Contacts of the helix formed by residues 67 - 80 (chain D) in PDB entry 1H2I
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 GLU 67 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51D TYR 4.6 2.0 + - - -
53D SER* 3.6 22.9 + - - +
65D TYR* 3.7 20.0 + - + -
66D ILE* 1.3 75.9 - - - +
68D GLY* 1.3 57.7 + - - +
69D HIS* 3.5 27.5 - - + +
70D ARG* 2.8 54.1 + - - +
71D VAL* 3.2 8.7 + - - +
152D LYS* 4.9 0.4 - - - +
167E LEU* 5.3 2.7 - - + +
169E LYS* 4.2 28.1 + - - +
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Residues in contact with GLY 68 (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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66D ILE 3.6 2.4 + - - -
67D GLU* 1.3 71.4 - - - +
69D HIS* 1.3 56.2 + - - +
71D VAL* 3.0 5.5 + - - +
72D ILE* 2.8 37.3 + - - +
148D THR* 4.1 25.2 - - - +
152D LYS* 4.1 13.3 - - - +
167E LEU* 5.7 0.4 - - - -
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Residues in contact with HIS 69 (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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67D GLU* 3.1 37.5 + - + +
68D GLY* 1.3 76.3 - - - +
70D ARG* 1.3 82.1 + - + +
72D ILE* 3.4 0.6 + - - -
73D ASN* 3.1 21.1 + - - -
46E ARG* 5.7 1.3 - - - -
160E ASN* 6.1 0.2 - - - -
164E ASN* 3.1 50.5 - - - +
165E CYS* 5.8 0.4 - - - -
167E LEU* 3.1 35.7 - - + +
168E ASP* 3.5 45.5 + - + -
169E LYS 5.1 0.2 - - - -
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Residues in contact with ARG 70 (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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195C ASP* 4.7 3.5 - - - +
50D GLU 3.8 17.1 + - - -
51D TYR* 3.7 42.8 + - + +
53D SER* 4.7 4.2 + - - -
66D ILE* 3.9 12.8 - - + -
67D GLU* 2.8 42.6 + - + +
69D HIS* 1.3 98.7 + - + +
71D VAL* 1.3 58.3 + - - +
73D ASN* 3.2 6.3 + - - +
74D LEU* 2.8 34.6 + - - +
168E ASP* 4.2 5.9 + - - -
170E ASP* 3.8 20.2 + - - -
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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
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66D ILE* 3.6 30.5 - - + -
67D GLU 3.8 4.9 - - - +
68D GLY* 3.0 7.1 + - - +
70D ARG* 1.3 77.7 - - - +
72D ILE* 1.3 65.0 + - + +
74D LEU* 3.1 12.2 + - + +
75D ALA* 2.9 22.0 + - - +
151D LEU* 5.5 1.8 - - + -
152D LYS* 3.8 33.0 - - + -
155D LEU* 3.9 34.3 - - + -
156D ARG* 6.1 1.1 - - - +
162D LEU* 4.3 13.2 - - + +
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Residues in contact with ILE 72 (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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68D GLY* 2.8 21.4 + - - +
69D HIS* 3.7 5.2 - - - +
70D ARG 3.3 0.2 - - - -
71D VAL* 1.3 79.1 - - + +
73D ASN* 1.3 57.1 + - - +
75D ALA* 3.3 6.5 + - - +
76D ASN* 2.9 32.9 + - - +
84D TRP* 4.1 9.1 - - + -
148D THR* 6.5 0.2 - - + -
151D LEU* 4.5 22.0 - - + -
156E ARG* 4.1 3.6 - - + +
157E SER* 3.4 45.3 - - - +
164E ASN* 3.6 30.1 - - - +
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Residues in contact with ASN 73 (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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195C ASP* 3.1 24.0 + - + +
69D HIS* 3.1 20.8 + - - +
70D ARG* 3.8 3.3 - - - +
72D ILE* 1.3 72.6 - - - +
74D LEU* 1.3 67.2 + - - +
76D ASN* 3.8 14.1 + - - +
77D GLU* 2.9 31.7 + - + +
46E ARG* 5.5 3.4 - - - +
159E GLY* 4.3 1.2 - - - -
160E ASN* 3.1 41.3 + - - +
164E ASN* 3.3 18.5 + - - +
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Residues in contact with LEU 74 (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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192C LYS* 3.7 32.3 - - + +
