Contacts of the helix formed by residues 69 - 84 (chain A) in PDB entry 1ECX
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 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A THR* 3.1 13.7 + - - -
68A SER* 1.3 93.2 + - - +
70A ALA* 1.3 65.3 + - - +
71A THR* 3.2 7.0 - - - -
72A GLU* 3.2 20.1 + - - +
73A SER* 3.2 10.0 + - - -
200A SER* 4.1 0.9 - - - +
202A HIS* 6.0 0.9 - - + -
209A GLY* 5.3 2.7 - - - +
210A VAL 3.8 4.9 - - - +
211A GLY* 3.2 18.4 - - - +
500A PLP 3.4 22.2 - - - +
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A CYS* 1.3 74.8 - - - +
71A THR* 1.3 57.0 + - - +
73A SER* 3.0 7.2 + - - -
74A ILE* 2.8 37.4 + - + +
179A VAL* 3.5 21.8 - - + -
198A SER* 4.8 0.4 - - - -
199A PHE 3.3 23.6 + - - +
200A SER* 3.2 22.0 + - - +
500A PLP 3.1 13.3 + - + +
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Residues in contact with THR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A CYS* 3.2 8.0 - - - -
70A ALA* 1.3 73.4 - - - +
72A GLU* 1.3 62.7 + - - +
74A ILE* 3.2 2.1 + - - +
75A ASN* 2.9 36.1 + - - +
99A HIS* 5.3 0.9 + - - -
101A ALA* 4.1 26.2 - - + +
500A PLP 2.7 40.7 + - - -
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR* 3.7 6.9 - - + +
68A SER* 2.7 46.3 + - - +
69A CYS* 3.2 13.8 + - - +
71A THR* 1.3 78.8 - - - +
73A SER* 1.3 58.1 + - - +
75A ASN* 3.7 5.5 - - - +
76A TRP* 2.8 36.2 + - + +
224A LEU* 4.5 13.5 - - + +
225A ILE* 3.9 13.8 - - + +
235A ARG* 2.6 45.8 + - - +
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Residues in contact with SER 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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67A THR* 2.7 20.0 + - - -
69A CYS 3.2 3.6 + - - -
70A ALA* 3.0 11.3 + - - -
72A GLU* 1.3 78.9 - - - +
74A ILE* 1.3 57.2 + - - +
76A TRP* 3.5 9.3 + - - +
77A ILE* 3.0 34.8 + - - +
198A SER* 3.6 20.4 - - - -
211A GLY 4.4 0.3 - - - -
212A ILE 4.1 4.9 + - - -
213A THR* 2.6 31.6 + - - -
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Residues in contact with ILE 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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70A ALA* 2.8 21.0 + - + +
71A THR* 3.7 4.5 - - - +
73A SER* 1.3 74.1 - - - +
75A ASN* 1.3 66.4 + - - +
77A ILE* 4.8 2.5 - - - -
78A LEU* 3.1 41.2 + - + +
101A ALA* 3.8 32.5 - - + +
102A VAL* 3.7 24.9 - - + -
105A THR* 4.6 0.4 - - - +
175A HIS* 4.2 10.3 - - + -
177A ASP* 3.9 26.7 - - - +
198A SER* 3.4 18.8 - - - +
500A PLP 4.2 8.3 - - + -
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Residues in contact with ASN 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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71A THR* 2.9 32.3 + - - +
72A GLU* 3.7 5.6 - - - +
74A ILE* 1.3 74.8 - - - +
76A TRP* 1.3 65.9 + - - +
79A LYS* 2.9 62.9 + - - +
101A ALA* 4.3 3.5 - - - +
105A THR* 3.1 23.4 + - - -
224A LEU* 4.0 13.6 - - + +
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Residues in contact with TRP 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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65A PHE* 3.7 27.8 - + + -
67A THR* 3.7 31.0 - - + -
72A GLU* 2.8 21.4 + - + +
73A SER* 3.6 4.5 - - - +
75A ASN* 1.3 76.8 - - - +
77A ILE* 1.3 51.8 + - + +
80A THR* 2.6 41.3 + - + +
213A THR* 3.9 23.6 - - + -
215A ILE* 3.7 17.0 - - + -
221A ILE* 3.6 11.6 - - + +
222A ARG 2.6 29.7 + - - -
224A LEU* 3.5 36.4 - - + +
234A LEU* 3.6 31.1 + - + -
235A ARG* 4.5 11.0 - - + -
