Contacts of the helix formed by residues 67 - 87 (chain B) in PDB entry 1Y67
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 LYS 67 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LYS 4.8 1.9 + - - -
42B ALA* 2.8 37.8 + - + +
44B GLU 3.4 18.8 + - - -
45B GLY 5.4 0.6 - - - -
46B THR* 3.7 9.2 - - + +
63B VAL* 4.4 1.8 - - - -
64B PRO* 2.8 32.0 + - + +
66B ASP* 1.3 93.7 - - - +
68B LYS* 1.3 65.9 + - - +
69B GLY 3.4 2.9 - - - -
70B ALA* 3.3 8.8 + - + +
71B LEU* 3.0 40.2 + - + +
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Residues in contact with LYS 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.5 31.0 - - + +
61B ASP* 4.4 10.0 - - - +
63B VAL* 3.8 14.4 - - + +
64B PRO 3.2 5.4 + - - +
65B ALA* 3.5 18.0 + - - +
67B LYS* 1.3 76.8 - - - +
69B GLY* 1.3 58.8 + - - +
71B LEU* 3.8 0.9 - - - +
72B ARG* 2.8 37.3 + - + +
161B ILE* 3.9 30.8 - - + +
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Residues in contact with GLY 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ALA 4.7 1.6 + - - -
66B ASP 5.1 1.6 + - - -
67B LYS 3.4 0.8 - - - -
68B LYS* 1.3 78.4 - - - +
70B ALA* 1.3 62.7 + - - +
72B ARG* 3.4 8.0 + - - +
73B ASN* 3.1 33.9 + - - -
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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
----------------------------------------------------------
38B ASN 5.3 0.7 - - - +
42B ALA* 4.0 20.0 - - + -
66B ASP 5.3 3.2 + - - +
67B LYS* 3.3 13.2 + - + +
69B GLY* 1.3 74.4 - - - +
71B LEU* 1.3 58.4 + - - +
73B ASN* 4.9 1.8 - - - +
74B ASN* 2.8 46.5 + - - +
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 3.9 9.2 - - - +
42B ALA* 3.7 25.8 - - + +
43B LEU* 3.7 35.9 - - + -
46B THR* 5.6 3.4 - - + -
48B PHE* 5.7 0.2 - - + -
56B LEU* 4.2 11.7 - - + -
57B ILE* 4.9 0.3 - - - +
60B LEU* 3.9 15.8 - - + +
63B VAL* 3.9 31.4 - - + -
67B LYS* 3.0 30.7 + - + +
68B LYS* 4.0 1.1 - - - +
70B ALA* 1.3 74.6 - - - +
72B ARG* 1.3 60.9 + - - +
75B ALA* 2.8 38.7 + - + +
76B GLY 3.4 0.3 + - - -
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.8 18.4 - - + +
68B LYS* 2.8 26.9 + - + +
69B GLY* 3.6 8.3 - - - +
71B LEU* 1.3 72.9 - - - +
73B ASN* 1.3 70.0 + - - +
76B GLY* 3.2 19.9 + - - -
152B GLN 4.0 3.5 - - - +
153B ASP* 2.8 40.8 + - - +
157B MET* 3.3 19.1 - - - +
161B ILE* 3.3 36.0 + - + +
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Residues in contact with ASN 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 3.5 55.5 - - + +
35B TYR* 4.1 1.0 - - - -
69B GLY* 3.1 20.4 + - - +
70B ALA* 4.0 3.5 - - - +
72B ARG* 1.3 88.8 + - - +
74B ASN* 1.3 65.4 + - - +
77B GLY* 2.9 19.8 + - - -
151B ASN* 5.3 2.4 + - - +
152B GLN* 3.2 16.2 + - - +
153B ASP* 4.8 3.1 - - - +
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Residues in contact with ASN 74 (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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130A PHE* 4.7 4.9 - - - -
35B TYR* 3.4 42.2 - - - +
38B ASN* 3.3 35.1 + - - +
39B ALA* 3.5 14.6 - - - +
70B ALA* 2.8 36.9 + - - +
73B ASN* 1.3 81.7 - - - +
75B ALA* 1.3 58.8 + - - +
76B GLY 3.2 0.9 - - - -
77B GLY 3.3 0.6 + - - +
78B HIS* 2.9 28.4 + - - +
