Contacts of the helix formed by residues 52 - 72 (chain B) in PDB entry 6YB9
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 GLY 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ASP* 3.2 10.6 + - - -
51B GLU* 1.3 76.1 - - - +
53B LYS* 1.3 63.0 + - - +
54B ALA 3.3 2.0 - - - -
55B ALA* 3.3 13.6 + - - +
56B ILE* 3.1 34.7 + - - +
246B LYS* 5.7 1.3 - - - -
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Residues in contact with LYS 53 (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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18B THR* 4.3 11.3 - - - +
36B LYS 4.4 3.3 + - - +
37B ASP* 3.3 2.2 + - - +
38B GLN 3.0 33.6 + - - +
39B ILE* 4.0 16.8 - - + +
50B LEU* 3.4 32.7 - - + +
51B GLU 3.3 3.4 + - - -
52B GLY* 1.3 77.4 - - - +
54B ALA* 1.3 53.9 + - - +
56B ILE* 3.1 8.8 + - - +
57B SER* 2.8 52.4 + - - +
210B ASP* 5.1 0.8 + - - -
212B ASP* 3.9 18.9 + - - -
249B PHE* 3.8 34.5 - - + -
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER* 3.5 27.8 - - - +
36B LYS* 3.7 25.0 + - - -
37B ASP* 2.9 20.4 + - - +
53B LYS* 1.3 77.7 - - - +
55B ALA* 1.3 56.1 + - - +
57B SER* 4.0 1.5 - - - -
58B ASN* 3.1 30.3 + - - +
84B THR* 4.0 15.2 - - + -
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLY* 3.3 15.5 + - - +
53B LYS 3.2 0.4 - - - -
54B ALA* 1.3 74.9 - - - +
56B ILE* 1.3 62.2 + - + +
59B LYS* 3.0 30.0 + - - +
83B GLU* 3.5 35.7 - - + +
84B THR* 3.9 10.2 - - + +
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Residues in contact with ILE 56 (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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51B GLU 5.8 0.2 - - - +
52B GLY* 3.1 25.9 + - - +
53B LYS* 3.6 7.0 - - - +
55B ALA* 1.3 74.8 - - + +
57B SER* 1.3 61.0 + - - +
59B LYS* 3.3 5.1 + - - +
60B ILE* 3.0 49.1 + - + +
246B LYS* 4.8 8.5 - - + +
249B PHE* 3.7 49.8 - - + +
250B GLU* 4.2 23.6 - - + +
253B ALA* 4.0 15.7 - - + -
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Residues in contact with SER 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER* 4.4 10.3 - - - -
53B LYS* 2.8 45.2 + - - +
54B ALA* 4.0 4.9 - - - -
56B ILE* 1.3 73.3 - - - +
58B ASN* 1.3 63.6 + - - +
60B ILE* 3.4 2.5 + - - +
61B THR* 3.0 27.8 + - - +
208B VAL* 6.4 1.6 - - - -
210B ASP* 3.4 33.8 + - - +
212B ASP* 5.0 0.2 + - - -
249B PHE* 5.3 1.6 - - - -
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Residues in contact with ASN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU 4.5 0.7 - - - +
35B SER* 4.4 6.6 + - - +
54B ALA 3.1 18.2 + - - +
57B SER* 1.3 78.8 - - - +
59B LYS* 1.3 55.7 - - - +
61B THR* 3.4 5.1 - - - +
62B SER* 2.8 37.8 + - - -
80B LYS* 3.7 10.9 - - - +
82B GLY 3.4 8.1 + - - -
83B GLU 3.2 18.6 + - - +
84B THR 3.7 4.6 - - - +
85B ALA* 2.7 52.0 + - - +
86B PHE* 3.5 17.2 - - - -
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Residues in contact with LYS 59 (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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55B ALA 3.0 20.0 + - - +
56B ILE* 3.7 5.4 - - - +
58B ASN* 1.3 73.9 - - - +
60B ILE* 1.3 60.2 + - + +
62B SER* 3.4 1.7 + - - -
63B CYS* 3.0 37.3 + - - -
80B LYS* 4.1 24.6 - - - +
83B GLU* 6.0 0.4 - - - +
253B ALA* 3.2 36.8 + - + +
254B GLU* 4.6 6.1 + - - +
256B VAL* 4.5 7.2 - - + -
257B GLU* 3.7 28.7 + - - -
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Residues in contact with ILE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE* 3.0 39.2 + - + +
57B SER* 3.9 4.3 - - - +
59B LYS* 1.3 74.8 - - - +
61B THR* 1.3 51.5 + - - +
62B SER 3.2 0.3 + - - -
63B CYS* 3.3 2.4 + - - +
64B ILE* 2.8 40.8 + - + +
209B ILE 3.7 3.1 - - - +
210B ASP* 3.7 21.8 - - + -
211B ASN* 4.0 19.3 - - + +
214B TRP* 4.0 23.3 - - + -
249B PHE 4.8 0.2 - - - +
252B VAL* 3.9 24.0 - - + -
253B ALA* 4.4 7.9 - - - +
256B VAL* 4.1 22.9 - - + -
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Residues in contact with THR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B SER 3.0 16.7 + - - +
58B ASN* 3.4 13.9 - - - +
60B ILE* 1.3 76.7 - - - +
62B SER* 1.3 57.7 + - - +
64B ILE* 4.5 1.6 - - - +
65B PHE* 2.8 54.1 + - + +
86B PHE* 3.8 31.4 - - + -
208B VAL* 3.4 14.2 - - + -
209B ILE 3.1 34.3 + - - -
210B ASP* 4.9 0.2 - - - -
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Residues in contact with SER 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN* 2.8 23.9 + - - -
59B LYS 3.7 3.6 - - - -
61B THR* 1.3 77.7 - - - +
63B CYS* 1.3 57.5 + - - +
66B GLN* 3.1 31.8 + - - +
77B PHE* 3.8 29.3 - - - -
80B LYS* 3.6 33.2 - - - +
