Contacts of the helix formed by residues 64 - 75 (chain A) in PDB entry 3Q7I
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 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A SER* 1.3 73.6 - - - +
65A LEU* 1.3 58.1 + - - +
66A LYS 3.4 2.0 - - - -
67A ASP* 3.1 17.3 + - - +
68A LYS* 2.8 44.3 + - - +
489A VAL* 3.6 18.4 + - - +
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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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60A ALA* 4.1 9.2 - - + +
63A SER* 3.0 18.5 + - - +
64A SER* 1.3 77.7 + - - +
66A LYS* 1.3 65.6 + - - +
68A LYS* 3.0 1.0 + - - -
69A ILE* 2.9 43.1 + - + +
300A PHE* 3.8 28.7 - - + -
306A VAL* 4.1 16.2 - - + -
485A PHE* 4.9 2.7 - - + -
486A VAL* 3.8 38.6 - - + -
489A VAL* 3.8 32.7 - - + +
490A LEU* 4.9 2.9 - - + -
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Residues in contact with LYS 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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60A ALA 5.3 0.2 + - - -
61A GLU* 6.0 4.5 - - - +
63A SER 4.7 3.6 + - - +
64A SER 3.4 0.4 - - - -
65A LEU* 1.3 78.5 - - - +
67A ASP* 1.3 80.3 + - - +
69A ILE* 3.5 7.1 + - - +
70A LYS* 3.4 43.2 + - - +
300A PHE* 3.8 22.1 - - + -
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Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 3.1 18.6 + - - +
66A LYS* 1.3 95.8 - - - +
68A LYS* 1.3 60.4 + - + +
70A LYS* 3.2 12.0 + - - +
71A GLN* 2.9 45.8 + - - +
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Residues in contact with LYS 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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64A SER* 2.8 39.2 + - - +
65A LEU 3.7 3.8 - - - +
67A ASP* 1.3 76.0 - - + +
69A ILE* 1.3 60.3 + - - +
71A GLN* 2.8 33.9 + - - +
72A MET* 2.9 24.6 + - - +
78A ILE* 4.7 15.6 - - + +
354A ILE* 6.6 0.2 - - - -
485A PHE* 3.5 13.5 - - + -
489A VAL* 3.9 30.3 - - + -
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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* 2.9 32.3 + - + +
66A LYS* 3.8 5.8 - - - +
67A ASP 3.3 0.2 - - - -
68A LYS* 1.3 75.8 - - - +
70A LYS* 1.3 65.8 + - + +
72A MET* 3.3 2.1 + - - +
73A PHE* 3.1 42.7 + - + -
295A PHE* 3.7 43.3 - - + +
296A LYS* 4.1 26.5 - - + +
300A PHE* 4.0 26.7 - - + -
306A VAL* 5.2 0.2 - - + -
485A PHE* 4.0 7.6 - - + -
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Residues in contact with LYS 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 LYS* 3.4 37.7 + - - +
67A ASP* 3.2 13.8 + - - +
69A ILE* 1.3 80.3 - - + +
71A GLN* 1.3 57.7 + - + +
73A PHE* 3.3 5.6 + - - +
74A ASN* 2.9 46.1 + - - +
296A LYS* 6.2 6.1 - - + +
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Residues in contact with GLN 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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67A ASP* 2.9 34.2 + - - +
68A LYS* 2.8 41.0 + - - +
69A ILE 3.2 0.4 - - - -
70A LYS* 1.3 74.1 - - + +
72A MET* 1.3 66.0 + - - +
74A ASN* 3.4 3.7 + - - -
75A GLY 3.2 3.6 + - - -
76A ALA* 3.0 47.5 + - + +
78A ILE* 3.7 12.9 - - + +
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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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68A LYS 2.9 16.6 + - - +
69A ILE 3.3 4.7 + - - +
71A GLN* 1.3 77.9 - - - +
73A PHE* 1.3 72.2 + - + +
75A GLY* 3.2 7.8 + - - -
76A ALA 5.2 0.8 - - - +
78A ILE* 3.9 17.0 - - + +
86A VAL* 3.5 34.0 + - + +
87A LEU* 3.4 12.6 - - - +
88A HIS* 4.2 8.5 - - + +
89A THR* 4.3 23.6 - - - +
482A HIS* 4.6 10.5 - - - +
485A PHE* 3.8 33.2 - - + -
496A TYR* 3.5 25.1 - - + +
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Residues in contact with PHE 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* 3.1 37.7 + - + +
70A LYS* 4.0 3.4 - - - +
72A MET* 1.3 89.0 - - + +
74A ASN* 1.3 63.4 + - - +
75A GLY 3.2 1.4 + - - -
87A LEU* 3.9 7.2 - - - +
89A THR* 3.7 41.5 + - + -
99A LEU* 3.8 15.6 - - - +
107A ARG* 5.5 2.1 + - - -
289A TYR* 6.5 0.2 - + - -
292A ASP* 3.7 33.4 - - + -
295A PHE* 4.1 15.5 - + - -
296A LYS* 3.9 45.5 - - + -
482A HIS* 4.6 0.2 - - - -
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Residues in contact with ASN 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 LYS* 2.9 32.7 + - - +
71A GLN* 4.1 5.3 - - - +
72A MET 3.2 0.2 - - - -
73A PHE* 1.3 79.5 - - - +
75A GLY* 1.3 60.9 + - - +
76A ALA* 3.4 2.8 + - + +
99A LEU* 3.6 11.3 - - - +
101A VAL* 4.2 1.4 - - - +
296A LYS* 5.8 2.3 - - - -
602A MES 3.3 67.3 + - - +
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Residues in contact with GLY 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 GLN 3.2 3.0 + - - -
72A MET 3.2 6.2 + - - -
73A PHE 3.2 1.8 + - - -
74A ASN* 1.3 78.8 - - - +
76A ALA* 1.3 67.9 + - - +
77A LYS* 3.7 5.2 + - - +
85A ALA* 3.5 13.3 - - - +
87A LEU* 3.9 22.2 - - - -
101A VAL* 3.9 23.0 - - - +
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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