Contacts of the helix formed by residues 78 - 96 (chain A) in PDB entry 1J1U
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 GLU 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A TYR* 4.1 15.8 + - - -
77A GLY* 1.3 76.8 - - - -
79A LEU* 1.3 68.3 + - - +
80A ASP* 3.4 19.7 - - - +
81A GLU* 2.8 23.5 + - - +
82A ILE* 3.0 21.8 + - - +
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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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68A ASP* 3.7 30.5 - - + +
69A LEU* 3.9 28.3 - - + -
72A TYR* 4.0 25.6 - - + -
77A GLY 4.0 1.2 + - - -
78A GLU* 1.3 77.5 + - - +
80A ASP* 1.3 59.1 + - - +
82A ILE* 3.7 3.7 - - + +
83A ARG* 2.8 65.6 + - - +
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Residues in contact with ASP 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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78A GLU* 3.4 19.2 - - - +
79A LEU* 1.3 79.8 - - - +
81A GLU* 1.3 82.2 + - - +
83A ARG* 3.3 8.2 + - - +
84A LYS* 3.1 21.3 + - - +
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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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76A LYS 4.8 2.6 - - - +
77A GLY* 3.4 11.4 - - - -
78A GLU* 2.8 47.1 + - - +
80A ASP* 1.3 85.4 + - - +
82A ILE* 1.3 67.3 + - + +
84A LYS* 3.3 18.9 + - - +
85A ILE* 2.9 36.5 + - + +
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Residues in contact with ILE 82 (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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37A PRO* 3.5 20.9 - - + +
68A ASP* 3.6 35.0 - - + +
71A ALA* 3.8 13.7 - - + -
72A TYR* 3.6 30.7 - - + +
76A LYS* 4.3 13.7 - - + +
77A GLY* 3.5 29.6 - - - +
78A GLU 3.0 16.5 + - - +
79A LEU* 3.7 5.6 - - - +
81A GLU* 1.3 77.9 - - + +
83A ARG* 1.3 60.0 + - - +
85A ILE* 3.3 6.4 + - + +
86A GLY 2.9 22.5 + - - -
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Residues in contact with ARG 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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68A ASP* 2.9 24.5 + - + +
79A LEU* 2.8 49.9 + - - +
80A ASP* 4.0 6.3 - - - +
82A ILE* 1.3 75.0 - - - +
84A LYS* 1.3 60.3 + - - +
86A GLY 3.1 0.5 + - - -
87A ASP* 2.9 26.2 + - - +
104A TYR* 3.3 28.2 + - + -
106A SER* 2.9 32.0 + - - -
110A LEU* 5.9 1.4 - - - +
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Residues in contact with LYS 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 ASP 3.1 14.5 + - - +
81A GLU* 3.5 22.8 - - - +
83A ARG* 1.3 78.4 - - - +
85A ILE* 1.3 72.8 + - - +
87A ASP* 3.3 8.1 + - - +
88A TYR* 3.2 19.8 + - - +
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Residues in contact with ILE 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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37A PRO* 3.8 5.8 - - + +
38A SER* 3.3 42.8 - - - +
39A GLY* 3.8 16.2 - - - +
81A GLU* 2.9 25.3 + - + +
82A ILE* 3.6 7.0 - - + +
84A LYS* 1.3 86.5 - - - +
86A GLY* 1.3 57.4 + - - +
88A TYR* 3.2 10.3 + - + +
89A ASN* 2.9 27.9 + - - +
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Residues in contact with GLY 86 (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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37A PRO* 3.7 18.8 - - - -
66A LEU* 4.0 9.0 - - - +
82A ILE 2.9 14.7 + - - -
83A ARG 3.4 5.4 - - - -
84A LYS 3.1 0.4 - - - -
85A ILE* 1.3 77.4 - - - +
87A ASP* 1.3 55.8 + - - +
89A ASN* 3.2 6.3 + - - +
90A LYS* 2.9 27.2 + - - +
104A TYR* 3.6 13.2 - - - -
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Residues in contact with ASP 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 ARG 2.9 9.6 + - - +
84A LYS* 3.3 10.2 + - - +
86A GLY* 1.3 72.9 - - - +
88A TYR* 1.3 67.9 + - - +
90A LYS* 3.2 14.0 + - - +
91A LYS* 3.2 48.7 + - - +
104A TYR* 3.1 15.7 + - - +
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Residues in contact with TYR 88 (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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38A SER 4.5 0.9 - - - -
