Contacts of the helix formed by residues 52 - 66 (chain B) in PDB entry 1YZ3
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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46B ASP 5.2 4.3 - - - -
49B ASN* 3.0 20.2 + - - -
50B PRO 3.4 0.4 - - - +
51B ASN* 1.3 84.2 - - - +
53B VAL* 1.3 63.5 + - - -
54B GLY 3.4 2.5 - - - -
55B PRO* 3.8 5.4 - - - +
56B TRP* 3.4 22.0 + - - +
256B TYR* 3.2 5.5 + - - -
261B HIS* 5.6 0.7 - - - -
262B LEU* 4.3 12.3 - - - -
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASN 5.7 0.4 - - - +
44B ARG* 4.1 27.3 + - + +
52B GLY* 1.3 70.4 - - - -
54B GLY* 1.3 71.0 + - - +
56B TRP* 3.8 1.5 - - + +
57B LYS* 3.0 33.9 + - + +
256B TYR* 3.2 37.0 + - + -
258B MET* 4.5 9.9 - - + -
262B LEU* 4.6 5.9 - - + +
272B VAL* 4.0 12.8 - - + -
3002B SKA 3.3 33.9 - - + -
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Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG 4.3 4.6 + - - -
46B ASP 5.5 0.2 + - - -
47B LEU* 3.6 18.4 - - - -
53B VAL* 1.3 87.2 - - - +
55B PRO* 1.3 70.2 - - - +
57B LYS* 3.2 11.7 + - - +
58B LEU* 3.0 25.6 + - - +
126B TYR* 4.5 10.8 - - - -
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Residues in contact with PRO 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASP 4.3 2.9 - - - +
47B LEU* 3.4 34.8 - - + +
49B ASN 3.3 19.7 - - - +
50B PRO* 3.9 10.8 - - + +
52B GLY* 3.8 11.4 - - - +
54B GLY* 1.3 88.4 - - - +
56B TRP* 1.3 51.5 + - - +
58B LEU* 3.3 2.1 + - - +
59B ARG* 2.8 58.6 + - - +
129B HIS* 3.8 23.0 + - + +
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Residues in contact with TRP 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLU* 5.7 0.2 + - - -
237A GLU* 3.6 38.3 - - + +
240A ARG* 5.4 0.2 - - - +
52B GLY 3.4 16.9 + - - +
53B VAL* 3.8 4.0 - - + +
54B GLY 3.3 0.6 - - - -
55B PRO* 1.3 78.1 - - - +
57B LYS* 1.3 88.5 + - + +
59B ARG* 3.2 16.1 + - - +
60B CYS* 3.0 42.7 + - - -
214B ILE* 5.4 1.3 - - + -
254B ARG* 3.7 18.6 - - + +
255B THR 3.7 17.5 + - - -
256B TYR* 3.5 38.8 - + + +
272B VAL* 3.5 39.5 - - + -
273B PHE 4.5 0.2 - - - -
274B PHE* 3.6 23.6 - - + -
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Residues in contact with LYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASN 5.4 0.6 + - - -
40B TYR* 3.5 30.9 - - - -
53B VAL* 3.0 26.1 + - + +
54B GLY* 3.7 12.5 - - - +
56B TRP* 1.3 94.9 - - + +
58B LEU* 1.3 64.7 + - + +
60B CYS* 3.0 16.0 + - - +
61B LEU* 3.2 18.8 + - - +
85B TYR* 3.7 27.1 + - + +
126B TYR* 5.0 3.7 + - - -
182B PHE* 3.9 22.9 - - + -
214B ILE* 4.2 18.7 - - + +
272B VAL* 4.8 0.7 - - + -
3002B SKA 3.6 24.9 - - + +
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Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 4.5 4.7 - - + -
54B GLY 3.0 18.4 + - - +
55B PRO 3.7 3.4 - - - +
57B LYS* 1.3 77.3 - - + +
59B ARG* 1.3 57.0 + - - +
61B LEU* 3.5 8.6 + - + +
62B ALA* 3.0 31.2 + - - +
85B TYR* 4.1 27.6 - - + +
88B LEU* 4.5 11.0 - - + -
89B SER* 4.6 4.3 + - - +
126B TYR* 3.9 36.3 - - + +
129B HIS* 3.7 34.3 - - + -
130B ALA* 4.4 9.0 - - + +
133B ILE* 3.3 13.0 - - + +
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Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A GLU* 2.8 42.8 + - - +
50B PRO* 3.0 33.2 + - - +
51B ASN* 5.0 2.4 + - - +
52B GLY 4.8 0.4 + - - -
55B PRO* 2.8 34.5 + - - +
56B TRP* 3.5 27.0 - - - +
58B LEU* 1.3 71.8 - - - +
