Contacts of the helix formed by residues 67 - 80 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51R TYR 4.5 2.4 + - - -
53R SER* 3.7 20.7 + - - +
65R TYR* 3.8 20.9 + - + -
66R ILE* 1.3 76.5 - - - +
68R GLY* 1.3 56.8 + - - +
69R HIS* 3.2 28.5 - - + +
70R ARG* 2.7 55.4 + - - +
71R VAL* 3.2 8.8 + - - +
152R LYS* 5.0 0.2 - - - +
167S LEU* 5.2 3.3 - - + +
169S LYS* 4.2 28.1 + - - +
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Residues in contact with GLY 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66R ILE 3.5 3.2 + - - -
67R GLU* 1.3 71.4 - - - +
69R HIS* 1.3 63.6 + - - +
71R VAL* 3.1 5.6 + - - +
72R ILE* 2.9 31.9 + - - +
148R THR* 4.0 26.7 - - - +
152R LYS* 4.2 12.4 - - - +
167S LEU* 5.7 1.2 - - - +
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Residues in contact with HIS 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67R GLU* 3.0 38.0 + - + +
68R GLY* 1.3 75.1 - - - +
70R ARG* 1.3 81.0 + - + +
72R ILE* 4.5 0.2 - - - -
73R ASN* 3.3 20.7 + - - -
46S ARG* 5.7 1.6 - - - -
160S ASN* 6.0 0.4 - - - -
164S ASN* 3.0 51.9 - - - +
165S CYS* 5.7 0.4 - - - -
167S LEU* 3.2 34.7 - - + +
168S ASP* 3.4 47.0 + - + -
169S LYS 5.0 0.4 - - - -
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Residues in contact with ARG 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195Q ASP* 4.5 2.7 - - - +
50R GLU 3.8 18.0 + - - -
51R TYR* 3.8 41.6 + - + +
53R SER* 4.9 4.4 + - - -
66R ILE* 3.9 13.2 - - + -
67R GLU* 2.7 49.2 + - + +
69R HIS* 1.3 92.1 + - + +
71R VAL* 1.3 54.6 + - - +
73R ASN* 3.2 6.6 + - - +
74R LEU* 2.8 38.2 + - - +
168S ASP* 4.1 6.1 + - - -
170S ASP* 3.7 21.0 + - - -
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Residues in contact with VAL 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66R ILE* 3.7 29.6 - - + -
67R GLU 3.8 5.4 - - - +
68R GLY 3.1 6.8 + - - +
70R ARG* 1.3 74.6 - - - +
72R ILE* 1.3 67.0 + - + +
74R LEU* 3.2 10.6 + - + +
75R ALA* 2.9 23.0 + - - +
151R LEU* 5.6 1.3 - - + -
152R LYS* 3.9 33.7 - - + -
155R LEU* 3.9 33.2 - - + -
156R ARG* 6.2 0.9 - - - +
162R LEU* 4.3 13.4 - - + +
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Residues in contact with ILE 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68R GLY* 2.9 21.2 + - - +
69R HIS 3.8 4.5 - - - +
71R VAL* 1.3 77.8 - - + +
73R ASN* 1.3 57.4 + - - +
75R ALA* 3.2 8.1 + - - +
76R ASN* 2.9 32.3 + - - +
84R TRP* 4.2 9.1 - - + -
148R THR* 6.5 0.7 - - + -
151R LEU* 4.5 21.1 - - + -
155R LEU* 5.9 0.7 - - + -
156S ARG* 4.2 3.6 - - + +
157S SER* 3.4 44.0 - - - +
164S ASN* 3.5 33.0 - - - +
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Residues in contact with ASN 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195Q ASP* 3.3 25.9 + - + +
69R HIS* 3.3 13.2 + - - +
70R ARG* 3.2 8.9 + - - +
71R VAL 3.2 0.4 - - - -
72R ILE* 1.3 76.7 - - - +
74R LEU* 1.3 67.6 + - - +
76R ASN* 4.2 12.7 + - - +
77R GLU* 3.1 30.0 + - + +
46S ARG* 5.5 3.0 - - - +
159S GLY* 4.4 1.0 - - - -
160S ASN* 3.1 40.9 + - - +
164S ASN* 3.3 18.1 + - - +
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Residues in contact with LEU 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192Q LYS* 3.9 24.8 + - + +