86B PHE* 4.0 9.2 - - - +
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Residues in contact with CYS 63 (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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59B LYS* 3.0 30.9 + - - +
60B ILE 3.7 3.1 - - - +
62B SER* 1.3 73.9 - - - +
64B ILE* 1.3 66.2 + - - +
66B GLN* 3.3 5.6 + - - +
67B LEU* 3.0 24.4 + - - +
256B VAL* 4.0 30.3 - - + +
257B GLU* 4.2 17.3 - - - -
260B LEU* 3.7 29.2 - - + +
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ILE* 2.8 27.1 + - + +
61B THR 4.1 2.2 - - - +
63B CYS* 1.3 71.1 - - - +
65B PHE* 1.3 58.8 + - + +
67B LEU* 3.3 8.5 + - + +
68B LEU* 3.0 39.0 + - + +
176B LEU* 3.8 23.3 - - + -
209B ILE* 3.7 29.6 - - + +
214B TRP* 3.9 29.2 - - + -
256B VAL* 3.8 20.0 - - + -
259B LEU* 3.9 20.0 - - + -
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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
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61B THR* 2.8 41.5 + - - +
62B SER 4.2 0.4 - - - +
64B ILE* 1.3 74.8 - - + +
66B GLN* 1.3 57.3 + - - +
68B LEU* 3.4 4.6 + - + +
69B GLN* 2.8 32.0 + - - +
75B THR* 3.5 17.6 - - + +
76B ALA 4.0 11.0 - - - -
77B PHE* 3.6 42.4 - + + -
86B PHE* 4.0 7.0 - + - -
205B LEU* 3.7 27.1 - - + -
206B ALA 3.7 13.9 - - - -
207B ASP 3.3 27.6 - - - -
208B VAL* 3.8 4.3 - - - -
209B ILE* 4.1 13.9 - - + -
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Residues in contact with GLN 66 (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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62B SER 3.1 20.7 + - - +
63B CYS* 3.7 5.5 - - - +
65B PHE* 1.3 77.7 - - - +
67B LEU* 1.3 57.5 + - - +
69B GLN* 3.4 6.1 + - - +
70B GLU* 2.9 64.5 + - + +
77B PHE* 4.4 16.4 - - + -
260B LEU* 4.0 20.7 - - + +
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Residues in contact with LEU 67 (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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63B CYS 3.0 14.0 + - - +
64B ILE* 3.4 10.3 - - + +
66B GLN* 1.3 74.2 - - - +
68B LEU* 1.3 65.0 + - - +
70B GLU* 3.4 4.8 + - - +
71B ALA* 3.1 22.7 + - - +
175B ILE* 5.0 6.1 - - + -
176B LEU* 4.0 25.6 - - + -
179B SER* 3.8 28.7 - - - +
259B LEU* 3.5 38.4 - - + +
260B LEU* 3.7 15.8 - - + +
396B HIS* 4.7 0.2 - - + -
397B LEU* 3.7 20.6 - - + -
400B SER* 5.6 4.0 - - - +
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Residues in contact with LEU 68 (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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64B ILE* 3.0 26.6 + - + +
65B PHE* 3.9 5.4 - - + +
67B LEU* 1.3 74.6 - - + +
69B GLN* 1.3 60.9 + - - +
71B ALA* 3.4 6.3 + - - +
72B GLY 3.2 5.2 + - - -
73B ILE* 3.0 47.1 + - + +
75B THR* 4.3 6.1 - - - +
172B ILE* 4.1 16.4 - - + +
175B ILE* 3.8 29.8 - - + -
176B LEU* 3.9 13.9 - - + -
205B LEU* 3.6 27.8 - - + -
209B ILE* 3.8 18.4 - - + -
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Residues in contact with GLN 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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65B PHE 2.8 16.4 + - - +
66B GLN* 3.8 6.4 - - - +
68B LEU* 1.3 77.6 - - - +
70B GLU* 1.3 59.2 + - + +
72B GLY* 3.1 19.2 + - - -
73B ILE 3.7 14.7 - - - +
75B THR* 3.1 26.3 + - - +
77B PHE* 2.8 47.4 + - - +
78B THR 4.7 3.3 - - - +
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Residues in contact with GLU 70 (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 GLN* 2.9 47.4 + - + +
67B LEU* 4.0 3.7 - - - +
69B GLN* 1.3 74.8 - - + +
71B ALA* 1.3 62.1 + - - +
260B LEU* 4.5 9.2 - - - +
401B LYS* 3.2 28.3 + - - +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU 3.1 13.4 + - - +
68B LEU* 3.5 12.3 - - - +
70B GLU* 1.3 77.7 - - - +
72B GLY* 1.3 55.6 + - - +
73B ILE 3.8 0.2 - - - -
175B ILE* 4.6 7.4 - - + -
397B LEU 5.4 0.4 - - - +
400B SER* 3.8 34.3 - - - +
401B LYS* 3.4 26.0 - - - +
404B ALA* 3.4 17.7 - - + +
405B SER 5.1 0.2 + - - -
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Residues in contact with GLY 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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68B LEU 3.2 0.2 + - - -
69B GLN 3.1 14.3 + - - -
70B GLU 4.7 0.2 - - - -
71B ALA* 1.3 78.2 - - - +
73B ILE* 1.3 63.3 - - - +
74B LYS* 3.6 9.1 + - - +
404B ALA* 4.2 2.2 - - - -
408B ASN* 2.8 30.9 + - - +
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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
------------------------------------------------------------
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