Contacts of the helix formed by residues 68 - 87 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D LYS* 3.7 18.8 - - - -
55D TYR 3.8 2.0 - - - -
56D ALA* 3.7 27.4 - - - -
63D ARG* 3.7 15.3 - - + -
65D PHE 3.7 20.9 - - - +
66D GLY* 4.5 0.2 - - - -
67D GLY* 1.3 76.4 - - - +
69D GLU* 1.3 60.4 + - - +
70D TYR 3.4 2.7 - - - -
71D VAL* 3.4 16.8 - - + -
72D ASP* 2.8 39.6 + - - +
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Residues in contact with GLU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ARG* 3.7 16.1 - - - +
29C HIS* 4.3 8.4 - - - -
67D GLY* 3.0 35.5 + - - -
68D CYS* 1.3 85.1 + - - +
70D TYR* 1.3 82.9 + - + +
72D ASP* 3.6 5.6 - - - +
73D ILE* 3.5 23.7 + - - +
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Residues in contact with TYR 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ALA* 3.6 17.8 - - - +
21C GLN* 3.5 57.6 + - + -
22C GLU* 3.9 24.1 + - + +
25C ARG* 3.7 30.7 - - + -
69D GLU* 1.3 95.1 + - + +
71D VAL* 1.3 64.5 + - - +
72D ASP 3.1 2.2 - - - -
73D ILE* 3.2 16.9 + - + +
74D VAL* 3.1 26.6 + - - +
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Residues in contact with VAL 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLU* 4.2 17.7 + - + +
51D LEU* 4.7 6.7 - - + -
54D LYS* 4.0 28.5 - - + -
56D ALA* 4.1 11.0 - - + -
63D ARG* 4.3 1.3 - - - +
67D GLY 4.8 0.2 - - - +
68D CYS* 3.4 38.6 - - + -
70D TYR* 1.3 76.5 - - - +
72D ASP* 1.3 63.1 + - - +
74D VAL* 4.1 5.8 - - - -
75D GLU* 3.0 25.3 + - - +
266D MET* 3.2 35.7 - - + +
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Residues in contact with ASP 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D PRO* 3.4 18.2 - - + +
61D GLY* 2.7 27.4 + - - -
63D ARG* 2.6 36.9 + - - +
68D CYS* 2.8 29.5 + - - +
69D GLU* 3.6 7.7 - - - +
71D VAL* 1.3 76.5 - - - +
73D ILE* 1.3 65.7 + - + +
75D GLU 3.6 0.3 + - - -
76D GLN* 3.1 24.6 + - - +
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Residues in contact with ILE 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLU* 5.0 3.8 - - + +
18C ALA* 3.5 20.4 - - + -
21C GLN* 4.3 9.2 - - - +
69D GLU 3.5 15.5 + - - +
70D TYR* 3.2 26.8 + - + +
72D ASP* 1.3 78.9 - - + +
74D VAL* 1.3 63.1 + - - +
76D GLN* 3.3 6.9 + - - +
77D LEU* 3.0 34.4 + - + +
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Residues in contact with VAL 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LEU* 4.1 11.7 - - + -
18C ALA* 4.1 18.8 - - + -
19C MET* 4.9 0.9 - - + -
51D LEU* 4.2 17.3 - - + -
70D TYR 3.1 15.7 + - - +
71D VAL* 3.5 13.2 - - - +
73D ILE* 1.3 77.8 - - - +
75D GLU* 1.3 62.9 + - - +
77D LEU* 3.2 12.7 + - - +
78D ALA* 3.2 19.4 + - - +
266D MET* 4.3 10.1 - - + +
269D ILE 4.4 2.7 - - - -
270D ALA* 3.6 39.3 - - + +
273D ALA* 4.3 1.6 - - + +
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Residues in contact with GLU 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D TYR* 3.8 5.0 - - - -
60D PRO* 3.3 22.2 - - + +
63D ARG* 2.8 31.9 + - - +
71D VAL 3.0 17.1 + - - +
72D ASP 4.1 2.2 - - - +
74D VAL* 1.3 76.7 - - - +
76D GLN* 1.3 57.8 + - - +
78D ALA* 3.4 2.4 + - - +
79D ILE* 3.0 42.5 + - + +
93D VAL* 3.7 15.4 + - + +
94D GLN* 2.6 36.4 + - - +
266D MET* 4.1 14.7 - - + +
269D ILE* 4.0 13.0 - - + -
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Residues in contact with GLN 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D PRO* 3.7 21.9 - - + +
72D ASP 3.1 19.3 + - - +
73D ILE* 3.6 6.7 - - - +
74D VAL 3.2 0.2 - - - -
75D GLU* 1.3 73.8 - - - +
77D LEU* 1.3 61.3 + - - +
79D ILE* 3.1 16.9 + - - +
80D ASP* 2.8 70.9 + - - +
83D LYS* 6.0 0.4 - - - +
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Residues in contact with LEU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLU* 3.7 27.4 - - + +
15C LEU* 3.7 46.2 - - + +
18C ALA* 5.4 0.2 - - + -
73D ILE* 3.0 28.4 + - + +
74D VAL* 3.2 7.8 + - - +
76D GLN* 1.3 76.3 - - - +
78D ALA* 1.3 56.6 + - - +
80D ASP* 4.0 5.5 - - + +
81D ARG* 2.5 64.8 + - - +
273D ALA* 4.4 7.0 - - + -
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Residues in contact with ALA 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D VAL 3.2 4.2 + - - +