195Q ASP* 4.1 5.8 - - - +
47R LEU* 3.5 19.7 - - + -
51R TYR* 3.6 36.3 - - + +
66R ILE* 5.1 2.5 - - + -
70R ARG 2.8 21.2 + - - +
71R VAL* 3.5 15.9 - - + +
73R ASN* 1.3 78.1 - - - +
75R ALA* 1.3 58.3 + - - +
77R GLU* 3.8 2.9 - - - +
78R MET* 2.8 33.6 + - + +
161R ALA 3.5 24.2 - - - +
162R LEU* 4.1 17.9 - - + +
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Residues in contact with ALA 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71R VAL 2.9 12.8 + - - +
72R ILE* 3.4 9.0 - - - +
74R LEU* 1.3 75.3 - - - +
76R ASN* 1.3 66.0 + - - +
78R MET* 3.1 0.6 + - - -
79R PHE* 2.9 34.7 + - + -
84R TRP* 3.5 36.9 - - + +
155R LEU* 4.7 6.7 - - + -
162R LEU* 4.0 15.7 - - + +
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Residues in contact with ASN 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72R ILE* 2.9 28.1 + - - +
73R ASN* 3.4 9.4 + - - +
75R ALA* 1.3 76.4 - - - +
77R GLU* 1.3 60.2 + - + +
80R GLY* 2.6 34.5 + - - -
81R TYR* 3.6 18.2 - - - +
84R TRP* 2.8 24.2 + - - +
40S GLN* 3.0 14.1 - - - +
121S HIS* 4.9 0.3 - - - -
157S SER 2.9 26.7 + - - +
158S PHE* 3.4 20.9 + - - +
159S GLY* 3.7 5.1 - - - +
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Residues in contact with GLU 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195Q ASP* 3.2 41.5 - - + +
196Q LEU* 3.1 15.3 - - - +
197Q GLU* 4.6 7.7 + - - +
200Q VAL* 4.5 2.4 - - - +
201Q GLU* 4.8 3.1 - - - +
204Q ARG* 3.0 21.8 + - - -
73R ASN* 3.1 20.3 + - + +
74R LEU 3.9 0.9 - - - +
76R ASN* 1.3 79.5 - - + +
78R MET* 1.3 59.0 + - - +
40S GLN* 4.1 7.9 + - - +
44S ARG* 2.5 55.7 + - - +
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Residues in contact with MET 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192Q LYS* 4.1 9.4 - - - -
195Q ASP 5.0 0.4 + - - -
197Q GLU* 3.9 18.4 - - + -
200Q VAL* 3.4 15.4 - - - +
204Q ARG* 3.2 15.0 + - - -
39R ILE* 3.8 12.2 - - + +
42R ALA* 3.7 33.0 - - + -
43R LEU* 3.8 26.5 - - + -
74R LEU* 2.8 21.2 + - + +
75R ALA 3.1 2.9 + - - +
77R GLU* 1.3 77.9 - - - +
79R PHE* 1.3 75.5 + - + +
161R ALA* 3.8 27.6 - - + +
162R LEU* 4.1 9.0 - - + -
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Residues in contact with PHE 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81Q TYR* 4.4 4.3 - + - -
204Q ARG* 3.7 18.0 + - - +
31R TYR* 3.9 16.3 + - - +
35R GLU* 4.6 2.3 - - - +
39R ILE* 4.1 22.0 - - + -
43R LEU* 4.5 3.8 - - + -
75R ALA* 2.9 22.0 + - + +
78R MET* 1.3 100.1 - - + +
80R GLY* 1.3 61.6 + - - +
82R ASN* 4.4 1.0 + - - -
83R GLY* 3.2 33.0 + - - +
84R TRP* 3.9 16.8 - + + -
115R LEU* 4.1 24.9 - - + -
116R LYS* 4.9 3.1 + - - -
155R LEU* 4.9 2.9 - - + -
158R PHE* 4.0 34.5 - + + -
162R LEU* 4.6 11.0 - - + -
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Residues in contact with GLY 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204Q ARG* 3.9 3.1 - - - +
76R ASN 2.6 24.5 + - - -
78R MET 3.7 0.8 - - - -
79R PHE* 1.3 73.6 - - - +
81R TYR* 1.3 56.7 + - - -
82R ASN* 2.9 10.8 - - - -
83R GLY* 2.7 21.5 + - - -
84R TRP* 3.6 10.4 - - - -
36S TYR* 3.8 13.7 - - - -
40S 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