Contacts of the helix formed by residues 65 - 79 (chain A) in PDB entry 1R47
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 SER 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A PRO 5.3 1.6 + - - -
63A CYS* 3.2 22.0 + - - -
64A ILE* 1.3 77.1 - - - +
66A GLU* 1.3 56.8 + - - +
67A LYS* 2.9 38.3 + - - +
68A LEU* 2.5 36.1 + - - +
69A PHE* 3.2 7.1 + - - -
112A ARG* 3.4 19.5 - - - -
113A PHE* 3.4 7.9 - - - -
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A SER* 1.3 71.8 - - - +
67A LYS* 1.3 66.5 + - + +
69A PHE* 4.2 2.6 - - - +
70A MET* 2.8 51.5 + - + +
112A ARG 3.0 11.6 + - - +
113A PHE* 3.0 27.2 - - + -
114A PRO* 2.8 34.6 - - + +
115A HIS* 3.0 39.1 + - - +
116A GLY 4.1 2.6 + - - -
120A LEU* 4.2 22.5 - - + +
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Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A CYS* 6.2 1.8 - - - -
60A PRO* 5.4 11.2 + - - +
63A CYS* 5.6 3.4 - - - -
65A SER* 2.9 25.7 + - - +
66A GLU* 1.3 87.5 - - + +
68A LEU* 1.3 63.7 + - - +
70A MET* 3.6 12.9 - - + +
71A GLU* 3.1 22.1 + - - +
111A GLN 5.6 4.9 - - - +
112A ARG* 5.2 1.3 - - - +
114A PRO* 5.9 2.7 - - + -
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TRP* 5.1 4.5 - - + -
46A HIS* 5.6 2.9 - - + -
50A PHE* 4.4 24.9 - - + -
60A PRO 6.0 0.4 - - - +
61A ASP 4.3 5.2 - - - +
62A SER 4.1 10.1 - - - +
63A CYS 3.1 32.3 - - - +
64A ILE* 4.0 9.9 - - + -
65A SER* 2.5 20.9 + - - +
67A LYS* 1.3 70.5 - - - +
69A PHE* 1.3 75.4 + - + +
71A GLU* 2.9 25.4 + - - +
72A MET* 3.1 25.6 + - + -
301A ARG* 4.0 21.1 - - - +
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Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TRP* 3.9 21.1 - + - -
46A HIS* 3.8 17.3 - + + -
64A ILE* 4.1 19.3 - - + -
65A SER 3.2 16.0 + - - -
66A GLU 4.2 3.6 - - - +
68A LEU* 1.3 86.0 - - + +
70A MET* 1.3 52.1 + - - +
72A MET* 2.7 14.5 + - - +
73A ALA* 2.6 35.6 + - - +
89A LEU* 4.1 19.7 - - + +
90A CYS* 3.5 21.8 - - - -
91A ILE* 3.4 46.7 - - + -
113A PHE* 4.3 9.4 - + - -
120A LEU* 4.8 12.3 - - + -
131A LEU* 5.8 1.3 - - + -
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Residues in contact with MET 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A GLU* 2.8 57.8 + - + +
67A LYS* 3.6 13.0 - - + +
69A PHE* 1.3 72.8 - - - +
71A GLU* 1.3 64.7 + - - +
73A ALA* 3.7 8.3 - - - +
74A GLU* 3.3 15.8 + - - +
115A HIS* 5.5 2.7 - - + -
120A LEU* 4.9 9.8 - - + +
123A TYR* 3.8 36.0 + - + -
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASP* 5.2 3.3 - - - +
67A LYS 3.1 9.9 + - - +
68A LEU* 2.9 12.6 + - - +
70A MET* 1.3 76.4 - - - +
72A MET* 1.3 67.2 + - - +
74A GLU* 2.9 14.8 + - - +
75A LEU* 2.8 26.6 - - + +
301A ARG* 2.9 47.3 + - + +
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Residues in contact with MET 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TRP* 4.0 23.1 - - + -
