Contacts of the helix formed by residues 47 - 65 (chain R) in PDB entry 1HI0
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 ASP 47 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43R LEU* 3.6 20.5 - - + +
44R LEU* 2.9 25.9 + - + +
45R SER 3.4 0.4 - - - -
46R VAL* 1.3 78.3 - - - +
48R PRO* 1.3 76.2 - - - +
49R ARG* 2.6 57.2 + - - +
50R PHE* 3.0 7.5 + - + +
51R LEU* 2.9 19.9 + - - +
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Residues in contact with PRO 48 (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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46R VAL 3.1 6.0 - - - +
47R ASP* 1.3 90.5 - - - +
49R ARG* 1.3 64.3 + - + +
51R LEU* 3.3 7.3 + - + +
52R SER* 2.9 26.1 + - - -
259R ASP* 5.8 11.9 - - + +
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Residues in contact with ARG 49 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43R LEU* 5.8 1.6 - - - +
47R ASP* 2.6 42.7 + - - +
48R PRO* 1.3 76.4 - - + +
50R PHE* 1.3 56.9 + - - +
52R SER* 3.3 6.7 - - - -
53R PHE* 2.8 29.3 + - - +
578R ALA* 3.3 28.5 + - - +
579R PHE* 3.4 37.3 - - + +
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Residues in contact with PHE 50 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39R THR* 3.8 28.5 - - + -
40R TYR* 5.9 0.9 - + - -
43R LEU* 4.0 18.2 - - + -
44R LEU 4.1 2.0 - - - -
45R SER* 3.5 24.2 - - - -
47R ASP* 3.0 22.0 + - + +
49R ARG* 1.3 78.9 - - - +
51R LEU* 1.3 52.2 + - - +
53R PHE* 2.9 16.3 + + - +
54R LYS* 2.7 51.4 + - + +
526R PHE* 3.7 44.2 - + + -
575R TRP* 3.9 20.0 - + - -
579R PHE* 3.6 15.6 - + + -
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Residues in contact with LEU 51 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45R SER 3.2 24.0 - - - +
46R VAL* 3.4 18.4 - - + +
47R ASP 2.9 18.1 + - - +
48R PRO* 3.9 7.2 - - + +
50R PHE* 1.3 71.8 - - - +
52R SER* 1.3 53.8 + - - +
54R LYS* 3.0 12.9 + - + +
55R ASN* 2.7 37.6 + - - +
89R HIS 5.1 1.3 - - - +
90R MET* 3.2 32.1 - - + -
259R ASP 4.0 9.0 - - - +
261R PRO* 3.6 38.4 - - + -
264R PHE* 3.6 11.9 - - + -
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Residues in contact with SER 52 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R PRO 2.9 18.6 + - - -
49R ARG* 3.3 8.7 - - - -
51R LEU* 1.3 77.3 - - - +
53R PHE* 1.3 63.5 + - - +
55R ASN* 3.1 9.0 + - - +
56R GLU* 2.9 24.8 + - - +
578R ALA* 5.0 6.2 - - - +
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Residues in contact with PHE 53 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49R ARG 2.8 13.4 + - - +
50R PHE* 3.1 22.2 - + - +
52R SER* 1.3 76.2 - - - +
54R LYS* 1.3 72.2 + - + +
56R GLU* 3.2 4.4 + - - +
57R LEU* 2.9 55.5 + - + +
87R MET* 5.7 0.2 - - - -
526R PHE* 3.6 40.6 - + + -
571R ILE* 3.8 10.3 - - + -
574R CYS* 3.5 33.0 - - + -
575R TRP* 3.5 39.9 - + - -
578R ALA* 3.6 14.8 - - + +
579R PHE* 4.3 2.2 - - + -
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Residues in contact with LYS 54 (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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45R SER 4.9 3.0 + - - -
50R PHE* 2.7 34.0 + - + +
51R LEU* 3.3 13.4 - - + +
53R PHE* 1.3 84.7 - - + +
55R ASN* 1.3 58.2 + - - +
57R LEU* 4.7 0.2 - - - -
58R SER* 2.9 32.2 + - - -
87R MET* 3.1 50.5 + - + +
88R ARG* 5.7 0.2 - - - -
89R HIS 3.6 9.7 + - - -
91R ASN* 3.1 30.3 - - - +
264R PHE* 4.1 15.7 - - + -
526R PHE* 3.1 26.0 + - + -
527R SER* 3.4 7.3 + - - -
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Residues in contact with ASN 55 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51R LEU 2.7 15.7 + - - +
52R SER* 3.1 12.5 + - - +
54R LYS* 1.3 72.9 - - - +
56R GLU* 1.3 69.5 - - - +
58R SER* 3.0 13.5 + - - -
59R ARG* 3.1 34.3 + - - +
88R ARG* 2.3 34.9 + - - +
261R PRO* 5.9 3.9 - - + +
262R ASP 4.6 2.9 - - - +
264R PHE* 3.9 13.1 - - + -
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Residues in contact with GLU 56 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52R SER* 2.9 16.1 + - - +
53R PHE* 3.8 3.1 - - - +
55R ASN* 1.3 83.2 - - - +
