Contacts of the helix formed by residues 77 - 94 (chain A) in PDB entry 5LUQ
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 77 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 4.0 6.6 + - + +
28A ALA* 3.2 49.0 + - - +
32A HIS* 5.9 0.2 - - - +
75A SER 2.4 12.4 + - - -
76A ILE* 1.3 86.9 - - - +
78A PHE* 1.3 65.4 + - - +
79A ARG* 3.3 2.0 - - - -
80A GLU* 3.0 38.3 + - - +
81A CYS* 3.3 13.5 + - - -
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Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP* 3.0 37.9 - - - +
24A ARG 5.7 0.2 - - - -
25A CYS 5.4 1.3 - - - -
26A GLY* 3.3 22.7 - - - -
27A ALA* 3.7 8.1 - - + -
69A VAL* 6.1 0.4 - - + -
70A ARG* 3.8 14.8 - - + +
73A LEU* 3.5 21.1 - - + -
74A ASN* 3.3 49.8 - - + +
75A SER 2.6 15.1 + - - +
76A ILE* 3.4 26.5 - - + -
77A GLU* 1.3 72.2 - - - +
79A ARG* 1.3 54.5 + - - +
81A CYS* 2.7 30.4 + - - +
82A ARG* 2.9 13.9 + - - +
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ARG* 4.3 5.4 - - - +
74A ASN 3.9 7.9 + - - +
75A SER* 3.3 40.6 - - - +
77A GLU* 4.9 0.9 - - - -
78A PHE* 1.3 75.5 - - - +
80A GLU* 1.3 57.1 + - + +
82A ARG* 2.9 45.4 + - - +
83A GLU* 2.9 30.7 + - - +
117A LYS* 3.7 28.8 + - - +
118A ASP* 5.1 10.2 + - - +
120A ALA* 5.3 5.7 - - - +
121A ALA* 3.8 26.5 - - - +
124A LYS* 5.4 4.9 - - - +
126A PRO* 6.0 0.9 - - + -
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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
----------------------------------------------------------
32A HIS* 3.1 33.1 + - + -
76A ILE 5.3 1.8 - - - +
77A GLU* 3.0 33.2 + - - +
79A ARG* 1.3 76.8 - - + +
81A CYS* 1.3 59.2 + - - +
83A GLU* 3.1 17.7 - - - +
84A GLU* 3.0 28.8 + - - +
126A PRO* 5.1 12.4 - - + +
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Residues in contact with CYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASP* 4.7 15.7 - - - +
27A ALA* 4.7 9.0 - - - -
28A ALA 4.1 10.8 - - - -
31A GLY* 3.5 28.7 - - - -
32A HIS* 4.5 6.1 - - - -
34A LEU* 6.4 0.2 - - + -
35A ILE* 3.2 24.1 - - + +
77A GLU* 3.6 15.3 - - - -
78A PHE* 2.7 15.9 + - - +
80A GLU* 1.3 68.9 - - - +
82A ARG* 1.3 65.2 + - - +
84A GLU* 3.1 2.1 + - - -
85A ILE* 2.9 26.8 + - + +
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Residues in contact with ARG 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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66A LEU* 4.9 12.1 - - + +
69A VAL* 6.3 0.4 - - + -
70A ARG* 3.3 47.0 - - + +
78A PHE 2.9 13.7 + - - +
79A ARG* 2.9 35.2 + - - +
81A CYS* 1.3 72.9 - - - +
83A GLU* 1.3 95.0 + - - +
85A ILE* 3.4 11.4 + - - +
86A LEU* 2.9 38.5 + - + +
114A VAL* 3.2 43.5 + - + +
117A LYS* 4.7 4.6 - - - +
118A ASP* 5.3 1.2 - - - +
130A LEU* 3.2 17.2 - - - +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 2.9 26.6 + - - +
80A GLU* 3.1 19.9 - - - +
82A ARG* 1.3 103.3 + - - +
84A GLU* 1.3 64.7 + - - +
86A LEU* 3.1 3.3 + - - +
87A LYS* 3.0 37.0 + - - +
126A PRO* 3.4 41.4 - - - +
129A ASP* 5.0 3.3 - - - +
130A LEU* 3.4 30.5 - - + +
133A LYS* 5.1 1.0 - - - +
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A HIS* 2.7 55.7 + - + +
35A ILE* 3.5 17.5 - - + +
36A ARG* 4.6 11.9 + - - -
80A GLU 3.0 11.0 + - - +
81A CYS 3.6 6.1 - - - +
83A GLU* 1.3 73.6 - - - +
85A ILE* 1.3 65.0 + - - +
87A LYS* 2.9 30.3 + - + +
88A PHE* 2.8 37.7 + - + -
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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
----------------------------------------------------------
23A ASP* 5.8 3.6 - - - +
34A LEU* 5.4 7.0 - - + -
35A ILE* 3.4 33.2 - - + +
38A LEU* 6.3 2.2 - - + -
62A ASP* 3.6 19.7 - - - +
66A LEU* 3.4 46.4 - - + -
69A VAL* 6.1 2.2 - - + -
81A CYS* 2.9 30.9 + - + +
82A ARG* 3.9 5.4 - - - +
84A GLU* 1.3 74.7 - - - +
86A LEU* 1.3 57.6 + - - +
88A PHE* 3.3 2.5 + - + +
89A LEU* 2.8 40.5 + - + +
92A PHE* 6.1 0.2 - - + -
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Residues in contact with LEU 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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66A LEU* 4.1 16.4 - - + -
