Contacts of the helix formed by residues 69 - 85 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B THR* 3.2 8.1 + - - -
68B SER* 1.3 93.5 + - - +
70B ALA* 1.3 67.4 + - - +
71B THR* 3.2 7.0 - - - -
72B GLU* 3.1 26.0 + - - +
73B SER 3.2 8.5 + - - -
200B SER* 4.0 1.8 - - - +
202B HIS* 5.8 2.0 - - + -
209B GLY* 5.4 2.2 - - - +
210B VAL 4.0 3.4 - - - +
211B GLY* 3.4 15.4 - - - +
501B PLP 3.4 21.3 - - - +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B CYS* 1.3 72.4 - - - +
71B THR* 1.3 57.4 + - - +
73B SER* 3.1 7.4 + - - -
74B ILE* 2.8 38.2 + - + +
179B VAL* 3.5 27.8 - - + -
198B SER* 4.8 0.4 - - - -
199B PHE 3.5 21.1 + - - +
200B SER* 2.9 23.2 + - - +
501B PLP 3.7 10.5 - - + +
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B CYS* 3.2 7.6 - - - -
70B ALA* 1.3 72.9 - - - +
72B GLU* 1.3 65.3 + - - +
74B ILE* 3.2 2.9 + - - +
75B ASN* 2.9 35.5 + - - +
99B HIS* 4.9 2.1 + - - -
101B ALA* 3.8 25.4 - - + +
501B PLP 2.6 40.9 + - - -
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B THR* 3.6 7.6 - - + +
68B SER* 2.7 52.5 + - - +
69B CYS* 3.1 13.7 + - - +
71B THR* 1.3 78.7 - - - +
73B SER* 1.3 64.9 + - - +
75B ASN* 3.2 7.1 + - - +
76B TRP* 2.9 25.1 + - + +
224B LEU* 4.1 13.0 - - + +
225B ILE* 4.1 13.7 - - + +
235B ARG* 2.8 38.0 + - - +
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Residues in contact with SER 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B THR* 2.6 30.9 + - - +
69B CYS 3.2 3.6 + - - -
70B ALA* 3.1 13.2 + - - -
72B GLU* 1.3 77.6 - - - +
74B ILE* 1.3 58.0 + - - +
76B TRP* 3.4 5.8 + - - +
77B ILE* 3.0 37.6 + - - +
198B SER* 3.8 15.0 - - - -
212B ILE 4.1 6.0 + - - -
213B THR* 2.7 24.8 + - - -
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA* 2.8 21.2 + - + +
71B THR* 3.6 4.0 - - - +
73B SER* 1.3 73.6 - - - +
75B ASN* 1.3 66.0 + - - +
77B ILE* 4.3 0.8 - - - +
78B LEU* 3.1 40.0 + - + +
101B ALA* 3.8 32.8 - - + +
102B VAL* 3.7 23.3 - - + -
175B HIS* 4.1 11.7 - - + -
177B ASP* 3.7 27.8 - - - +
198B SER* 3.4 21.1 - - - +
501B PLP 4.0 10.3 - - + -
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Residues in contact with ASN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B THR* 2.9 32.2 + - - +
72B GLU* 3.5 10.3 - - - +
74B ILE* 1.3 75.2 - - - +
76B TRP* 1.3 56.2 + - - +
79B LYS* 2.8 75.2 + - - +
101B ALA 4.3 2.9 - - - +
105B THR* 3.4 22.5 + - - -
224B LEU* 3.9 12.9 - - + +
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Residues in contact with TRP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B PHE* 3.8 23.3 - + + -
67B THR* 3.7 32.5 - - + -
72B GLU* 2.9 19.8 + - + +
73B SER* 3.5 4.7 - - - +
75B ASN* 1.3 77.2 - - - +
77B ILE* 1.3 61.9 + - + +
80B THR* 2.9 38.2 + - + -
213B THR* 3.9 23.8 - - + -
215B ILE* 3.7 22.2 - - + -
221B ILE* 3.5 11.9 - - + +
222B ARG 2.6 28.8 + - - -
224B LEU* 3.5 30.1 - - + +
234B LEU* 3.6 31.6 + - + -
235B ARG* 4.4 12.1 - - + -
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B SER 3.0 22.5 + - - +
74B ILE* 4.3 2.0 - - - +
76B TRP* 1.3 77.8 - - + +
78B LEU* 1.3 65.0 + - + +
81B VAL* 3.0 34.7 + - + +
142B LEU* 4.9 2.6 - - + +
175B HIS* 4.2 16.4 - - + -