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Residues in contact with ALA 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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3B TYR* 4.7 0.2 - - + -
39B ALA* 3.9 9.8 - - + +
53B VAL* 3.4 17.4 - - + +
56B LEU* 3.9 25.8 - - + -
57B ILE* 3.7 16.6 - - + -
60B LEU* 5.5 0.2 - - + -
71B LEU* 2.8 28.5 + - + +
74B ASN* 1.3 71.6 - - - +
76B GLY* 1.3 57.6 + - - +
78B HIS* 3.3 1.2 + - - -
79B ALA* 2.9 27.5 + - - +
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Residues in contact with GLY 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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57B ILE* 3.8 5.2 - - - +
71B LEU 3.4 0.4 + - - -
72B ARG 3.2 21.4 + - - -
74B ASN 3.2 0.4 - - - -
75B ALA* 1.3 78.8 - - - +
77B GLY* 1.3 52.0 + - - +
79B ALA* 3.7 2.3 - - - +
80B ASN* 2.8 41.2 + - - +
152B GLN 3.4 16.6 - - - -
157B MET* 3.7 11.4 - - - -
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Residues in contact with GLY 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B TYR* 3.7 17.7 - - - -
73B ASN 2.9 20.5 + - - -
74B ASN 3.3 2.9 + - - -
76B GLY* 1.3 73.0 - - - +
78B HIS* 1.3 61.5 + - - +
80B ASN* 3.9 0.2 - - - +
81B HIS* 2.7 32.9 + - - +
152B GLN* 3.4 21.9 - - - +
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Residues in contact with HIS 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TYR* 3.6 40.2 - + + +
4B THR 3.6 21.2 + - - -
6B PRO* 4.2 4.5 - - + -
32B HIS* 3.0 30.0 + - - -
35B TYR* 3.9 3.7 - - + +
36B VAL* 3.5 19.0 - - + +
53B VAL* 3.7 24.2 - - + +
74B ASN 2.9 17.0 + - - +
75B ALA* 3.7 4.5 - - - +
76B GLY 3.2 0.4 - - - -
77B GLY* 1.3 74.1 - - - +
79B ALA* 1.3 62.9 + - - +
82B SER* 2.7 47.5 + - - -
102C GLY* 6.5 0.2 - - - -
106C ASP* 4.5 4.6 + - - -
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Residues in contact with ALA 79 (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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53B VAL* 3.9 24.1 - - + +
54B GLU* 5.0 3.6 - - + +
57B ILE* 3.9 26.7 - - + -
75B ALA 2.9 17.6 + - - +
76B GLY 3.7 3.1 - - - +
78B HIS* 1.3 76.3 - - - +
80B ASN* 1.3 67.1 + - - +
82B SER* 3.5 2.8 + - - -
83B MET* 3.2 23.4 + - - +
154B ASN* 4.6 4.2 + - - +
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Residues in contact with ASN 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 GLY 2.8 21.8 + - - +
77B GLY 3.9 0.4 - - - +
79B ALA* 1.3 73.3 - - - +
81B HIS* 1.3 57.9 + - - +
83B MET* 3.4 4.4 + - - +
84B PHE* 3.0 26.7 + - - +
134B TRP* 3.5 31.8 - - + +
136B TRP* 3.4 16.0 - - + -
152B GLN* 2.9 48.3 + - - +
153B ASP 3.6 5.5 + - - -
154B ASN* 2.7 36.5 + - - +
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Residues in contact with HIS 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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27B HIS* 3.0 25.7 + + - -
31B HIS* 5.1 0.6 - - - +
32B HIS* 3.6 27.8 - + + +
35B TYR* 3.4 27.5 - + - -
77B GLY 2.7 27.6 + - - +
80B ASN* 1.3 72.1 - - - +
82B SER* 1.3 67.4 + - - +
84B PHE* 3.1 7.0 + + - +
85B TRP* 3.1 43.1 + + - +
134B TRP* 3.8 12.9 - + - -
152B GLN* 3.6 14.4 - - - -
173B ASP* 3.4 2.1 + - - -
229B FE 2.2 28.6 - - - -