50A PHE* 4.6 1.6 - - + -
68A LEU* 3.1 20.7 + - + +
69A PHE* 2.7 15.4 + - - +
71A GLU* 1.3 74.9 - - - +
73A ALA* 1.3 63.2 + - - +
75A LEU* 2.9 19.0 + - - +
76A MET* 3.0 16.8 + - - +
89A LEU* 4.5 13.2 - - + -
298A ASN 4.6 0.4 - - - +
299A ASP* 3.1 35.0 - - - +
300A LEU* 3.6 39.7 - - + +
301A ARG* 3.6 25.6 - - + +
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PHE 2.6 15.0 + - - +
70A MET* 3.7 9.0 - - - +
72A MET* 1.3 72.9 - - - +
74A GLU* 1.3 66.5 + - - +
76A MET* 3.5 6.0 + - - -
77A VAL* 3.3 18.2 - - - +
89A LEU* 3.4 25.8 - - + +
123A TYR* 4.2 16.8 - - + -
124A VAL* 5.2 8.1 - - + -
127A LYS* 4.9 4.5 - - + -
129A LEU* 3.6 16.3 - - + +
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A MET 3.3 7.2 + - - +
71A GLU* 2.9 14.3 + - - +
73A ALA* 1.3 81.6 - - - +
75A LEU* 1.3 68.1 + - + +
77A VAL* 3.1 9.2 - - - +
78A SER* 3.0 38.8 + - - -
123A TYR* 3.7 14.5 + - - +
127A LYS* 2.7 37.0 + - - +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLU* 2.8 30.7 - - + +
72A MET* 2.9 11.6 + - - +
74A GLU* 1.3 77.1 - - + +
76A MET* 1.3 60.3 + - - +
77A VAL 2.8 2.2 - - - -
78A SER* 2.5 38.7 + - - +
79A GLU* 3.1 11.8 + - + +
81A TRP* 3.9 3.7 - - + +
300A LEU* 3.6 18.6 - - + +
301A ARG* 3.3 48.9 - - + +
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Residues in contact with MET 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TRP* 4.4 11.0 - - + -
72A MET 3.0 7.9 + - - +
73A ALA 3.5 6.7 + - - +
75A LEU* 1.3 77.4 - - - +
77A VAL* 1.3 56.6 + - - +
81A TRP* 2.6 45.5 + - + -
82A LYS* 2.9 10.0 + - - +
86A TYR* 3.9 37.0 - - + +
87A GLU* 4.8 2.2 - - - -
88A TYR 4.2 20.2 - - - +
89A LEU* 3.9 35.7 - - - -
129A LEU* 4.3 18.2 - - + -
296A MET* 5.1 1.8 - - + -
300A LEU* 3.6 20.4 - - + -
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Residues in contact with VAL 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ALA 3.3 16.8 - - - +
74A GLU* 3.1 7.2 - - - +
75A LEU 2.6 4.4 + - - -
76A MET* 1.3 72.1 - - - +
78A SER* 1.3 67.8 + - - +
80A GLY* 3.4 9.7 + - - -
82A LYS* 4.5 16.9 - - + +
83A ASP* 5.2 2.8 - - - +
127A LYS* 3.7 45.3 - - + +
129A LEU* 4.0 10.3 - - + -
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Residues in contact with SER 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLU* 3.0 31.0 + - - -
75A LEU* 2.5 22.7 + - - +
77A VAL* 1.3 70.1 - - - +
79A GLU* 1.3 62.9 + - - -
80A GLY* 2.6 16.5 + - - -
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 3.1 9.6 + - + +
78A SER* 1.3 79.1 - - - +
80A GLY* 1.3 61.6 + - - +
81A TRP* 3.4 21.5 - - - +
300A LEU 5.5 5.6 - - - +
303A ILE* 6.4 1.8 - - + -
308A LYS* 3.4 33.0 + - + +
312A GLN* 3.3 17.0 + - - +
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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