Contacts of the helix formed by residues 59 - 80 (chain B) in PDB entry 6CNC
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 LYS 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LYS* 3.4 37.9 - - + +
56B GLY 3.7 8.8 + - - +
57B LEU 3.6 2.8 - - - -
58B VAL* 1.3 74.0 - - - +
60B GLN* 1.3 71.5 + - - +
61B HIS 3.3 1.1 - - - -
62B LEU* 2.7 13.2 + - - -
63B ASP* 2.4 56.7 + - + +
379B LEU* 5.7 1.0 - - - +
518B THR 3.6 6.5 - - - -
519B HIS* 3.2 43.0 + - + +
520B ILE* 2.9 35.2 + - - +
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Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LYS* 5.9 0.2 - - - +
57B LEU 3.3 11.5 + - - +
58B VAL* 3.0 26.7 - - - +
59B LYS* 1.3 83.1 - - + +
61B HIS* 1.3 68.1 + - + +
64B SER* 3.5 10.9 + - - -
196B VAL* 4.7 3.4 - - + -
379B LEU* 3.2 44.4 - - + +
471B THR* 5.6 4.2 + - - +
514B LEU* 3.8 13.0 - - + +
515B ALA 5.8 0.6 + - - -
516B LEU 5.9 0.4 + - - -
518B THR* 3.6 31.7 + - - +
520B ILE* 3.4 26.2 - - + -
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Residues in contact with HIS 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B VAL* 3.5 20.9 - - + +
60B GLN* 1.3 77.8 - - + +
62B LEU* 1.3 66.1 + - - +
65B PHE* 3.3 13.0 + - - +
155B MET* 3.0 19.5 - - - +
183B GLY* 3.4 28.3 - - - +
193B VAL* 4.2 3.6 - - + +
194B ILE 2.9 31.1 + - - -
195B LEU* 4.6 0.2 - - - -
196B VAL* 3.3 30.8 + - + +
380B ALA* 4.3 19.8 - - + +
469B MET 5.1 1.3 + - - -
470B MET* 3.6 30.9 - - - -
471B THR* 4.3 6.5 - - - -
472B ARG 5.7 0.4 - - - -
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLY* 6.5 0.4 - - - -
58B VAL* 3.2 28.5 - - + +
59B LYS* 2.7 12.7 + - - +
61B HIS* 1.3 71.6 - - - +
63B ASP* 1.3 70.0 + - - +
65B PHE* 2.9 15.4 + - - +
66B ASN* 2.9 22.3 + - - +
155B MET* 3.5 8.1 - - + -
156B LEU 4.7 0.2 - - - +
157B ARG* 3.3 34.5 - - + +
158B SER* 5.0 0.9 - - - +
181B PRO 5.0 2.7 - - - +
182B GLY 4.3 2.9 - - - -
183B GLY* 3.6 32.5 - - - +
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Residues in contact with ASP 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LYS* 4.8 5.0 - - - +
59B LYS* 2.4 56.0 + - + +
62B LEU* 1.3 72.9 - - - +
64B SER* 1.3 56.9 + - - +
66B ASN* 3.1 17.3 + - - +
67B TYR* 2.8 31.3 + - - +
519B HIS* 5.4 1.4 + - - -
522B THR* 6.2 4.0 - - + -
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Residues in contact with SER 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLN 3.6 13.5 + - - -
61B HIS 4.9 0.2 - - - -
62B LEU 3.3 1.0 - - - -
63B ASP* 1.3 77.8 - - - +
65B PHE* 1.3 58.2 + - - +
67B TYR* 3.5 9.1 + - - +
68B PHE* 2.9 23.2 + - - +
379B LEU* 3.1 31.0 - - - +
381B GLY* 3.4 31.9 - - - -
382B GLN* 4.4 11.8 + - - -
522B THR* 5.2 9.8 - - - +
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Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B HIS 3.3 20.6 + - - +
62B LEU 2.9 3.4 + - - +
64B SER* 1.3 79.1 - - - +
66B ASN* 1.3 64.5 + - - +
68B PHE* 3.3 6.7 - + + +
69B VAL* 3.0 48.5 + - + +
152B MET* 4.0 11.4 - - + -
154B ILE* 3.6 16.4 - - + -
155B MET* 3.4 36.6 - - + -