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Residues in contact with ILE 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 SER 3.0 21.8 + - - +
74A ILE* 4.2 2.2 - - - +
76A TRP* 1.3 77.6 - - + +
78A LEU* 1.3 71.6 + - + +
80A THR* 4.1 3.1 - - - -
81A VAL* 3.0 32.6 + - + +
142A LEU* 5.3 1.8 - - + -
175A HIS* 3.9 23.1 - - + +
196A TYR* 3.6 56.1 - - + -
197A ALA 4.5 1.3 - - - +
198A SER* 4.3 5.6 - - - +
213A THR* 3.8 27.8 - - + -
214A TYR 4.5 1.1 - - - +
215A ILE* 5.0 1.1 - - + -
221A ILE* 4.3 11.0 - - + -
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Residues in contact with LEU 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 ILE* 3.1 32.5 + - + +
77A ILE* 1.3 80.9 - - + +
79A LYS* 1.3 58.7 + - - +
81A VAL* 4.1 1.6 - - - +
82A ALA* 3.0 31.9 + - - +
102A VAL* 4.2 9.6 - - + -
105A THR* 3.3 35.4 - - + -
106A MET* 3.7 28.9 - - + -
109A LEU* 4.1 7.8 - - + +
142A LEU* 3.4 30.3 - - + +
144A SER* 4.0 12.8 - - - +
175A HIS* 4.4 9.0 - - + +
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Residues in contact with LYS 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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75A ASN* 2.9 51.8 + - + +
76A TRP 4.4 0.7 - - - +
78A LEU* 1.3 77.7 - - - +
80A THR* 1.3 58.0 + - + +
82A ALA* 3.2 7.3 + - - +
83A GLU* 2.8 28.6 + - - +
105A THR* 4.2 16.6 - - + +
108A TYR* 3.6 46.6 - - + -
109A LEU* 4.4 7.0 - - + +
224A LEU* 4.6 18.1 - - + +
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Residues in contact with THR 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 TRP* 2.6 29.3 + - + +
79A LYS* 1.3 72.4 - - + +
81A VAL* 1.3 65.1 + - - +
83A GLU* 3.1 15.0 + - - +
84A THR* 3.0 28.0 + - - +
221A ILE* 3.0 23.2 - - - +
222A ARG* 3.0 42.6 - - + +
223A PRO 3.8 11.4 - - - +
224A LEU* 4.3 9.0 - - + +
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Residues in contact with VAL 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 ILE* 3.0 21.9 + - + +
78A LEU 4.1 0.7 - - - +
80A THR* 1.3 78.2 + - - +
82A ALA* 1.3 64.2 + - - +
84A THR* 2.6 25.3 + - - -
85A PHE* 2.9 19.7 - - + -
141A PHE* 3.8 24.0 - - + -
142A LEU* 4.3 14.8 - - + -
173A LEU* 4.2 7.6 - - + -
196A TYR* 2.9 42.2 - - + +
220A PRO* 3.8 13.5 - - + +
221A ILE* 4.9 2.9 - - + +
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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 LEU 3.0 21.0 + - - +
79A LYS 3.3 4.7 - - - +
81A VAL* 1.3 78.3 - - - +
83A GLU* 1.3 58.7 + - - +
85A PHE* 2.8 22.7 + - - +
86A GLU 3.5 0.3 + - - -
109A LEU* 4.0 23.3 - - + -
114A PHE* 3.5 33.6 - - + -
141A PHE* 3.6 18.4 - - + -
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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
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79A LYS 2.8 13.8 + - - +
80A THR* 3.2 25.8 - - - +
82A ALA* 1.3 75.6 - - - +
84A THR* 1.3 58.2 + - + +
85A PHE 3.1 4.3 + - - -
86A GLU* 3.3 44.2 + - - +
114A PHE* 4.6 0.9 - - - -
222A ARG* 4.2 27.2 + - - +
223A PRO 5.2 1.9 - - - +
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Residues in contact with THR 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 THR 3.0 13.9 + - - +
81A VAL 2.6 19.1 + - - -
83A GLU* 1.3 73.9 - - - +
85A PHE* 1.3 70.4 + - - +
86A GLU 3.5 0.7 - - - -
88A ARG* 3.0 28.3 + - - -
220A PRO* 3.8 18.5 - - + +
221A ILE 4.6 2.5 - - - +
222A ARG* 3.5 48.0 - - + +
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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