195C ASP* 4.0 6.0 + - - +
47D LEU* 3.6 20.0 - - + -
51D TYR* 3.8 27.4 - - + +
66D ILE* 5.0 5.2 - - + -
70D ARG 2.8 18.9 + - - +
71D VAL* 3.4 17.3 - - + +
73D ASN* 1.3 76.1 - - - +
75D ALA* 1.3 57.8 + - - +
77D GLU* 3.3 3.3 + - - +
78D MET* 2.8 34.0 + - + +
161D ALA 3.5 24.2 - - - +
162D LEU* 4.1 17.0 - - + +
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Residues in contact with ALA 75 (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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71D VAL 2.9 13.2 + - - +
72D ILE 3.5 8.3 - - - +
74D LEU* 1.3 77.2 - - - +
76D ASN* 1.3 57.5 + - - +
78D MET* 3.1 0.8 + - - -
79D PHE* 2.8 43.3 + - + -
84D TRP* 3.5 35.8 - - + -
155D LEU* 4.7 7.0 - - + -
162D LEU* 3.9 16.3 - - + +
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Residues in contact with ASN 76 (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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72D ILE* 2.9 30.6 + - - +
73D ASN* 3.3 8.6 + - - +
75D ALA* 1.3 74.5 - - - +
77D GLU* 1.3 63.7 + - + +
80D GLY* 2.7 33.6 + - - -
81D TYR* 3.6 19.1 - - - +
84D TRP* 2.9 23.9 + - - +
40E GLN* 3.1 12.4 - - - +
121E HIS* 4.9 0.5 - - - -
157E SER 3.0 24.9 + - - +
158E PHE* 3.6 19.8 + - - +
159E GLY* 3.7 5.8 - - - +
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Residues in contact with GLU 77 (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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195C ASP* 3.6 41.1 - - + +
196C LEU* 3.6 12.3 - - - +
197C GLU* 4.5 8.2 + - - +
200C VAL* 4.3 3.1 - - - +
201C GLU* 4.6 3.3 - - - +
204C ARG* 2.8 20.8 + - - -
73D ASN* 2.9 24.0 + - + +
74D LEU 3.8 2.2 - - - +
76D ASN* 1.3 82.5 - - + +
78D MET* 1.3 59.0 + - - +
40E GLN* 3.9 9.7 + - - +
44E ARG* 2.5 56.1 + - - +
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Residues in contact with MET 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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192C LYS* 4.3 6.3 - - - -
197C GLU* 4.1 19.5 - - + +
200C VAL* 3.3 13.2 - - - +
204C ARG* 3.2 17.2 + - - -
39D ILE* 3.8 13.5 - - + +
42D ALA* 3.5 32.3 - - + +
43D LEU* 3.8 26.5 - - + -
74D LEU* 2.8 20.6 + - + +
75D ALA 3.8 2.5 - - - +
77D GLU* 1.3 77.2 - - - +
79D PHE* 1.3 79.1 + - + +
161D ALA* 3.8 30.5 - - + -
162D LEU* 4.2 7.0 - - + -
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Residues in contact with PHE 79 (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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81C TYR* 4.4 4.7 - + - -
204C ARG* 3.6 19.1 + - - +
31D TYR* 3.8 18.7 + - - +
35D GLU* 4.6 3.0 - - - +
39D ILE* 4.1 20.0 - - + -
43D LEU* 4.5 4.3 - - + -
75D ALA* 2.8 29.1 + - + +
78D MET* 1.3 96.8 - - + +
80D GLY* 1.3 61.2 - - - +
82D ASN* 4.5 1.0 + - - -
83D GLY* 3.2 32.4 - - - +
84D TRP* 3.9 17.5 - + + +
115D LEU* 4.1 25.6 - - + -
116D LYS* 5.0 3.5 - - - -
155D LEU* 5.1 2.5 - - + -
158D PHE* 4.0 33.4 - + + -
162D LEU* 4.6 7.6 - - + -
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Residues in contact with GLY 80 (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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204C ARG* 3.6 14.2 - - - +
76D ASN 2.7 23.9 + - - -
79D PHE* 1.3 73.7 - - - +
81D TYR* 1.3 64.5 + - - -
82D ASN* 2.9 11.4 - - - -
83D GLY 2.8 11.4 + - - -
84D TRP* 3.5 12.0 - - - -
36E TYR* 4.0 3.4 - - - -
40E GLN* 3.4 10.8 - - - -
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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
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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