82A ARG* 2.9 40.7 + - + +
83A GLU* 3.1 5.3 + - - +
85A ILE* 1.3 74.6 - - - +
87A LYS* 1.3 63.0 + - - +
89A LEU* 3.4 21.2 + - + +
90A CYS* 3.0 25.3 + - - +
107A ILE* 4.6 7.9 - - + +
110A THR* 5.4 4.0 - - + -
111A CYS* 4.2 20.0 - - - -
114A VAL* 4.0 10.5 - - + -
130A LEU* 4.6 3.1 - - + -
133A LYS* 4.9 6.1 - - + -
134A LEU* 3.4 29.2 - - + -
137A THR* 3.9 8.5 - - + +
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Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 3.0 28.5 + - - +
84A GLU* 2.9 23.5 + - + +
86A LEU* 1.3 75.6 - - - +
88A PHE* 1.3 68.0 + - + +
90A CYS* 2.9 30.5 - - - -
91A ILE* 3.1 11.4 + - - +
129A ASP* 3.4 41.7 + - - +
130A LEU* 5.5 0.2 - - - +
133A LYS* 3.3 43.0 - - + +
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Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.4 39.5 - - + +
36A ARG* 4.5 20.4 - - + -
39A GLY* 4.4 10.8 - - - -
40A GLN* 5.7 5.6 - - + -
43A VAL* 5.5 2.7 - - + -
84A GLU* 2.8 52.3 + - + +
85A ILE* 3.8 4.5 - - + +
87A LYS* 1.3 78.3 - - + +
89A LEU* 1.3 56.4 + - - +
91A ILE* 3.0 20.4 - - + +
92A PHE* 2.9 50.1 + + + -
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Residues in contact with LEU 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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59A PHE* 5.0 1.3 - - + -
62A ASP* 3.7 24.0 - - + +
63A PHE* 3.4 39.0 - - + -
66A LEU* 3.4 26.0 - - + -
85A ILE* 2.8 27.2 + - + +
86A LEU* 3.7 20.6 - - + +
88A PHE* 1.3 74.5 - - - +
90A CYS* 1.3 59.9 + - - +
92A PHE* 2.6 41.6 + - + +
93A LEU* 2.9 18.0 + - + +
107A ILE* 4.6 8.7 - - + -
137A THR* 5.7 0.7 - - + -
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Residues in contact with CYS 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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86A LEU 3.0 14.6 + - - -
87A LYS* 2.9 28.3 - - - -
89A LEU* 1.3 75.4 - - - +
91A ILE* 1.3 67.6 + - - +
92A PHE 3.5 0.2 + - - -
93A LEU* 3.6 14.7 + - - +
94A GLU* 3.7 22.0 + - - +
133A LYS* 4.3 23.6 - - - -
136A GLN* 4.5 11.7 - - + -
137A THR* 3.4 34.7 - - + +
140A SER* 4.9 3.0 + - - +
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Residues in contact with ILE 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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43A VAL* 4.7 9.4 - - + -
87A LYS 3.1 13.9 + - - +
88A PHE* 3.0 33.4 - - + +
90A CYS* 1.3 82.5 - - - +
92A PHE* 1.3 71.6 + - + +
93A LEU 3.5 0.2 - - - -
94A GLU* 4.5 10.2 + - - +
95A LYS* 3.3 43.2 + - - +
133A LYS* 5.9 4.3 - - - +
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Residues in contact with PHE 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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38A LEU 4.1 5.4 - - - -
39A GLY* 3.6 23.3 - - - -
43A VAL* 3.6 32.8 - - + -
59A PHE* 3.2 46.8 - + + -
62A ASP* 4.3 8.5 - - - -
63A PHE* 5.7 1.1 - - + -
85A ILE* 5.3 0.9 - - + -
88A PHE* 2.9 43.7 + - + -
89A LEU* 2.6 39.2 + - + +
91A ILE* 1.3 81.3 - - + +
93A LEU* 1.3 59.9 + - + -
95A LYS* 3.6 6.3 + - + +
96A MSE 3.0 32.2 + - - +
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PHE* 6.2 0.2 - - + -
63A PHE* 4.0 20.6 - - + -
89A LEU* 2.9 16.5 + - + +
90A CYS* 3.6 8.9 + - - +
91A ILE 3.5 0.6 - - - -
92A PHE* 1.3 76.3 - - + +
94A GLU* 1.3 68.8 + - + +
96A MSE 3.1 12.1 + - - +
97A GLY 3.3 17.0 - - - +
100A ILE* 3.5 35.0 - - + -
104A SER* 5.2 11.0 - - - -
107A ILE* 4.2 22.9 - - + -
137A THR* 5.2 13.0 - - - +
140A SER* 5.2 15.5 - - - +
141A SER* 5.6 2.5 - - - +
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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
----------------------------------------------------------
90A CYS* 3.7 19.1 + - - +
91A ILE* 4.5 10.0 + - - +
92A PHE 3.7 0.2 - - - -
93A LEU* 1.3 78.5 - - - +
95A LYS* 1.3 66.1 + - + +
97A GLY* 3.9 8.5 + - - +
136A GLN* 5.0 2.1 - - - +
140A SER* 3.4 34.9 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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