Contacts of the helix formed by residues 68 - 87 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LYS* 3.7 17.9 - - - -
55C TYR 3.8 2.9 - - - -
56C ALA* 3.7 28.3 - - - -
63C ARG* 3.7 17.7 - - + -
65C PHE* 3.6 20.2 - - - +
67C GLY* 1.3 76.2 - - - +
69C GLU* 1.3 60.9 + - - +
70C TYR 3.4 2.5 - - - -
71C VAL* 3.4 15.9 - - + -
72C ASP* 2.8 38.8 + - - +
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Residues in contact with GLU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLY* 3.0 37.0 + - - -
68C CYS* 1.3 84.5 + - - +
70C TYR* 1.3 83.6 + - + +
72C ASP* 3.6 5.6 - - - +
73C ILE* 3.5 24.5 + - - +
25D ARG* 3.8 16.1 - - - +
29D HIS* 4.4 8.0 - - - -
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Residues in contact with TYR 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C CYS* 4.6 0.2 - - - +
69C GLU* 1.3 93.8 + - + +
71C VAL* 1.3 65.8 + - - +
72C ASP 3.1 1.8 - - - -
73C ILE* 3.2 16.6 + - + +
74C VAL* 3.1 26.8 + - - +
18D ALA* 3.6 18.4 - - - +
21D GLN* 3.4 50.3 + - + -
22D GLU* 3.9 31.5 + - + +
25D ARG* 3.8 28.7 - - + -
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 4.8 6.1 - - + -
54C LYS* 4.0 28.5 - - + -
56C ALA* 4.2 10.3 - - + -
63C ARG* 3.9 1.5 + - - +
67C GLY 4.8 0.2 - - - +
68C CYS* 3.4 39.3 - - + +
70C TYR* 1.3 76.1 - - - +
72C ASP* 1.3 62.9 + - - +
74C VAL* 3.5 6.5 - - + +
75C GLU* 3.0 25.8 + - - +
266C MET* 3.3 36.8 - - + +
22D GLU* 4.2 17.7 + - + +
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Residues in contact with ASP 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C PRO* 3.2 19.1 - - + +
61C GLY* 2.7 27.7 + - - -
63C ARG* 2.6 36.1 + - - +
68C CYS* 2.8 29.0 + - - +
69C GLU* 3.6 8.0 - - - +
70C TYR 3.1 0.2 - - - -
71C VAL* 1.3 76.4 - - - +
73C ILE* 1.3 64.3 + - + +
76C GLN* 3.1 24.3 + - - +
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Residues in contact with ILE 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLU 3.5 15.7 + - - +
70C TYR* 3.2 27.2 + - + +
72C ASP* 1.3 78.7 - - + +
74C VAL* 1.3 62.8 + - - +
76C GLN* 3.3 6.8 + - - +
77C LEU* 3.0 34.2 + - + +
14D GLU* 5.0 4.7 - - - +
18D ALA* 3.6 19.7 - - + -
21D GLN* 4.4 7.9 - - - +
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Residues in contact with VAL 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C LEU* 4.2 17.0 - - + -
70C TYR 3.1 17.0 + - - +
71C VAL* 3.5 12.6 - - - +
72C ASP 3.3 0.2 - - - -
73C ILE* 1.3 77.8 - - - +
75C GLU* 1.3 62.4 + - - +
77C LEU* 3.2 7.0 + - - +
78C ALA* 3.2 19.4 + - - +
266C MET* 4.3 11.0 - - + +
269C ILE 4.4 2.2 - - - -
270C ALA* 3.6 38.6 - - + +
273C ALA* 4.3 1.3 - - + +
15D LEU* 4.0 17.3 - - + -
18D ALA* 4.1 15.9 - - + -
19D MET* 4.9 4.5 - - + +
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Residues in contact with GLU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C TYR* 3.7 5.2 - - - -
60C PRO* 3.2 21.5 - - + +
63C ARG* 2.8 27.3 + - - +
71C VAL 3.0 17.1 + - - +
72C ASP 4.2 2.7 - - - +
74C VAL* 1.3 76.4 - - - +
76C GLN* 1.3 57.0 + - - +
78C ALA* 3.4 2.6 + - - +
79C ILE* 3.0 42.2 + - + +
93C VAL* 3.7 15.9 + - + +
94C GLN* 2.6 36.2 + - - +
266C MET* 4.1 15.0 - - + +
269C ILE* 4.0 12.3 - - + -
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Residues in contact with GLN 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C PRO* 3.7 23.1 - - + +
72C ASP 3.1 19.8 + - - +
73C ILE* 3.6 6.7 - - - +
75C GLU* 1.3 74.4 - - - +
77C LEU* 1.3 60.4 + - - +
79C ILE* 3.2 16.4 + - - +
80C ASP* 2.8 70.8 + - - +
83C LYS* 6.0 0.2 - - - +
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C ILE* 3.0 28.1 + - + +
74C VAL* 3.2 8.0 + - - +
76C GLN* 1.3 77.4 - - - +
78C ALA* 1.3 57.3 + - - +
80C ASP* 4.0 4.9 - - + +
81C ARG* 2.5 65.3 + - - +
273C ALA* 4.3 7.2 - - + -
14D GLU* 4.0 25.4 - - + +
15D LEU* 3.7 47.3 - - + +
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Residues in contact with ALA 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C VAL 3.2 3.6 + - - +
75C GLU 3.7 7.0 - - - +
77C LEU* 1.3 78.7 - - - +