158B SER* 3.6 28.3 - - - -
160B LYS* 5.9 0.9 - - + -
185B PHE* 3.4 30.3 - + - -
380B ALA* 5.5 1.8 - - + -
381B GLY* 4.1 6.0 - - - +
384B ILE* 3.9 16.6 - - + -
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Residues in contact with ASN 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 2.9 23.3 + - - +
63B ASP* 3.5 22.3 + - - +
65B PHE* 1.3 74.0 - - - +
67B TYR* 1.3 67.1 + - - +
69B VAL* 3.0 8.7 + - - +
70B ASP* 2.9 26.0 + - - +
157B ARG 5.6 0.2 + - - -
158B SER* 3.7 11.8 - - - -
159B ASN* 2.8 61.1 + - - +
164B TYR* 6.1 0.4 - - - -
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Residues in contact with TYR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ASP 2.8 20.0 + - - +
64B SER* 3.9 7.9 - - - +
66B ASN* 1.3 73.8 - - - +
68B PHE* 1.3 57.8 + - - +
70B ASP* 4.9 2.0 - - - -
71B THR* 2.9 68.4 + - + +
72B ASP* 3.6 22.0 + - - -
382B GLN* 5.3 13.0 - - + -
522B THR* 5.8 16.8 - - + -
523B ASP* 4.9 19.6 + - + +
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Residues in contact with PHE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B SER 2.9 16.1 + - - +
65B PHE* 3.3 14.1 - + - +
66B ASN 3.1 0.2 - - - -
67B TYR* 1.3 79.6 - - - +
69B VAL* 1.3 83.3 + - + +
70B ASP 2.8 7.5 + - - -
71B THR 3.3 0.2 + - - -
72B ASP* 3.2 33.7 + - + +
73B LEU* 3.4 43.2 + - + -
76B ILE* 5.9 1.3 - - + -
152B MET* 3.5 25.8 - - + -
381B GLY* 3.6 22.4 - - - -
384B ILE* 3.7 14.8 - - + -
385B SER* 3.3 35.7 - - - -
388B PHE* 4.2 11.9 - + + -
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 3.0 41.7 + - + +
66B ASN* 3.0 25.6 + - - +
68B PHE* 1.3 93.1 - - + +
70B ASP* 1.3 60.7 + - + +
73B LEU* 3.5 23.4 - - + +
98B ILE* 5.9 0.2 - - - +
99B ARG* 6.1 0.9 - - - -
100B VAL* 4.4 20.0 + - + +
152B MET* 5.1 5.4 - - + -
154B ILE* 5.6 2.0 - - + -
159B ASN* 4.7 7.4 - - - +
160B LYS* 4.4 24.8 - - + -
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Residues in contact with ASP 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASN 2.9 15.9 + - - +
67B TYR* 4.4 2.2 - - - +
68B PHE 2.8 0.4 + - - -
69B VAL* 1.3 83.1 - - + +
71B THR* 1.3 71.2 + - - +
73B LEU 4.9 0.2 - - - -
74B LYS* 3.4 27.4 + - - +
159B ASN* 5.3 5.9 + - - +
160B LYS* 6.4 1.8 - - - +
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 2.9 50.7 + - + +
70B ASP* 1.3 77.6 + - - +
72B ASP* 1.3 76.2 + - - +
74B LYS* 2.8 21.1 + - - +
75B LYS* 3.1 13.1 + - + +
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Residues in contact with ASP 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 4.2 21.0 + - - -
68B PHE* 3.2 30.1 + - + +
71B THR* 1.3 87.6 - - - +
73B LEU* 1.3 52.1 + - - +
75B LYS* 2.6 43.8 + - - +
76B ILE* 2.7 30.8 + - + +
381B GLY 5.6 0.3 - - - -
382B GLN* 5.4 7.8 + - - +
385B SER* 4.2 17.7 + - - -
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Residues in contact with LEU 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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68B PHE* 3.4 34.8 + - + +
69B VAL* 3.5 32.8 - - + +
71B THR 3.3 0.4 - - - -