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Residues in contact with SER 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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6B PRO* 4.0 8.7 - - - +
32B HIS* 3.6 9.8 - - - -
53B VAL* 5.3 4.2 - - - +
78B HIS* 2.7 46.7 + - - -
79B ALA* 3.7 6.3 - - - -
81B HIS* 1.3 78.3 - - - +
83B MET* 1.3 61.2 + - - +
85B TRP* 3.8 6.9 + - - +
86B GLN* 3.6 28.0 + - - +
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Residues in contact with MET 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 ALA 3.2 14.0 + - - +
80B ASN* 3.6 7.6 - - - +
82B SER* 1.3 73.5 - - - +
84B PHE* 1.3 67.1 + - - +
86B GLN* 3.0 5.4 + - - +
87B ILE* 3.0 27.5 + - + +
136B TRP* 4.0 19.1 - - + -
154B ASN* 5.4 3.1 - - - +
168B PRO* 4.1 13.7 - - + +
169B ILE* 3.4 13.9 - - - +
170B LEU* 3.2 48.5 - - - +
171B GLY* 3.5 4.9 - - - +
206B ARG* 3.7 34.5 - - - +
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Residues in contact with PHE 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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19B ILE* 5.0 5.2 - - + -
24B MET* 5.9 0.7 - - - -
27B HIS* 3.8 26.7 - + - -
80B ASN 3.0 17.7 + - - +
81B HIS* 3.1 8.2 + + - +
83B MET* 1.3 76.6 - - - +
85B TRP* 1.3 84.6 + + - +
86B GLN 3.3 0.5 + - - -
87B ILE* 3.3 23.4 + - + +
88B MET* 3.5 32.0 + - + +
134B TRP* 3.7 22.2 - + + -
171B GLY 3.6 16.8 - - - -
173B ASP* 3.8 16.4 - - + -
178B ALA* 5.5 0.2 - - + -
190B TYR* 3.8 20.0 - - - -
194B PHE* 3.8 24.5 - + - -
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Residues in contact with TRP 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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6B PRO* 4.4 8.7 - - + -
7B GLN 5.6 1.6 - - - +
8B LEU* 3.5 26.9 - - + -
9B PRO* 3.7 9.3 - - + +
10B TYR* 2.8 26.2 + - - +
24B MET* 3.6 32.3 - - + -
27B HIS* 3.5 38.1 - + + -
28B HIS* 3.7 28.4 - + + -
32B HIS* 3.0 28.5 + + - -
81B HIS* 3.1 35.8 + + - -
82B SER* 4.3 7.2 - - - +
83B MET 3.3 0.2 - - - -
84B PHE* 1.3 94.5 - + - +
86B GLN* 1.3 58.5 + - + +
88B MET* 3.2 20.5 - - + +
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Residues in contact with GLN 86 (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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9B PRO* 4.4 15.8 - - + +
82B SER* 3.6 16.7 + - - +
83B MET* 3.0 8.0 + - - +
85B TRP* 1.3 78.6 - - + +
87B ILE* 1.3 58.2 + - - +
88B MET 3.3 8.2 + - - +
199B ASN* 4.2 5.2 + - - +
202B GLU* 3.3 28.5 - - - +
206B ARG* 2.8 35.0 + - - +
103C GLU* 5.8 8.1 - - - +
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Residues in contact with ILE 87 (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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83B MET* 3.0 27.0 + - + +
84B PHE* 3.3 17.5 + - + +
86B GLN* 1.3 75.4 - - - +
88B MET* 1.3 63.3 + - + +
169B ILE 3.7 22.0 - - - +
170B LEU* 3.6 20.9 - - + -
171B GLY 3.5 28.0 - - - +
194B PHE* 4.0 5.2 - - + -
198B VAL* 3.5 7.8 - - - +
199B ASN* 2.7 28.4 + - - -
202B GLU* 3.8 10.8 - - + -
203B VAL* 4.1 6.5 - - + -
206B ARG* 3.8 22.9 - - - +
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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