79C ILE* 1.3 58.1 + - - +
81C ARG* 4.4 0.7 - - - -
82C ALA* 3.0 31.2 + - - +
93C VAL* 3.9 14.7 - - + +
269C ILE* 3.8 26.5 - - + +
272C LYS* 4.7 3.4 - - + -
273C ALA* 3.8 29.1 - - + +
276C LEU* 3.5 5.5 - - + +
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Residues in contact with ILE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C TYR* 5.6 4.3 - - + -
60C PRO* 4.5 12.6 - - + -
75C GLU* 3.0 42.7 + - + +
76C GLN* 3.6 18.8 - - - +
78C ALA* 1.3 73.9 - - - +
80C ASP* 1.3 65.7 + - - +
82C ALA* 3.3 4.3 + - - +
83C LYS* 3.1 41.3 + - + +
91C ALA* 3.8 31.6 - - + +
92C ASN* 5.5 0.4 - - - -
93C VAL* 3.7 21.3 - - + +
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Residues in contact with ASP 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C GLN* 2.8 53.5 + - - +
77C LEU* 4.0 6.5 - - + +
79C ILE* 1.3 73.3 - - - +
81C ARG* 1.3 62.7 + - + +
83C LYS* 3.2 20.4 + - - +
84C GLU* 3.0 23.7 + - - +
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Residues in contact with ARG 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C LEU* 2.5 64.7 + - - +
78C ALA* 4.1 2.7 - - - +
80C ASP* 1.3 74.9 - - + +
82C ALA* 1.3 59.3 + - - +
84C GLU* 3.3 3.0 + - - +
85C LEU* 2.9 33.3 + - - +
273C ALA* 3.3 25.9 + - - +
276C LEU* 4.0 16.4 - - + -
277C LYS* 3.9 22.6 - - - +
280C MET* 3.7 27.0 - - + +
12D ASP* 2.5 42.0 + - - -
14D GLU* 4.5 7.7 + - - +
15D LEU* 4.4 0.8 - - - +
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Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ALA 3.0 20.6 + - - +
79C ILE* 3.5 5.6 - - - +
80C ASP 3.2 0.2 - - - -
81C ARG* 1.3 77.5 - - - +
83C LYS* 1.3 61.3 + - - +
85C LEU* 4.8 0.7 - - - -
86C PHE* 3.3 30.8 + - - +
91C ALA* 4.0 14.4 - - + -
238C LEU* 4.4 14.8 - - + -
240C LEU* 4.2 12.3 - - + +
276C LEU* 3.5 21.0 - - + +
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Residues in contact with LYS 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C GLN* 6.0 0.2 - - - +
79C ILE* 3.1 21.1 + - + +
80C ASP* 3.6 24.7 + - - +
81C ARG 3.2 0.2 - - - -
82C ALA* 1.3 76.6 - - - +
84C GLU* 1.3 54.1 + - - +
87C GLY* 2.7 31.9 + - - -
88C ALA* 3.1 26.1 + - - +
89C ASP* 3.3 38.4 + - - +
90C TYR* 3.5 8.5 - - - +
91C ALA* 3.5 16.4 - - + +
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Residues in contact with GLU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ASP 3.0 16.7 + - - +
81C ARG* 3.9 5.1 - - - +
83C LYS* 1.3 78.5 - - - +
85C LEU* 1.3 61.2 + - - +
86C PHE 3.4 0.3 + - - -
87C GLY* 3.8 6.0 + - - -
280C MET* 4.2 20.2 - - + +
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ARG 2.9 17.0 + - - +
82C ALA* 4.1 3.6 - - - +
84C GLU* 1.3 77.8 - - - +
86C PHE* 1.3 73.7 + - + +
209C ALA* 4.1 32.5 - - + +
215C ASN* 5.4 0.5 + - - -
231C LEU* 4.5 1.1 - - + -
276C LEU* 3.8 26.9 - - + +
279C ALA* 3.6 42.6 - - + +
280C MET* 4.1 21.0 - - + +
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Residues in contact with PHE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ALA* 3.3 20.4 + - - +
83C LYS 4.7 0.2 - - - +
84C GLU 3.3 0.2 - - - -
85C LEU* 1.3 96.2 - - + +
87C GLY* 1.3 64.0 + - - +
88C ALA* 4.7 2.7 - - + +
201C MET* 3.4 27.6 - - + -
205C ALA* 3.6 25.1 - - + -
208C VAL* 4.2 13.2 - - + -
209C ALA* 4.1 19.3 - - + -
215C ASN* 3.2 24.4 + - - +
217C VAL* 3.9 13.8 - - + +
218C PRO* 5.5 0.2 - - - +
225C THR* 5.3 0.9 - - + -
231C LEU* 4.2 22.7 - - + -
238C LEU* 4.9 5.6 - - + -
240C LEU* 3.6 28.9 - - + -
276C LEU* 4.7 4.9 - - + -
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Residues in contact with GLY 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LYS 2.7 16.2 + - - -
84C GLU* 3.8 5.7 + - - -
85C LEU 3.7 1.2 - - - -
86C PHE* 1.3 76.7 - - - +
88C ALA* 1.3 58.4 + - - -
217C VAL* 4.2 1.1 - - - +
242C LYS* 3.0 35.4 + - - +
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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
------------------------------------------------------------
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