Contacts of the helix formed by residues 63 - 79 (chain G) in PDB entry 1HQ3
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 ARG 63 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61G LEU 4.0 1.4 + - - -
62G ILE* 1.3 77.2 - - + +
64G LYS* 1.3 65.4 + - - +
65G LEU* 6.1 0.2 - - - +
66G PRO* 3.4 27.8 - - + +
67G PHE* 3.1 20.4 + - - +
28H GLY 5.6 1.6 - - - +
33H ALA* 5.0 1.4 - - + +
36H ARG* 4.8 12.2 - - - +
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Residues in contact with LYS 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G LEU* 4.1 13.6 + - - +
62G ILE 4.5 2.2 + - - +
63G ARG* 1.3 69.7 - - - +
65G LEU* 1.3 62.0 + - - +
67G PHE* 3.2 1.7 + - - +
68G GLN* 2.9 30.7 + - - +
89G VAL* 5.4 1.0 - - - +
90G MET* 3.4 35.2 - - + -
93G GLN* 3.9 22.7 + - - +
601G CL 3.4 24.4 - - - +
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Residues in contact with LEU 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G LYS* 1.3 74.9 - - - +
66G PRO* 1.3 75.8 - - + +
68G GLN* 3.1 14.0 + - - +
69G ARG* 2.9 63.0 + - + +
611G CL 4.1 11.4 - - + -
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Residues in contact with PRO 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G ILE* 5.6 0.7 - - + -
63G ARG* 3.4 40.6 - - + +
65G LEU* 1.3 97.6 - - + +
67G PHE* 1.3 61.0 + - - +
69G ARG* 3.2 11.6 + - + +
70G LEU* 3.0 22.1 + - - +
25H ASN* 4.7 4.7 - - - +
28H GLY* 3.9 31.4 - - - +
29H ILE* 5.3 2.8 - - - +
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Residues in contact with PHE 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G ILE* 4.3 26.4 - - + +
63G ARG 3.1 19.3 + - - +
64G LYS 3.6 4.5 - - - +
66G PRO* 1.3 75.0 - - - +
68G GLN* 1.3 65.5 + - - +
70G LEU* 3.0 8.6 + - + +
71G VAL* 2.9 36.5 + - + +
89G VAL* 3.8 11.9 - - + -
92G LEU 3.8 1.8 - - - -
93G GLN* 3.3 61.0 - - + +
96G SER* 3.6 24.2 - - - -
29H ILE* 4.6 8.3 - - + -
58H LEU* 5.0 2.9 - - + -
62H LEU* 4.0 28.3 - - + -
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Residues in contact with GLN 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G LYS 2.9 14.2 + - - +
65G LEU* 3.4 18.7 - - + +
67G PHE* 1.3 77.7 - - - +
69G ARG* 1.3 57.4 + - - +
71G VAL* 3.2 4.5 + - - +
72G ARG* 2.9 54.2 + - + +
86G SER* 5.0 8.0 + - - -
89G VAL* 3.9 37.7 - - + +
611G CL 3.3 26.1 - - + +
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Residues in contact with ARG 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G LEU* 2.9 49.5 + - + +
66G PRO* 3.5 10.1 - - + +
67G PHE 3.2 0.2 - - - -
68G GLN* 1.3 76.7 - - - +
70G LEU* 1.3 58.9 + - - +
72G ARG* 3.4 6.3 + - - +
73G GLU* 2.9 30.5 + - - +
611G CL 3.4 26.5 - - - +
20H LYS* 4.3 21.1 - - - +
22H LEU* 4.1 16.3 - - + +
25H ASN* 3.8 26.2 + - - +
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Residues in contact with LEU 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G PRO 3.0 11.3 + - - +
67G PHE* 3.0 13.3 + - + +
69G ARG* 1.3 77.4 - - - +
71G VAL* 1.3 63.1 + - - +
73G GLU* 3.2 7.7 + - - +
74G ILE* 2.9 37.9 + - + +
25H ASN* 4.0 13.9 - - + +
26H ILE* 3.8 39.7 - - + +
29H ILE* 4.0 28.9 - - + -
58H LEU* 4.2 3.6 - - + -
59H LYS* 5.6 4.7 - - + -
62H LEU* 3.5 29.2 - - + -
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Residues in contact with VAL 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G PHE* 2.9 43.7 + - + +
68G GLN* 3.5 10.5 - - - +
70G LEU* 1.3 77.5 - - - +
72G ARG* 1.3 63.7 + - + +
74G ILE* 3.3 3.2 + - - +
