Contacts of the helix formed by residues 68 - 87 (chain A) in PDB entry 1EQB
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 CYS 68 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LYS* 3.8 17.9 - - - -
55A TYR 3.8 2.5 - - - -
56A ALA* 3.7 28.9 - - - -
63A ARG* 3.7 16.6 - - + -
65A PHE* 3.7 19.5 - - - +
66A GLY 3.4 0.2 - - - -
67A GLY* 1.3 76.3 - - - +
69A GLU* 1.3 61.4 + - - +
70A TYR 3.4 2.2 - - - -
71A VAL* 3.4 15.7 - - + -
72A ASP* 2.8 38.1 + - - +
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLY* 3.0 36.2 + - - -
68A CYS* 1.3 84.2 + - - +
70A TYR* 1.3 83.6 + - + +
72A ASP* 3.6 5.1 - - - +
73A ILE* 3.5 24.6 + - - +
25B ARG* 3.8 16.1 - - - +
29B HIS* 4.4 7.4 - - - -
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Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A CYS* 4.6 0.2 - - - +
69A GLU* 1.3 95.7 + - + +
71A VAL* 1.3 65.3 + - - +
72A ASP 3.0 1.3 - - - -
73A ILE* 3.2 16.5 + - + +
74A VAL* 3.1 27.2 + - - +
18B ALA* 3.6 18.3 - - - +
21B GLN* 3.4 51.3 + - + -
22B GLU* 3.9 31.3 + - + +
25B ARG* 3.8 28.7 - - + -
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Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 4.7 6.7 - - + -
54A LYS* 4.0 28.9 - - + -
56A ALA* 4.1 9.9 - - + -
63A ARG* 4.2 1.3 - - - +
67A GLY 4.8 0.2 - - - +
68A CYS* 3.4 39.0 - - + +
70A TYR* 1.3 76.1 - - - +
72A ASP* 1.3 63.6 + - - +
74A VAL* 4.1 6.3 - - + -
75A GLU* 2.9 26.0 + - - +
266A MET* 3.2 35.7 - - + +
22B GLU* 4.2 17.0 + - + +
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Residues in contact with ASP 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PRO* 3.2 19.4 - - + +
61A GLY* 2.7 27.7 + - - -
63A ARG* 2.6 36.0 + - - +
68A CYS* 2.8 29.3 + - - +
69A GLU* 3.6 8.1 - - - +
70A TYR 3.0 0.2 - - - -
71A VAL* 1.3 76.9 - - - +
73A ILE* 1.3 64.8 + - + +
75A GLU 4.0 0.2 - - - -
76A GLN* 3.1 24.3 + - - +
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Residues in contact with ILE 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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69A GLU 3.5 15.0 - - - +
70A TYR* 3.2 27.1 + - + +
72A ASP* 1.3 78.3 - - + +
74A VAL* 1.3 62.6 + - - +
76A GLN* 3.2 6.3 + - - +
77A LEU* 3.0 34.3 + - + +
14B GLU* 5.0 5.6 - - - +
17B GLN* 6.0 2.0 - - - +
18B ALA* 3.6 19.7 - - + -
21B GLN* 4.4 8.1 - - - +
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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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51A LEU* 4.3 16.2 - - + -
70A TYR 3.1 16.1 + - - +
71A VAL* 3.5 11.9 - - - +
73A ILE* 1.3 77.4 - - - +
75A GLU* 1.3 63.2 + - - +
77A LEU* 3.2 10.6 + - - +
78A ALA* 3.2 19.4 + - - +
266A MET* 4.3 11.4 - - + +
269A ILE 4.4 2.7 - - - -
270A ALA* 3.6 38.4 - - + +
273A ALA* 4.3 0.9 - - - +
15B LEU* 3.9 14.4 - - + -
18B ALA* 4.0 16.2 - - + -
19B MET* 4.9 4.9 - - + +
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Residues in contact with GLU 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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59A TYR* 3.8 5.4 - - - -
60A PRO* 3.3 22.4 - - + +
63A ARG* 2.7 32.7 + - - +
71A VAL 2.9 16.7 + - - +
72A ASP 4.1 2.0 - - - +
74A VAL* 1.3 77.7 - - - +
76A GLN* 1.3 57.3 + - - +
78A ALA* 3.4 3.1 + - - +
79A ILE* 3.0 36.3 + - + +
93A VAL* 3.7 16.3 - - + +
94A GLN* 2.6 36.1 + - - +
266A MET* 4.1 14.6 - - + +
269A ILE* 4.0 13.2 - - + -
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Residues in contact with GLN 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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60A PRO* 3.7 21.9 - - + +
72A ASP 3.1 19.2 + - - +
73A ILE* 3.5 6.1 - - - +
74A VAL 3.2 0.2 - - - -
75A GLU* 1.3 74.4 - - - +
77A LEU* 1.3 61.5 + - - +
79A ILE* 3.2 17.4 + - - +
80A ASP* 2.8 71.2 + - - +
83A LYS* 5.9 0.6 - - - +
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Residues in contact with LEU 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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73A ILE* 3.0 26.1 + - + +
74A VAL* 3.4 7.6 - - - +
76A GLN* 1.3 76.5 - - - +
78A ALA* 1.3 56.4 + - - +
80A ASP* 3.4 5.4 + - + +
81A ARG* 2.6 63.8 + - - +
273A ALA* 4.3 7.6 - - + -
14B GLU* 3.4 27.6 - - + +
15B LEU* 3.4 48.2 - - + +
18B ALA* 5.5 0.2 - - + -
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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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74A VAL 3.2 3.4 + - - +
75A GLU 3.7 8.1 - - - +
76A GLN 3.3 0.2 - - - -
