Contacts of the helix formed by residues 56 - 69 (chain B) in PDB entry 5Y7G
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 PRO 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B GLU 4.0 4.0 - - - +
55B LEU* 1.3 88.2 - - + +
57B GLU* 1.3 66.6 + - - +
58B ALA* 3.3 4.5 - - + +
59B SER* 3.0 29.6 + - - +
60B GLN* 3.0 11.3 + - - +
93B PRO* 4.1 21.3 - - + -
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Residues in contact with GLU 57 (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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20B PHE* 3.9 34.7 - - + -
23B LEU* 4.5 11.5 - - + +
24B HIS* 5.4 5.2 - - - -
55B LEU 3.8 0.8 + - - -
56B PRO* 1.3 72.9 - - - +
58B ALA* 1.3 63.9 + - - +
60B GLN* 3.7 13.1 - - - +
61B ALA* 3.1 25.5 + - - +
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 5.8 1.3 - - - -
56B PRO* 3.3 4.1 - - + +
57B GLU* 1.3 79.4 - - - +
59B SER* 1.3 61.1 + - - +
61B ALA* 3.4 3.7 + - - +
62B LEU* 3.2 17.3 + - - +
83B GLU 5.3 3.4 - - - +
84B ILE* 3.2 44.2 - - + +
90B ALA* 4.0 8.3 - - + -
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Residues in contact with SER 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 3.6 7.2 - - - +
56B PRO* 3.0 32.9 + - - +
57B GLU 3.3 0.2 - - - -
58B ALA* 1.3 76.9 - - - +
60B GLN* 1.3 66.5 + - - +
62B LEU* 3.2 13.9 + - - +
63B LEU 3.4 8.8 + - - -
90B ALA* 2.9 32.3 - - - +
93B PRO* 3.9 18.5 - - - +
94B LEU* 4.0 13.6 - - - +
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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
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23B LEU* 3.7 18.2 - - + +
27B ARG* 3.5 31.7 + - - +
52B PHE* 2.9 55.2 - - + +
53B ALA 4.0 2.8 - - - +
55B LEU* 3.5 28.4 - - + +
56B PRO 3.0 14.4 + - - +
57B GLU* 3.7 13.8 - - - +
59B SER* 1.3 81.2 + - - +
61B ALA* 1.3 64.5 + - - +
63B LEU* 3.6 8.0 + - - +
64B VAL* 3.6 8.8 + - - +
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Residues in contact with ALA 61 (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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20B PHE* 3.9 11.9 - - + -
22B TYR* 3.3 36.8 + - + +
23B LEU* 3.7 22.7 - - + -
57B GLU 3.1 20.0 + - - +
58B ALA* 3.6 5.4 - - - +
59B SER 3.2 0.2 - - - -
60B GLN* 1.3 76.0 - - - +
62B LEU* 1.3 65.0 + - - +
64B VAL 3.3 9.0 + - - -
65B ARG* 3.3 4.2 + - - +
84B ILE* 3.9 6.5 - - + -
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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
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58B ALA 3.2 11.5 + - - +
59B SER 3.2 9.6 + - - +
61B ALA* 1.3 75.0 - - - +
63B LEU* 1.3 64.8 + - - +
65B ARG* 2.9 18.0 + - + +
66B MET* 3.1 23.8 + - + +
79B LEU* 4.4 31.9 - - + +
81B TYR* 4.6 5.8 - - + -
84B ILE* 3.5 27.7 - - + +
87B THR* 4.1 18.2 - - + +
90B ALA* 4.4 4.0 - - + -
91B VAL* 3.8 42.8 - - + +
94B LEU* 4.5 3.4 - - + -
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Residues in contact with LEU 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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26B PHE* 6.5 0.7 - - + -
48B PHE* 4.7 7.0 - - + -
52B PHE* 4.0 19.1 - - + -
55B LEU* 4.5 0.9 - - + -