39A GLY* 3.6 23.4 + - - -
40A LYS* 5.4 2.9 + - - -
41A ILE* 4.5 10.5 + - + +
84A LYS 3.2 10.4 + - - +
85A ILE* 3.2 12.8 + - + +
87A ASP* 1.3 80.9 + - - +
89A ASN* 1.3 86.0 + - - +
91A LYS* 2.9 21.1 + - + +
92A VAL* 3.0 39.6 + - + +
216A ASP* 2.8 31.1 + - - -
306A LEU* 4.7 8.3 - - + -
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Residues in contact with ASN 89 (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 PHE* 5.6 2.1 - - - +
36A GLU 4.5 0.5 - - - +
37A PRO* 3.1 11.3 - - - +
38A SER 2.6 48.0 + - - -
41A ILE* 3.5 18.5 - - - +
66A LEU* 4.7 4.4 - - + +
85A ILE 2.9 17.9 + - - -
86A GLY* 3.2 9.8 + - - +
88A TYR* 1.3 85.3 - - - +
90A LYS* 1.3 64.9 + - - +
92A VAL* 3.0 9.5 + - - +
93A PHE* 3.0 42.7 + - + -
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Residues in contact with LYS 90 (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 LEU* 4.3 12.0 - - + +
86A GLY 2.9 13.2 + - - +
87A ASP* 3.4 18.4 + - - +
88A TYR 3.2 0.2 - - - -
89A ASN* 1.3 77.5 - - - +
91A LYS* 1.3 70.4 + - + +
93A PHE* 3.3 4.8 + - - +
94A GLU* 2.9 53.8 + - - +
102A TYR* 3.7 48.9 + - + +
104A TYR* 5.8 2.0 - - + +
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Residues in contact with LYS 91 (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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87A ASP* 3.2 44.4 + - - +
88A TYR* 2.9 14.3 + - + +
90A LYS* 1.3 90.6 - - + +
92A VAL* 1.3 60.2 + - - +
94A GLU* 3.3 25.8 + - - +
95A ALA* 2.9 29.1 + - - +
306A LEU* 4.0 11.9 - - + +
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Residues in contact with VAL 92 (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 ILE* 3.7 32.8 - - + -
88A TYR* 3.0 39.3 + - + +
89A ASN 3.4 6.5 - - - +
91A LYS* 1.3 76.1 - - - +
93A PHE* 1.3 58.0 + - + +
95A ALA* 3.0 4.7 + - - +
96A MET* 2.9 34.4 + - + +
215A VAL* 3.7 19.3 - - + -
302A ILE* 4.6 5.4 - - + -
306A LEU* 3.7 26.2 - - + -
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Residues in contact with PHE 93 (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 PHE* 3.6 35.0 - + + -
41A ILE* 4.0 40.8 - - + -
45A HIS* 4.2 7.2 - + + -
49A ILE* 3.6 30.7 - - + -
64A ILE* 4.0 11.2 - - + -
66A LEU* 4.5 6.7 - - + -
89A ASN* 3.0 31.8 + - + -
90A LYS* 3.7 2.7 - - - +
92A VAL* 1.3 76.9 - - + +
94A GLU* 1.3 63.2 + - - +
96A MET* 3.2 20.5 + - + +
97A GLY 3.5 0.3 + - - -
98A LEU* 3.2 20.4 + - + +
102A TYR* 3.3 35.2 - + + +
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Residues in contact with GLU 94 (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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90A LYS* 2.9 43.5 + - - +
91A LYS* 3.4 30.7 + - - +
93A PHE* 1.3 77.9 - - - +
95A ALA* 1.3 58.3 + - - +
97A GLY* 2.8 22.2 + - - -
98A LEU 3.5 19.9 + - - +
99A LYS* 5.3 3.8 - - - +
100A ALA 5.3 0.3 - - - +
102A TYR* 3.7 14.0 - - + +
305A ARG* 4.4 3.1 + - - -
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Residues in contact with ALA 95 (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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91A LYS 2.9 14.1 + - - +
92A VAL 3.0 10.5 + - - +
94A GLU* 1.3 75.2 - - - +
96A MET* 1.3 58.5 + - - +
97A GLY 3.0 0.2 - - - -
302A ILE* 3.9 21.6 + - + +
305A ARG* 3.1 46.9 + - + +
306A LEU* 3.5 23.3 - - + -
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Residues in contact with MET 96 (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 ILE* 3.6 30.5 - - + -
45A HIS 4.7 0.2 - - - -
46A TYR* 3.6 51.8 + - + +
49A ILE* 3.7 32.8 - - + -
53A ILE* 3.8 12.4 - - - +
92A VAL* 2.9 21.8 + - + +
93A PHE* 3.5 15.9 - - + +
94A GLU 3.1 0.4 - - - -
95A ALA* 1.3 76.1 - - - +
97A GLY* 1.3 59.5 + - - +
98A LEU 3.6 0.4 - - - -
215A VAL* 3.7 12.1 - - + -
302A ILE* 3.9 22.2 - - + -
305A ARG* 5.0 0.4 - - - -
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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