60B CYS* 1.3 65.8 + - - +
63B GLN* 2.9 50.6 + - - +
129B HIS* 4.9 2.4 + - - -
133B ILE* 3.5 25.6 - - + -
254B ARG* 5.5 0.4 - - - +
256B TYR* 6.0 0.4 - - - -
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Residues in contact with CYS 60 (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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237A GLU* 5.7 0.2 - - - -
56B TRP* 3.0 52.7 + - - -
57B LYS* 3.0 8.7 + - - +
59B ARG* 1.3 76.0 - - - +
61B LEU* 1.3 61.8 + - - +
63B GLN* 4.1 1.4 - - - +
64B THR* 3.0 30.3 + - - -
214B ILE* 5.7 0.2 - - + -
254B ARG* 3.9 28.0 + - - +
274B PHE* 3.5 37.8 - - + -
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS 3.2 17.1 + - - +
58B LEU* 3.9 9.6 - - + +
60B CYS* 1.3 74.7 - - - +
62B ALA* 1.3 65.0 + - - +
64B THR* 3.4 3.0 + - - -
65B PHE* 3.0 36.1 + - + -
85B TYR* 4.5 10.1 - - + +
86B GLN* 4.0 35.2 - - + +
89B SER* 4.3 11.0 - - - +
179B VAL* 5.2 4.7 - - + -
212B LEU* 4.0 28.9 - - + -
214B ILE* 4.0 22.9 - - + -
274B PHE* 4.1 13.5 - - + -
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU 3.0 19.5 + - - +
59B ARG 3.9 1.3 - - - +
61B LEU* 1.3 75.3 - - - +
63B GLN* 1.3 60.2 + - + +
65B PHE* 3.3 3.5 + - - +
66B ALA* 2.9 30.3 + - - +
89B SER* 3.5 21.7 + - - +
133B ILE* 3.6 28.9 - - + +
134B GLU* 4.4 10.6 - - + +
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Residues in contact with GLN 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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237A GLU* 4.6 3.4 + - - +
240A ARG* 4.4 2.9 + - - -
241A GLU* 5.3 6.3 + - - -
59B ARG* 2.9 47.3 + - - +
60B CYS 4.1 0.2 - - - +
62B ALA* 1.3 74.6 - - + +
64B THR* 1.3 66.2 + - - +
66B ALA* 3.4 14.4 + - - +
67B THR* 3.4 16.5 + - - +
254B ARG* 3.1 36.5 + - - +
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Residues in contact with THR 64 (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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60B CYS 3.0 19.8 + - - -
61B LEU* 3.8 4.7 - - - -
62B ALA 3.3 0.2 - - - -
63B GLN* 1.3 76.3 - - - +
65B PHE* 1.3 60.1 + - - +
67B THR* 2.8 30.9 + - - -
68B GLY 4.3 0.2 + - - -
70B VAL* 4.0 16.1 - - + +
212B LEU* 3.8 23.1 - - + -
252B ASP* 4.8 2.1 + - - -
254B ARG* 4.9 3.4 + - - +
274B PHE* 3.3 21.6 - - - -
276B TRP* 3.8 33.3 - - + -
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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 LEU* 3.0 33.6 + - + +
62B ALA 3.8 3.6 - - - +
64B THR* 1.3 78.2 - - - +
66B ALA* 1.3 57.0 + - - +
67B THR 3.1 0.2 - - - -
68B GLY* 2.9 21.8 + - - -
70B VAL* 3.7 42.5 + - + +
75B LEU* 4.8 4.5 - - + -
86B GLN 5.4 1.1 - - - -
89B SER* 3.8 18.8 - - - +
90B ALA* 3.3 34.8 - - + -
93B HIS* 3.6 38.0 - + + +
94B PHE* 3.8 15.5 - + - -
179B VAL* 4.8 1.6 - - + -
212B LEU* 3.4 29.4 - - + -
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Residues in contact with ALA 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 ALA 2.9 18.3 + - - +
63B GLN* 3.8 10.1 - - - +
64B THR 3.2 0.8 - - - -
65B PHE* 1.3 72.1 - - - +
67B THR* 1.3 59.5 + - - +
68B GLY* 3.0 6.6 + - - -
93B HIS* 5.5 2.0 - - - -
136B LYS* 6.6 0.2 - - - -
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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
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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