196B TYR* 3.3 55.9 - - + -
197B ALA 4.4 2.5 - - - +
198B SER* 4.0 16.8 - - - +
213B THR* 3.8 29.2 - - + +
214B TYR 4.8 0.2 - - - +
215B ILE* 5.0 0.7 - - + -
221B ILE* 4.4 14.6 - - + -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ILE* 3.1 37.1 + - + +
77B ILE* 1.3 76.7 - - + +
79B LYS* 1.3 64.8 + - - +
81B VAL* 4.3 0.2 - - - +
82B ALA* 3.1 26.5 + - - +
92B ILE* 6.6 0.2 - - + -
102B VAL* 4.2 10.8 - - + +
105B THR* 3.8 28.7 - - + -
106B MET* 4.1 21.8 - - + -
109B LEU* 3.9 9.5 - - + +
142B LEU* 3.7 28.8 - - + +
144B SER* 4.0 19.7 - - - +
175B HIS* 4.2 12.6 - - + +
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ASN* 2.8 54.4 + - - +
76B TRP 4.5 0.2 - - - +
78B LEU* 1.3 75.3 - - - +
80B THR* 1.3 60.9 + - + +
82B ALA* 3.3 2.8 + - - +
83B GLU* 2.9 28.0 + - - +
105B THR* 3.9 16.6 - - + +
108B TYR* 3.6 46.1 - - + +
109B LEU* 4.5 9.1 - - + +
224B LEU* 4.5 17.5 - - + +
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Residues in contact with THR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B TRP* 2.9 30.0 + - + +
79B LYS* 1.3 75.8 - - + +
81B VAL* 1.3 62.7 + - - +
83B GLU* 3.2 16.4 - - - +
84B THR* 3.1 27.0 + - - +
221B ILE* 3.4 8.3 - - - +
222B ARG* 3.2 51.6 + - - +
223B PRO 3.9 12.3 - - - +
224B LEU* 4.1 10.5 - - + +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ILE* 3.0 24.6 + - + +
78B LEU 4.3 0.9 - - - +
80B THR* 1.3 82.3 + - - +
82B ALA* 1.3 64.8 + - - +
84B THR* 2.8 24.6 + - - +
85B PHE* 3.2 22.4 - - + -
141B PHE* 4.1 17.3 - - + -
142B LEU* 4.4 12.1 - - + -
173B LEU* 4.3 6.5 - - + -
196B TYR* 3.2 38.4 - - + +
220B PRO* 3.5 14.8 - - + +
221B ILE* 4.6 2.0 - - + -
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LEU 3.1 20.6 + - - +
79B LYS 3.6 4.3 - - - +
81B VAL* 1.3 76.5 - - - +
83B GLU* 1.3 62.3 + - - +
85B PHE* 3.1 10.9 + - - +
86B GLU* 3.4 4.9 + - - +
92B ILE* 4.5 0.7 - - + -
109B LEU* 3.8 21.8 - - + -
114B PHE* 3.2 37.3 - - + -
141B PHE* 3.7 21.1 - - + -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LYS 2.9 13.5 + - - +
80B THR* 3.2 29.4 - - - +
81B VAL 3.1 0.4 - - - -
82B ALA* 1.3 79.0 - - - +
84B THR* 1.3 59.3 + - - +
85B PHE 3.5 0.3 + - - -
86B GLU* 3.7 31.1 + - - +
114B PHE* 5.7 0.2 - - - -
222B ARG* 4.1 28.8 + - - +
223B PRO 5.2 2.3 - - - +
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Residues in contact with THR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B THR 3.1 15.9 + - - +
81B VAL* 2.8 19.5 + - - -
83B GLU* 1.3 77.2 - - - +
85B PHE* 1.3 69.6 + - - +
86B GLU 3.4 1.3 + - - +
88B ARG* 3.0 25.0 + - - -
220B PRO* 3.7 14.2 - - + +
221B ILE 4.5 11.4 - - - +
222B ARG* 3.1 47.4 + - + +
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Residues in contact with PHE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B VAL* 3.2 21.5 + - + +
82B ALA 3.1 10.4 + - - +
84B THR* 1.3 92.2 + - - +
86B GLU* 1.3 65.0 + - - +
88B ARG* 3.2 31.8 + - - +
89B LYS* 2.9 51.1 + - + +
141B PHE* 3.6 46.0 - + + -
171B GLU 5.4 5.2 - - - -
173B LEU* 4.1 25.6 - - + -
220B PRO* 4.2 12.1 - - + -
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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