75G ALA* 3.0 21.5 + - - +
84G PHE* 3.8 37.2 - - + -
89G VAL* 4.7 9.2 - - + -
92G LEU* 3.9 20.9 - - + -
62H LEU* 4.6 5.2 - - + -
66H ILE* 3.9 15.6 - - + +
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Residues in contact with ARG 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G GLN* 2.9 45.9 + - + +
69G ARG* 4.0 2.2 - - - +
71G VAL* 1.3 75.2 - - + +
73G GLU* 1.3 65.7 + - - +
75G ALA* 3.3 6.5 + - - +
76G GLN* 3.0 26.2 + - + +
82G LEU 4.6 3.6 + - - +
83G ARG* 4.2 14.3 - - - +
84G PHE* 3.6 49.9 + - + +
89G VAL* 5.7 0.4 - - + +
611G CL 3.7 21.5 - - - +
22H LEU* 3.6 18.4 - - + -
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Residues in contact with GLU 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G ARG 2.9 18.1 + - - +
70G LEU* 3.2 10.7 + - + +
72G ARG* 1.3 76.0 - - - +
74G ILE* 1.3 66.0 + - + +
76G GLN* 3.2 19.4 + - - +
77G ASP* 3.5 7.6 - - - +
22H LEU* 3.5 30.9 - - + +
23H ARG* 3.2 5.7 - - - -
24H ASP* 3.4 16.5 + - - -
25H ASN* 2.6 47.7 + - - +
26H ILE* 4.9 2.6 + - - +
59H LYS* 4.9 11.1 + - - -
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Residues in contact with ILE 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G LEU* 2.9 38.5 + - + +
71G VAL 3.7 3.8 - - - +
73G GLU* 1.3 81.0 - - + +
75G ALA* 1.3 62.3 + - - +
76G GLN 3.3 1.0 + - - -
77G ASP* 3.4 16.4 + - - +
78G PHE* 3.6 28.8 - - + -
59H LYS* 4.4 16.8 - - + +
62H LEU* 3.7 29.2 - - + -
63H GLU* 4.0 27.1 - - + +
66H ILE* 3.5 19.3 - - + -
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Residues in contact with ALA 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G VAL 3.0 11.2 + - - +
72G ARG 3.7 4.3 - - - +
73G GLU 3.3 0.4 - - - -
74G ILE* 1.3 77.1 - - - +
76G GLN* 1.3 65.8 + - - +
77G ASP 3.0 1.3 + - - -
78G PHE* 3.3 12.8 + - - +
79G LYS 3.1 22.6 + - - +
82G LEU* 4.1 15.4 - - + +
84G PHE* 3.5 37.5 - - + -
66H ILE* 4.3 4.5 - - + -
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Residues in contact with GLN 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72G ARG* 3.0 19.1 + - + +
73G GLU* 3.2 9.4 + - - +
75G ALA* 1.3 76.2 - - - +
77G ASP* 1.3 65.6 + - - +
79G LYS 3.5 16.7 + - - +
80G THR* 4.3 6.3 + - - +
20H LYS 2.9 28.5 + - - +
21H VAL* 3.9 10.5 - - - +
22H LEU* 3.2 42.7 + - + +
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Residues in contact with ASP 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73G GLU 3.5 10.2 - - - +
74G ILE* 3.5 14.8 - - - +
75G ALA 3.1 0.6 - - - -
76G GLN* 1.3 79.8 - - - +
78G PHE* 1.3 74.7 + - + +
79G LYS* 2.9 3.1 + - - -
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Residues in contact with PHE 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G ILE* 3.6 39.7 - - + -
75G ALA* 3.3 6.3 + - - +
77G ASP* 1.3 81.6 - - + +
79G LYS* 1.3 65.0 + - + +
82G LEU* 5.2 0.2 - - + -
63H GLU* 3.8 23.1 - - + -
66H ILE* 4.0 15.7 - - + -
67H ARG* 3.8 46.4 - - + -
70H VAL* 4.2 21.3 - - + -
74H GLU* 4.3 8.3 - - - +
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Residues in contact with LYS 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75G ALA 3.1 16.5 + - - +
76G GLN* 3.5 12.5 - - - +
77G ASP 2.9 4.6 + - - -
78G PHE* 1.3 83.2 - - + +
80G THR* 1.3 79.9 + - - +
81G ASP* 3.4 10.3 + - - +
82G LEU* 3.5 40.1 - - + +
70H VAL* 6.0 0.2 - - + -
74H GLU* 3.2 31.2 - - + +
78H ARG 5.3 3.4 - - - -
79H LYS* 3.5 23.3 - - - +
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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