 + - - -
85A LYS* 3.0 31.7 + - - +
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Residues in contact with LEU 82 (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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35A TRP* 3.9 17.5 - - + -
39A CYS* 3.8 24.5 - - - -
44A VAL* 3.7 24.5 - - + -
50A VAL* 4.1 23.8 - - + -
55A VAL* 4.8 2.5 - - + -
58A VAL* 3.8 31.9 - - + -
78A ALA 3.0 24.9 + - - +
79A LEU* 4.7 0.7 - - + -
81A GLU* 1.3 78.8 - - - +
83A ALA* 1.3 61.6 + - - +
85A LYS* 3.2 23.3 + - + +
86A ARG* 3.3 14.9 + - - +
99A ILE* 3.5 18.5 - - + +
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Residues in contact with ALA 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 LEU 2.7 22.8 + - - +
80A GLU* 3.4 10.3 - - - +
82A LEU* 1.3 73.3 - - - +
84A THR* 1.3 57.3 + - + +
86A ARG 3.2 0.3 + - - -
87A PHE* 2.7 44.7 + - - +
95A ALA* 3.8 20.2 - - + +
96A PHE* 4.4 3.6 - - + -
99A ILE* 3.5 23.7 - - + +
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Residues in contact with THR 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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80A GLU* 2.9 29.8 + - + +
81A GLU* 2.7 28.8 + - - -
83A ALA* 1.3 73.3 - - + +
85A LYS* 1.3 61.6 + - - +
86A ARG 3.4 0.2 - - - -
88A LYS* 3.1 40.9 - - + +
95A ALA* 5.9 2.9 - - + -
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Residues in contact with LYS 85 (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 SER* 2.8 21.7 + - - +
50A VAL* 3.6 19.5 - - + -
54A ASP* 2.8 39.1 + - - +
58A VAL* 4.7 4.2 - - - +
61A LYS* 5.0 4.9 - - - +
81A GLU* 3.0 49.0 + - - +
82A LEU* 3.2 17.0 - - + +
83A ALA 3.1 0.2 - - - -
84A THR* 1.3 79.4 - - - +
86A ARG* 1.3 57.8 + - - +
88A LYS* 4.2 13.0 - - - -
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Residues in contact with ARG 86 (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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43A LYS 3.1 19.0 + - - -
44A VAL* 2.7 46.8 + - - +
46A ASP* 3.2 27.8 + - - +
48A LYS* 4.6 8.7 - - - +
49A SER* 3.7 18.2 - - - +
50A VAL* 4.1 7.0 - - + -
82A LEU 3.3 8.0 + - - +
83A ALA 3.2 1.8 + - - -
85A LYS* 1.3 77.9 - - - +
87A PHE* 1.3 81.1 + - + +
88A LYS* 3.1 15.5 + - - +
102A LEU* 3.9 23.4 - - - +
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Residues in contact with PHE 87 (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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83A ALA* 2.7 27.9 + - - +
84A THR* 4.9 0.2 - - - -
86A ARG* 1.3 92.9 - - + +
88A LYS* 1.3 62.5 + - - +
90A LYS* 3.7 31.0 + - + +
95A ALA* 3.5 42.1 - - + +
98A ALA* 3.7 23.3 - - + -
99A ILE* 3.9 21.3 - - + -
102A LEU* 3.7 27.4 - - + -
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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