77A LEU* 1.3 80.3 - - - +
79A ILE* 1.3 56.6 + - - +
81A ARG* 4.4 0.9 - - - -
82A ALA* 3.0 31.5 + - - +
93A VAL* 3.9 14.3 - - + +
269A ILE* 3.8 25.8 - - + +
272A LYS* 4.7 3.6 - - + -
273A ALA* 3.7 29.3 - - + +
276A LEU* 3.5 5.1 - - + +
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Residues in contact with ILE 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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59A TYR* 5.6 4.5 - - + -
60A PRO* 4.6 12.1 - - + -
75A GLU* 3.0 42.2 + - + +
76A GLN* 3.2 19.0 + - - +
78A ALA* 1.3 76.6 - - - +
80A ASP* 1.3 64.6 + - - +
82A ALA* 3.3 3.5 + - - +
83A LYS* 3.0 42.0 + - + +
91A ALA* 3.8 30.7 - - + +
92A ASN* 5.5 0.7 - - - -
93A VAL* 3.7 21.5 - - + +
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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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76A GLN* 2.8 53.5 + - - +
77A LEU* 4.0 6.5 - - + +
79A ILE* 1.3 74.3 - - - +
81A ARG* 1.3 62.1 + - + +
83A LYS* 3.2 20.0 + - - +
84A GLU* 3.0 23.5 + - - +
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Residues in contact with ARG 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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77A LEU* 2.6 57.0 + - - +
78A ALA* 4.1 3.1 - - - +
80A ASP* 1.3 75.5 - - + +
82A ALA* 1.3 64.4 + - - +
84A GLU* 3.3 2.6 + - - +
85A LEU* 2.9 27.7 + - - +
273A ALA* 3.3 25.5 + - - +
276A LEU* 4.0 15.5 - - + +
277A LYS* 3.8 22.2 - - - +
280A MET* 3.7 27.1 - - + +
12B ASP* 2.3 44.6 + - - -
14B GLU* 4.5 5.5 - - - +
15B LEU* 4.2 6.5 - - - +
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Residues in contact with ALA 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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78A ALA 3.0 21.0 + - - +
79A ILE* 3.5 5.6 - - - +
80A ASP 3.2 0.2 - - - -
81A ARG* 1.3 77.8 - - - +
83A LYS* 1.3 61.3 + - - +
85A LEU* 4.8 0.7 - - - -
86A PHE* 3.3 30.6 + - - +
91A ALA* 4.1 14.6 - - + -
238A LEU* 4.4 13.5 - - + -
240A LEU* 4.3 11.5 - - + +
276A LEU* 3.5 22.6 - - + +
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Residues in contact with LYS 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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76A GLN* 6.0 0.4 - - - +
79A ILE* 3.0 22.0 + - + +
80A ASP* 3.6 23.6 + - - +
81A ARG 3.2 0.4 - - - -
82A ALA* 1.3 77.1 - - - +
84A GLU* 1.3 53.3 + - - +
87A GLY* 2.7 32.7 + - - -
88A ALA* 3.1 26.0 + - - +
89A ASP* 3.4 38.0 + - - +
90A TYR* 3.6 8.3 - - - +
91A ALA* 3.6 15.9 - - + +
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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
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80A ASP 3.0 16.7 + - - +
81A ARG* 3.9 4.7 - - - +
83A LYS* 1.3 79.8 - - - +
85A LEU* 1.3 61.7 + - - +
86A PHE 3.4 0.5 + - - -
87A GLY* 3.7 6.0 + - - -
280A MET* 4.2 21.1 - - + +
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Residues in contact with LEU 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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81A ARG 2.9 18.1 + - - +
82A ALA* 4.1 3.4 - - - +
84A GLU* 1.3 78.1 - - - +
86A PHE* 1.3 74.8 + - + +
209A ALA* 4.1 32.0 - - + +
215A ASN* 5.4 0.5 + - - -
231A LEU* 4.5 1.1 - - + -
276A LEU* 3.9 25.8 - - + +
279A ALA* 3.6 43.1 - - + +
280A MET* 4.1 21.7 - - + +
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Residues in contact with PHE 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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82A ALA* 3.3 21.8 + - - +
83A LYS 4.6 0.2 - - - +
85A LEU* 1.3 96.9 - - + +
87A GLY* 1.3 60.5 + - - +
88A ALA* 3.4 2.9 + - + +
201A MET* 3.4 27.6 - - + -
205A ALA* 3.5 24.7 - - + -
208A VAL* 4.2 14.4 - - + -
209A ALA* 4.1 19.1 - - + -
215A ASN* 3.2 24.9 + - - +
217A VAL* 3.8 13.9 - - + +
218A PRO* 5.5 0.2 - - - +
225A THR* 5.3 0.7 - - + -
231A LEU* 4.1 23.1 - - + -
238A LEU* 4.9 5.4 - - + -
240A LEU* 3.6 29.2 - - + -
276A LEU* 4.7 5.2 - - + -
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Residues in contact with GLY 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 LYS 2.7 15.9 + - - -
84A GLU* 3.7 5.7 + - - -
85A LEU 3.7 1.4 - - - -
86A PHE* 1.3 76.5 - - - +
88A ALA* 1.3 57.8 + - - -
217A VAL* 4.2 1.1 - - - +
242A LYS* 3.0 36.4 + - - +
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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
------------------------------------------------------------
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