59B SER 3.4 3.4 + - - +
60B GLN 3.7 9.4 - - - +
61B ALA 3.3 0.6 - - - -
62B LEU* 1.3 78.6 - - - +
64B VAL* 1.3 57.7 + - + +
66B MET* 3.3 6.3 + - + +
67B VAL* 3.0 38.1 + - + +
94B LEU* 3.6 33.7 - - + +
99B TRP* 3.5 38.1 - - + -
100B VAL* 4.5 3.1 - - + -
166B LEU* 3.5 33.2 - - + -
168B CYS* 5.3 2.2 - - + -
172B CYS* 6.2 2.0 - - - -
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 3.5 32.5 - - + +
23B LEU* 3.6 27.6 - - + -
26B PHE* 3.7 37.0 - - + -
52B PHE* 4.2 2.0 - - + -
60B GLN 3.6 5.2 - - - +
61B ALA 3.3 7.1 + - - +
62B LEU 3.2 1.0 - - - -
63B LEU* 1.3 74.9 - - + +
65B ARG* 1.3 66.9 + - - +
67B VAL* 3.3 6.6 + - + +
68B MET* 3.0 40.7 + - + +
187B TRP* 6.4 0.4 - - + -
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Residues in contact with ARG 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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19B PRO 5.8 0.2 + - - -
21B TYR* 4.4 15.6 + - - -
22B TYR* 3.2 36.2 - - + +
61B ALA 3.3 11.9 + - - +
62B LEU* 2.9 11.9 + - + +
64B VAL* 1.3 78.1 - - - +
66B MET* 1.3 63.9 + - + +
68B MET* 3.1 22.7 + - - +
69B ARG* 3.0 30.1 + - - +
79B LEU* 5.5 0.2 - - + -
81B TYR* 3.7 49.2 + - + +
83B GLU* 2.4 27.9 + - - -
84B ILE* 4.1 5.8 - - + -
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Residues in contact with MET 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 3.1 28.9 + - + +
63B LEU* 3.9 4.7 - - + +
65B ARG* 1.3 73.2 - - - +
67B VAL* 1.3 65.9 + - - +
69B ARG* 3.3 17.4 + - - +
71B GLY 3.9 4.3 - - - +
74B PHE* 3.7 35.7 - - + -
79B LEU* 3.7 33.7 - - + -
91B VAL* 5.2 1.6 - - - -
94B LEU* 5.1 1.3 - - - -
100B VAL* 3.6 28.0 - - + -
164B TYR* 4.8 5.4 - - + -
165B GLU 4.7 0.2 - - - -
166B LEU* 3.4 45.3 - - + +
169B MET* 5.2 0.7 - - - +
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 5.4 10.1 - - + -
63B LEU* 3.0 26.4 + - + +
64B VAL* 3.8 6.7 - - + +
65B ARG 3.3 0.2 - - - -
66B MET* 1.3 76.1 - - - +
68B MET* 1.3 61.2 - - + +
69B ARG 3.5 4.5 + - - +
166B LEU* 3.6 18.6 - - + -
169B MET* 3.8 29.4 - - + +
172B CYS* 4.0 29.8 - - + -
173B ASP* 5.8 0.2 - - - +
187B TRP* 4.0 24.0 + - + +
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Residues in contact with MET 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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22B TYR* 4.0 26.5 - - + +
64B VAL* 3.0 35.6 + - + +
65B ARG* 3.1 30.0 + - - +
67B VAL* 1.3 79.6 - - + +
69B ARG* 1.3 62.1 + - + +
186B ASP* 5.1 8.8 - - - +
187B TRP* 3.7 39.7 - - + -
188B SER* 5.6 1.8 - - - +
191B VAL* 6.4 1.8 - - - -
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Residues in contact with ARG 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 ARG* 3.0 19.4 + - - +
66B MET 3.3 6.1 + - - +
67B VAL 3.3 4.9 - - - +
68B MET* 1.3 81.3 - - + +
70B LYS* 1.3 68.0 + - - +
71B GLY 3.1 12.5 - - - +
74B PHE* 3.8 34.9 - - + -
78B LYS* 2.9 42.2 + - - +
79B LEU* 3.3 14.4 - - - +
81B TYR* 3.2 27.9 + - - -
169B MET* 6.0 1.2 - - - +
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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
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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