72B ASP* 1.3 77.3 - - - +
74B LYS* 1.3 62.9 + - + +
75B LYS 3.3 0.2 + - - -
76B ILE* 3.3 12.2 + - - +
77B ILE* 3.6 9.0 + - - +
98B ILE* 3.8 34.7 - - + +
100B VAL* 4.1 23.3 - - + -
129B ILE* 5.2 4.3 - - + -
152B MET* 5.9 2.0 - - + -
388B PHE* 3.5 39.0 - - + -
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Residues in contact with LYS 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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70B ASP* 3.4 26.0 - - - +
71B THR* 2.8 15.5 + - - +
73B LEU* 1.3 75.5 - - + +
75B LYS* 1.3 59.5 + - - +
77B ILE* 3.6 10.1 - - - +
78B LYS* 3.2 23.3 + - - +
96B VAL 5.4 4.4 + - - -
97B ASP* 4.2 15.5 + - - +
98B ILE* 4.5 20.1 - - + +
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Residues in contact with LYS 75 (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 THR* 3.1 10.7 + - + +
72B ASP* 2.6 35.0 + - - +
74B LYS* 1.3 71.4 - - - +
76B ILE* 1.3 72.7 + - - +
78B LYS* 3.0 14.2 + - + +
79B ALA* 2.9 29.8 + - + +
224B THR* 5.8 5.7 - - - +
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Residues in contact with ILE 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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68B PHE* 5.9 1.1 - - + -
72B ASP* 2.7 33.0 + - + +
73B LEU* 3.3 8.7 + - + +
75B LYS* 1.3 86.2 - - - +
77B ILE* 1.3 60.2 + - + +
79B ALA* 3.0 22.4 + - + +
80B ASN* 3.2 12.3 + - - +
385B SER* 5.5 8.3 - - - +
388B PHE* 4.5 18.4 - - + -
389B GLU* 3.3 52.9 - - + +
392B PHE* 4.3 18.0 - - + -
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Residues in contact with ILE 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 LEU 3.6 2.6 + - - +
74B LYS* 3.6 12.1 - - - +
76B ILE* 1.3 73.7 - - + +
78B LYS* 1.3 65.0 + - + +
79B ALA 3.0 2.5 - - - -
80B ASN 2.9 34.3 - - - +
81B GLN* 3.0 9.3 + - + +
95B TYR* 4.1 11.9 - - + -
96B VAL* 3.2 42.0 - - - +
97B ASP 3.8 3.6 - - - +
98B ILE* 3.3 44.9 - - + +
388B PHE* 6.0 3.6 - - + -
392B PHE* 4.1 24.5 - - + -
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Residues in contact with LYS 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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74B LYS 3.2 17.2 + - - +
75B LYS* 3.0 17.1 + - + +
77B ILE* 1.3 83.4 - - - +
79B ALA* 1.3 56.3 + - - +
81B GLN* 2.8 19.8 + - - +
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Residues in contact with ALA 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 LYS* 2.9 12.3 + - + +
76B ILE* 3.0 13.0 + - + +
78B LYS* 1.3 79.1 - - - +
80B ASN* 1.3 74.5 + - - +
81B GLN* 3.7 5.1 + - - +
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Residues in contact with ASN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 3.2 5.5 + - - +
77B ILE* 2.9 14.4 - - - +
79B ALA* 1.3 91.9 + - - +
81B GLN* 1.3 57.8 + - - +
82B LEU 3.6 8.7 + - - +
83B ILE* 5.6 3.1 - - + -
95B TYR* 3.3 17.9 - - - -
392B PHE* 4.2 18.6 - - + -
393B LYS* 3.9 28.7 - - - +
396B ASN* 4.6 6.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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