Contacts of the helix formed by residues 68 - 85 (chain b) in PDB entry 5JPQ
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 ASN 68 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64b LEU* 4.0 13.0 - - + -
65b PRO* 3.0 25.8 + - + +
66b PRO 3.5 1.2 - - - -
67b ASP* 1.3 77.8 - - - +
69b GLU* 1.3 66.9 + - - +
70b VAL* 3.1 4.9 + - + +
71b ARG* 3.9 15.0 - - + +
72b ARG* 2.9 25.6 + - - +
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Residues in contact with GLU 69 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67b ASP 3.4 4.8 + - - -
68b ASN* 1.3 71.7 - - - +
70b VAL* 1.3 64.0 + - - +
72b ARG* 4.1 4.7 - - - +
73b LYS* 3.4 20.4 + - - +
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Residues in contact with VAL 70 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68b ASN* 3.1 5.3 - - + +
69b GLU* 1.3 76.1 - - - +
71b ARG* 1.3 56.6 + - - +
73b LYS* 3.0 6.1 + - - +
74b HIS* 2.6 40.7 + - + +
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Residues in contact with ARG 71 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61b LEU* 4.3 15.0 - - + +
64b LEU* 4.2 14.8 - - + -
65b PRO 4.2 6.3 - - - +
66b PRO* 5.2 4.0 - - + +
68b ASN* 3.1 20.2 + - + +
70b VAL* 1.3 74.5 - - - +
72b ARG* 1.3 55.3 + - - +
73b LYS 2.8 8.8 + - - -
74b HIS* 4.9 1.6 - - - -
75b GLU* 2.7 46.1 + - + +
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Residues in contact with ARG 72 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66b PRO 5.2 6.8 + - - +
67b ASP* 5.2 5.2 - - - -
68b ASN 2.9 19.5 + - - +
69b GLU* 4.1 5.6 - - - +
71b ARG* 1.3 76.4 - - - +
73b LYS* 1.3 58.1 + - - +
75b GLU* 5.0 1.1 - - - -
76b THR* 3.6 18.9 + - - -
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Residues in contact with LYS 73 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69b GLU 3.4 15.8 + - - +
70b VAL* 3.0 4.9 + - - +
71b ARG 2.8 3.6 + - - -
72b ARG* 1.3 76.6 - - - +
74b HIS* 1.3 62.7 + - - +
75b GLU 3.4 0.2 - - - -
76b THR* 3.7 3.0 + - - -
77b LEU* 3.2 25.2 + - - +
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Residues in contact with HIS 74 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61b LEU* 6.0 3.8 - - + -
70b VAL* 2.6 22.6 + - + +
71b ARG* 4.9 1.3 - - - -
73b LYS* 1.3 71.8 - - - +
75b GLU* 1.3 58.5 + - - +
77b LEU* 3.7 5.1 - - - +
78b LEU* 2.8 31.7 + - - +
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Residues in contact with GLU 75 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61b LEU* 4.9 14.0 - - + +
71b ARG* 2.7 34.8 + - + +
72b ARG* 5.0 1.1 - - - -
74b HIS* 1.3 72.8 - - - +
76b THR* 1.3 61.1 + - - +
78b LEU* 3.1 8.3 + - - +
79b LEU* 3.1 22.3 + - - +
94b LEU* 5.3 13.0 - - + -
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Residues in contact with THR 76 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71b ARG 3.9 1.8 + - - -
72b ARG 3.6 19.0 + - - -
73b LYS 3.7 3.7 + - - -
74b HIS 3.4 0.2 - - - -
75b GLU* 1.3 76.3 - - - +
77b LEU* 1.3 52.7 + - - +
79b LEU* 3.0 11.0 + - - +
80b ASP* 2.8 34.8 + - - +
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Residues in contact with LEU 77 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73b LYS 3.2 16.7 + - - +
74b HIS* 3.8 6.5 - - - +
75b GLU 3.3 0.2 - - - -
76b THR* 1.3 78.4 - - - +
78b LEU* 1.3 62.6 + - - +
80b ASP* 3.5 9.7 + - - +
81b LYS* 3.2 21.5 + - - +
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Residues in contact with LEU 78 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57b PHE* 6.1 6.1 - - + -
74b HIS 2.8 14.5 + - - +
75b GLU* 3.1 12.3 + - - +
77b LEU* 1.3 76.5 - - - +
79b LEU* 1.3 56.4 + - - +
81b LYS* 3.2 9.5 + - - +
82b LEU* 3.1 24.8 + - - +
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Residues in contact with LEU 79 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75b GLU 3.1 11.4 + - - +
76b THR* 3.0 11.3 + - - +
78b LEU* 1.3 72.9 - - - +
80b ASP* 1.3 58.1 + - - +
81b LYS 3.1 1.1 - - - -
82b LEU* 2.8 28.8 + - - +
83b TYR* 2.9 13.5 + - - +
92b ALA* 4.7 19.3 - - + +
94b LEU* 6.5 0.9 - - - -
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Residues in contact with ASP 80 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76b THR 2.8 16.3 + - - +
77b LEU* 3.6 14.6 - - - +
79b LEU* 1.3 69.7 - - - +
81b LYS* 1.3 56.8 + - - +
83b TYR* 3.3 9.5 + - - +
84b ASP* 3.0 26.7 + - - +
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Residues in contact with LYS 81 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77b LEU 3.2 12.0 + - - +
78b LEU* 3.3 12.1 - - - +
79b LEU 3.1 0.2 - - - -
80b ASP* 1.3 73.6 - - - +
82b LEU* 1.3 64.2 + - - +
83b TYR 3.1 2.4 + - - -
84b ASP* 3.4 8.2 + - - +
85b MET* 3.3 22.7 + - - +
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Residues in contact with LEU 82 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78b LEU 3.1 12.2 + - - +
79b LEU* 2.8 14.9 + - - +
81b LYS* 1.3 77.8 - - - +
83b TYR* 1.3 54.8 + - - +
85b MET* 3.7 3.3 - - - -
86b GLY 2.9 6.1 + - - -
87b ILE* 2.8 43.3 + - + +
88b LEU* 4.0 13.0 + - + +
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Residues in contact with TYR 83 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79b LEU 2.9 10.5 + - - +
80b ASP* 3.3 13.9 - - - +
81b LYS 3.1 0.2 - - - -
82b LEU* 1.3 74.5 - - - +
84b ASP* 1.3 61.0 + - - +
85b MET 3.1 1.8 - - - -
86b GLY* 2.8 20.2 + - - -
88b LEU* 4.4 10.7 - - - +
152b ARG* 4.0 8.8 - - - +
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Residues in contact with ASP 84 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80b ASP 3.0 15.2 + - - +
81b LYS* 3.4 8.7 + - - +
83b TYR* 1.3 75.4 - - - +
85b MET* 1.3 51.3 + - - +
86b GLY 3.3 0.2 - - - -
151b THR* 3.2 13.4 - - - -
152b ARG* 2.7 36.0 + - - +
153b ASN* 4.4 0.9 + - - +
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Residues in contact with MET 85 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81b LYS 3.3 13.9 + - - +
82b LEU* 4.2 3.8 - - - +
83b TYR 3.1 0.2 - - - -
84b ASP* 1.3 77.5 - - - +
86b GLY* 1.3 67.6 + - - +
87b ILE* 4.9 3.4 - - + +
109b ARG* 4.1 14.2 - - + +
149b LEU* 5.9 5.8 - - + +
150b VAL 4.0 20.2 - - - +
151b THR* 4.2 3.4 - - - +
152b ARG* 4.6 2.9 - - - -
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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