75D GLU 3.7 7.6 - - - +
76D GLN 3.2 0.4 - - - -
77D LEU* 1.3 77.9 - - - +
79D ILE* 1.3 58.3 + - - +
81D ARG* 4.4 0.9 - - - -
82D ALA* 3.0 31.5 + - - +
93D VAL* 3.9 14.6 - - + -
269D ILE* 3.8 26.5 - - + +
272D LYS* 4.7 3.4 - - + -
273D ALA* 3.8 28.6 - - + +
276D LEU* 3.5 5.9 - - + +
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Residues in contact with ILE 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D TYR* 5.6 4.7 - - + -
60D PRO* 4.6 13.0 - - + -
75D GLU* 3.0 41.7 + - + +
76D GLN* 3.6 18.4 - - - +
78D ALA* 1.3 77.2 - - - +
80D ASP* 1.3 63.7 + - - +
82D ALA* 3.4 3.6 + - - +
83D LYS* 3.1 42.1 + - + +
91D ALA* 3.9 29.2 - - + +
92D ASN* 5.5 0.4 - - - -
93D VAL* 3.7 22.2 - - + +
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Residues in contact with ASP 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLN* 2.8 53.0 + - - +
77D LEU* 4.1 6.0 - - + +
79D ILE* 1.3 73.6 - - - +
81D ARG* 1.3 63.6 + - + +
83D LYS* 3.2 21.1 + - - +
84D GLU* 3.0 23.3 + - - +
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Residues in contact with ARG 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ASP* 2.4 43.0 + - - -
14C GLU* 3.9 8.9 + - - -
15C LEU* 4.3 5.1 - - - +
77D LEU* 2.5 59.2 + - - +
78D ALA* 4.1 2.9 - - - +
80D ASP* 1.3 77.0 - - + +
82D ALA* 1.3 58.6 + - - +
84D GLU* 3.2 3.3 + - - +
85D LEU* 2.9 34.0 + - - +
273D ALA* 3.2 26.9 + - - +
276D LEU* 4.0 15.9 - - + -
277D LYS* 3.8 21.7 - - - +
280D MET* 3.7 26.6 - - + +
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Residues in contact with ALA 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ALA 3.0 19.8 + - - +
79D ILE* 3.5 5.8 - - - +
80D ASP 3.2 0.2 - - - -
81D ARG* 1.3 78.1 - - - +
83D LYS* 1.3 61.7 + - - +
85D LEU* 4.8 1.1 - - - -
86D PHE* 3.3 30.6 + - - +
91D ALA* 4.0 14.6 - - + -
238D LEU* 4.4 13.9 - - + -
240D LEU* 4.2 12.2 - - + +
276D LEU* 3.5 21.5 - - + +
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Residues in contact with LYS 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D GLN* 6.0 0.4 - - - +
79D ILE* 3.1 21.8 + - + +
80D ASP* 3.2 24.0 + - - +
82D ALA* 1.3 77.3 - - - +
84D GLU* 1.3 57.8 + - - +
87D GLY* 2.7 28.4 + - - -
88D ALA* 3.1 25.2 + - - +
89D ASP* 3.4 37.6 + - - +
90D TYR* 3.5 8.3 - - - +
91D ALA* 3.6 16.6 - - + +
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Residues in contact with GLU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ASP 3.0 16.3 + - - +
81D ARG* 3.9 5.8 - - - +
83D LYS* 1.3 77.0 - - - +
85D LEU* 1.3 64.5 + - - +
86D PHE 3.4 0.3 + - - -
87D GLY* 3.8 5.6 + - - -
280D MET* 4.2 21.0 - - + +
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Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D ARG 2.9 17.8 + - - +
82D ALA* 4.2 3.8 - - - +
84D GLU* 1.3 78.5 - - - +
86D PHE* 1.3 75.2 + - + +
209D ALA* 4.1 30.7 - - + +
215D ASN* 5.5 0.7 + - - -
231D LEU* 4.5 1.3 - - + -
276D LEU* 3.8 26.0 - - + +
279D ALA* 3.6 42.2 - - + +
280D MET* 4.1 21.3 - - + +
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Residues in contact with PHE 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ALA* 3.3 20.9 + - - +
83D LYS 4.7 0.2 - - - +
85D LEU* 1.3 97.8 - - + +
87D GLY* 1.3 61.1 + - - +
88D ALA* 3.7 2.4 + - + +
201D MET* 3.4 27.4 - - + -
205D ALA* 3.6 25.8 - - + -
208D VAL* 4.2 13.9 - - + -
209D ALA* 4.1 18.8 - - + -
215D ASN* 3.2 24.9 + - - +
217D VAL* 3.8 13.9 - - + +
218D PRO* 5.5 0.2 - - - +
225D THR* 5.3 0.4 - - + -
231D LEU* 4.1 22.2 - - + -
238D LEU* 4.9 5.4 - - + -
240D LEU* 3.6 29.8 - - + -
276D LEU* 4.7 5.2 - - + -
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Residues in contact with GLY 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D LYS 2.7 16.6 + - - -
84D GLU* 3.8 5.3 + - - -
85D LEU 3.7 1.4 - - - -
86D PHE* 1.3 75.9 - - - +
88D ALA* 1.3 58.5 + - - -
217D VAL* 4.1 1.6 - - - +
242D LYS* 3.1 34.7 + - - +
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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