57R LEU* 1.3 57.8 + - - +
59R ARG* 3.8 4.1 - - - +
60R TYR* 3.0 34.9 + - + +
573R ARG* 3.7 12.3 + - - +
574R CYS* 3.4 28.1 - - - +
577R ASN* 3.0 35.4 + - - +
578R ALA* 5.8 0.2 - - - +
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Residues in contact with LEU 57 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53R PHE* 2.9 49.5 + - + +
54R LYS 4.1 1.8 - - - +
56R GLU* 1.3 69.7 - - - +
58R SER* 1.3 68.0 + - - +
60R TYR* 3.9 1.3 - - + +
61R LEU* 3.0 48.3 + - + +
87R MET* 4.1 18.2 - - + -
522R LEU* 4.1 9.0 - - + -
526R PHE* 4.4 1.3 - - + -
570R ALA* 3.9 29.8 - - + -
571R ILE* 3.7 17.9 - - + +
574R CYS* 3.9 14.3 - - + -
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Residues in contact with SER 58 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54R LYS 2.9 22.8 + - - -
55R ASN 3.0 6.2 + - - -
57R LEU* 1.3 77.3 - - - +
59R ARG* 1.3 66.8 + - - +
61R LEU* 4.0 1.0 - - - +
62R THR* 2.7 33.7 + - - -
84R PHE* 3.4 26.4 - - - +
85R PHE* 4.0 10.8 - - - -
87R MET* 3.6 15.4 - - - -
88R ARG* 3.3 19.7 + - - -
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Residues in contact with ARG 59 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55R ASN* 3.1 44.9 + - - +
56R GLU* 3.8 4.3 - - - +
58R SER* 1.3 82.4 + - - +
60R TYR* 1.3 63.3 + - - +
62R THR* 3.3 2.3 + - - -
63R ASP* 2.9 25.1 + - - +
85R PHE* 3.9 16.1 - - + -
88R ARG* 3.2 6.3 - - - +
213R LEU* 4.4 13.1 - - + +
220R PHE* 3.4 30.7 - - + -
262R ASP* 5.2 6.3 + - - +
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Residues in contact with TYR 60 (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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56R GLU* 3.0 21.5 + - + +
57R LEU* 3.9 3.8 - - + +
59R ARG* 1.3 77.5 - - - +
61R LEU* 1.3 79.7 + - + +
63R ASP* 3.0 5.3 + - - +
64R HIS* 2.8 75.4 + + + -
65R PHE* 4.6 5.4 - + - -
570R ALA* 3.9 18.6 - - + -
573R ARG* 3.1 37.0 + - - +
574R CYS* 5.2 1.1 - - - -
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Residues in contact with LEU 61 (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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57R LEU* 3.0 42.1 + - + +
60R TYR* 1.3 77.3 - - + +
62R THR* 1.3 58.8 + - - +
65R PHE* 2.8 64.7 + - + +
84R PHE* 3.6 22.1 - - + -
522R LEU* 3.6 31.0 - - + -
567R VAL* 4.0 25.6 - - + -
570R ALA* 4.0 16.4 - - + -
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Residues in contact with THR 62 (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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58R SER 2.7 21.7 + - - -
59R ARG 3.6 4.0 - - - -
61R LEU* 1.3 76.8 - - - +
63R ASP* 1.3 62.4 + - - +
65R PHE 3.9 0.8 - - - -
66R PRO* 3.8 19.8 - - + +
83R ASN* 3.2 26.7 - - + +
84R PHE* 3.0 28.0 + - - -
85R PHE* 3.2 29.1 - - + -
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Residues in contact with ASP 63 (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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59R ARG 2.9 18.0 + - - +
60R TYR* 3.4 6.1 - - - +
62R THR* 1.3 81.3 - - - +
64R HIS* 1.3 78.2 + - + +
65R PHE 3.5 0.3 + - - -
66R PRO* 3.8 9.0 - - - +
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Residues in contact with HIS 64 (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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60R TYR* 2.8 63.2 + + + +
63R ASP* 1.3 88.8 - - + +
65R PHE* 1.3 91.5 + - + +
66R PRO* 3.5 5.6 - - - +
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Residues in contact with PHE 65 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60R TYR* 4.6 7.9 - + - -
61R LEU* 2.8 44.3 + - + +
62R THR* 3.9 1.8 - - - +
63R ASP 3.3 0.4 - - - -
64R HIS* 1.3 102.8 - - + +
66R PRO* 1.3 68.8 - - - +
78R ASN* 3.8 8.3 - - + +
80R VAL* 3.4 29.5 - - + +
82R THR 4.8 0.5 - - - +
83R ASN* 5.7 0.5 - - - -
84R PHE* 3.5 11.0 - - + -
563R ILE* 3.3 39.9 - - + -
566R ASP* 3.6 33.2 - - + -
567R VAL* 5.5 0.2 - - + -
570R ALA* 5.9 0.2 - - + -
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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