Contacts of the helix formed by residues 57 - 69 (chain G) in PDB entry 1HNX
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 GLU 57 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18G TYR* 6.0 0.9 - - + -
51G GLN* 4.0 9.0 - - - +
55G GLY 5.8 0.2 - - - +
56G GLN* 1.3 83.1 - - - +
58G PRO* 1.3 80.7 - - + +
59G LEU* 4.5 7.4 - - + +
60G LYS* 3.2 28.9 + - - +
61G VAL* 3.4 8.1 + - - +
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Residues in contact with PRO 58 (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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18G TYR* 3.0 29.4 - - + +
47G CYS* 3.2 40.8 - - + +
50G ILE* 4.0 20.4 - - + -
51G GLN* 3.7 23.3 - - + +
56G GLN 3.6 1.4 - - - -
57G GLU* 1.3 83.2 - - + +
59G LEU* 1.3 57.5 + - - +
60G LYS 2.6 2.3 + - - -
61G VAL* 2.6 28.1 + - - +
62G PHE* 2.8 13.1 + - - -
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Residues in contact with LEU 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G TYR* 3.2 54.9 - - + +
20G ASP* 4.7 3.1 - - + +
23G VAL* 4.1 16.4 - - + -
43G PHE* 6.0 1.6 - - + -
47G CYS* 5.1 1.1 - - - -
57G GLU* 3.3 6.0 - - + -
58G PRO* 1.3 80.5 - - - +
60G LYS* 1.3 57.4 + - - +
62G PHE* 3.5 9.8 - - + +
63G LYS* 3.2 52.7 + - + +
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Residues in contact with LYS 60 (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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56G GLN* 5.1 12.1 + - + +
57G GLU* 3.2 28.1 + - - +
58G PRO 2.6 5.9 + - - -
59G LEU* 1.3 73.8 - - - +
61G VAL* 1.3 65.1 + - + +
62G PHE 3.0 1.6 - - - -
63G LYS* 3.8 5.8 - - + +
64G GLN* 2.9 42.7 + - + +
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Residues in contact with VAL 61 (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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50G ILE* 3.4 37.5 - - + -
54G THR* 4.3 1.3 - - + +
56G GLN* 3.6 40.4 - - + +
57G GLU 3.5 13.7 - - - +
58G PRO* 2.6 11.7 + - + +
60G LYS* 1.3 74.9 - - - +
62G PHE* 1.3 63.6 - - - +
64G GLN* 3.6 6.0 - - - +
65G ALA* 3.1 19.1 + - - +
124G LEU* 4.5 1.3 - - + -
125G MET* 4.0 28.5 - - + +
128G ALA* 4.0 9.4 - - + +
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Residues in contact with PHE 62 (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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22G LEU* 3.7 32.8 - - + -
23G VAL* 4.4 14.1 - - + -
26G PHE* 3.5 48.5 - + + -
43G PHE* 4.2 16.4 - + + -
47G CYS* 6.0 0.4 - - - -
50G ILE* 5.3 2.2 - - + +
58G PRO 2.8 10.7 + - - +
59G LEU* 3.5 22.0 - - + +
61G VAL* 1.3 76.7 - - - +
63G LYS* 1.3 73.8 + - + +
65G ALA* 2.7 32.7 + - - +
66G VAL* 3.1 21.2 + - + -
101G LEU* 4.3 0.4 - - + -
104G LEU* 5.0 0.2 - - + -
124G LEU* 3.5 30.5 - - + -
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Residues in contact with LYS 63 (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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20G ASP* 2.7 31.3 + - - -
22G LEU* 4.6 10.3 - - + -
59G LEU* 3.2 40.3 + - + +
60G LYS* 4.2 6.3 - - + +
62G PHE* 1.3 93.4 - - + +
64G GLN* 1.3 62.2 + - - +
66G VAL* 3.8 8.4 - - - +
67G GLU* 3.2 23.4 + - - +
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Residues in contact with GLN 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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56G GLN* 6.2 0.2 - - - +
60G LYS* 2.9 40.0 + - + +
61G VAL* 3.6 7.0 - - - +
63G LYS* 1.3 77.0 - - - +
65G ALA* 1.3 59.5 + - - +
67G GLU* 3.5 13.1 + - - +
68G ASN* 2.6 49.6 + - - +
128G ALA* 4.0 19.7 + - + +
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Residues in contact with ALA 65 (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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61G VAL 3.1 8.2 + - - +
62G PHE 2.7 15.3 + - - +
64G GLN* 1.3 73.5 - - - +
66G VAL* 1.3 54.8 + - - +
68G ASN* 2.6 29.6 + - - +
69G VAL* 3.2 14.1 + - - +
104G LEU* 4.4 2.9 - - + -
124G LEU* 3.5 28.5 - - + +
127G ALA* 3.4 29.2 - - + -
128G ALA* 3.9 4.4 - - - +
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Residues in contact with VAL 66 (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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22G LEU* 4.2 19.5 - - + -
62G PHE* 3.1 25.3 + - + +
63G LYS* 3.8 9.0 - - - +
65G ALA* 1.3 78.6 - - - +
67G GLU* 1.3 64.6 + - - +
69G VAL* 3.0 14.7 + - - -
70G LYS* 3.2 39.6 + - - +
97G GLN* 5.3 2.9 - - + -
100G ALA* 3.8 12.3 - - + +
101G LEU* 3.9 26.2 - - + -
104G LEU* 4.2 14.5 - - + +
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Residues in contact with GLU 67 (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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63G LYS 3.2 14.8 + - - +
64G GLN* 3.6 15.9 - - - +
65G ALA 2.9 1.0 + - - -
66G VAL* 1.3 82.1 - - - +
68G ASN* 1.3 65.1 + - - +
70G LYS* 3.8 33.1 + - - +
72G ARG* 5.9 0.5 + - - -
138G LYS* 5.9 0.3 - - - -
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Residues in contact with ASN 68 (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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64G GLN* 2.6 37.9 + - - +
65G ALA 2.6 13.1 + - - +
67G GLU* 1.3 75.5 - - - +
69G VAL* 1.3 56.0 + - + +
70G LYS 3.2 7.4 + - - -
127G ALA 3.2 27.1 + - - +
128G ALA 3.6 12.6 + - - -
130G GLY* 5.6 3.6 - - - -
135G VAL* 4.0 16.7 - - + +
138G LYS* 3.6 23.4 + - - +
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Residues in contact with VAL 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 ALA 3.3 17.0 - - - +
66G VAL 3.0 6.6 + - - +
68G ASN* 1.3 75.7 - - - +
70G LYS* 1.3 57.3 + - - +
71G PRO* 3.4 1.7 - - - +
100G ALA* 3.5 11.3 - - + +
103G TRP* 3.2 41.0 - - + -
104G LEU* 3.2 28.5 - - + -
127G ALA* 4.0 10.5 - - + -
134G ALA* 3.5 37.2 - - + +
135G VAL* 4.4 5.4 - - + +
138G LYS* 3.8 7.0 - - + -
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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