Contacts of the helix formed by residues 61 - 74 (chain A) in PDB entry 1INR
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 GLY 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ASP 3.0 16.7 + - - -
56A PHE* 3.3 21.6 - - - -
58A GLY 3.0 14.5 + - - -
59A TYR 3.3 1.8 + - - -
60A LEU* 1.3 74.8 - - - +
62A CYS* 1.4 56.9 + - - +
64A ALA* 3.3 3.5 - - - +
65A LEU* 3.0 28.7 + - - +
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Residues in contact with CYS 62 (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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59A TYR 4.9 0.4 + - - -
60A LEU 3.4 1.0 - - - -
61A GLY* 1.4 70.0 - - - +
63A GLN* 1.3 70.5 + - - +
65A LEU* 4.0 2.5 - - - +
66A SER* 2.9 27.4 + - - -
111A PHE 5.3 1.6 - - - +
112A LEU* 3.7 21.4 - - + +
113A PRO* 3.7 22.9 - - + -
114A CYS* 1.9 62.1 - - + -
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Residues in contact with GLN 63 (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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59A TYR 3.7 6.9 + - - -
60A LEU* 3.4 45.3 + - + +
62A CYS* 1.3 77.6 - - - +
64A ALA* 1.4 55.7 + - - +
66A SER* 3.8 3.3 - - - -
67A GLU* 2.9 34.4 + - - +
114A CYS* 3.4 26.9 - - + +
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Residues in contact with ALA 64 (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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52A LEU* 5.4 4.5 - - + -
55A ASP* 4.2 18.4 - - + +
56A PHE* 3.9 19.7 - - + -
60A LEU* 3.2 11.5 + - + +
61A GLY 3.3 10.3 - - - +
62A CYS 3.2 0.2 - - - -
63A GLN* 1.4 76.7 - - - +
65A LEU* 1.3 65.5 + - - +
67A GLU* 3.8 6.1 - - - +
68A MET* 2.9 26.4 + - - +
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Residues in contact with LEU 65 (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 PHE* 3.7 35.0 - - + -
61A GLY 3.0 13.3 + - - +
62A CYS* 4.0 3.4 - - - +
64A ALA* 1.3 77.5 - - - +
66A SER* 1.3 53.8 + - - +
68A MET* 3.1 2.6 + - + +
69A ILE* 2.8 57.6 + - + +
105A LEU* 4.1 19.3 - - + -
111A PHE 5.6 0.4 - - - +
112A LEU* 3.5 26.9 - - + -
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Residues in contact with SER 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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62A CYS 2.9 19.7 + - - -
63A GLN* 3.8 3.4 - - - -
65A LEU* 1.3 77.8 - - - +
67A GLU* 1.3 62.1 + - - +
69A ILE* 3.3 6.5 + - - +
70A GLN* 3.2 22.7 + - - +
102A ARG* 4.2 4.0 + - - -
112A LEU* 5.1 3.4 - - - -
114A CYS* 4.0 14.1 + - - -
115A GLU* 3.0 32.8 + - - +
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Residues in contact with GLU 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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63A GLN* 2.9 20.3 + - - +
64A ALA* 4.0 4.8 - - - +
66A SER* 1.3 76.2 + - - +
68A MET* 1.4 57.5 + - + +
70A GLN* 3.3 19.6 + - - +
71A PHE* 2.8 34.1 + - + +
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Residues in contact with MET 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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48A LEU* 4.2 11.4 - - + -
52A LEU* 4.2 30.1 - - + -
56A PHE* 4.0 24.9 - - + -
64A ALA* 2.9 24.7 + - - +
65A LEU* 3.1 6.5 + - + +
67A GLU* 1.4 73.1 - - + +
69A ILE* 1.4 62.8 + - + +
71A PHE* 3.3 34.0 + - + +
72A TYR* 3.1 47.5 + - + -
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Residues in contact with ILE 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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65A LEU* 2.8 48.3 + - + +
66A SER* 3.8 6.5 - - - +
67A GLU 3.3 0.2 - - - -
68A MET* 1.4 75.2 - - - +
70A GLN* 1.3 63.2 + - - +
72A TYR* 3.5 3.2 + - - +
73A LEU* 3.0 37.6 + - + +
98A LEU* 3.7 38.1 - - + +
101A LEU* 5.6 2.5 - - + -
102A ARG* 3.7 43.1 - - + +
105A LEU* 4.8 7.4 - - + -
112A LEU* 5.1 2.0 - - + -
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Residues in contact with GLN 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 SER* 3.2 14.2 + - - +
67A GLU* 3.7 21.5 - - - +
69A ILE* 1.3 78.5 - - - +
71A PHE* 1.3 56.6 + - - +
73A LEU* 4.2 4.7 - - - +
74A GLU* 2.8 64.0 + - + +
75A GLU* 5.3 5.3 + - - -
102A ARG* 4.4 12.7 - - - +
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Residues in contact with PHE 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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47A LEU* 5.4 11.4 - - + -
48A LEU* 5.2 6.5 - - + -
67A GLU* 2.8 22.8 + - + +
68A MET* 3.3 35.0 + - + +
70A GLN* 1.3 74.1 - - - +
72A TYR* 1.3 66.8 + + - +
75A GLU* 2.9 70.9 + - + +
76A VAL* 2.9 30.8 + - + -
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Residues in contact with TYR 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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47A LEU* 5.8 1.2 - - - +
48A LEU* 3.5 30.4 - - + +
68A MET* 3.1 46.0 + - + +
69A ILE* 3.9 4.0 - - - +
71A PHE* 1.3 81.8 - + - +
73A LEU* 1.3 59.8 + - - +
74A GLU 3.3 0.3 + - - -
76A VAL* 3.6 33.0 - - + -
77A MET* 2.9 55.1 + - + +
98A LEU* 4.5 7.4 - - + -
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Residues in contact with LEU 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 ILE* 3.0 29.5 + - + +
70A GLN* 4.2 3.4 - - - +
72A TYR* 1.3 76.4 - - - +
74A GLU* 1.3 58.0 + - + +
77A MET* 4.7 6.3 - - - +
78A PRO* 3.4 18.4 - - - +
95A GLY* 3.5 37.2 - - - +
98A LEU* 3.7 17.3 - - + -
99A LYS* 3.8 29.8 - - + -
102A ARG* 3.5 29.2 - - - +
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Residues in contact with GLU 74 (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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70A GLN* 2.8 48.7 + - - +
73A LEU* 1.3 79.9 - - + +
75A GLU* 1.3 68.7 + - + +
78A PRO* 3.6 15.6 - - - +
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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