Contacts of the helix formed by residues 56 - 69 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLU 4.2 3.1 - - - +
55A LEU* 1.3 87.6 - - + +
57A GLU* 1.3 61.5 + - - +
58A ALA* 3.2 9.9 - - + +
59A SER* 3.3 18.6 - - - +
60A GLN* 3.0 27.7 + - - +
93A PRO* 4.3 19.7 - - + -
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 4.4 25.1 - - + +
23A LEU* 3.6 15.8 - - - +
24A HIS* 6.0 0.2 - - - -
27A ARG* 3.1 37.8 + - - +
55A LEU 3.8 0.6 + - - +
56A PRO* 1.3 73.5 - - - +
58A ALA* 1.3 63.4 + - - +
60A GLN* 4.6 5.6 - - - +
61A ALA* 3.2 23.6 + - - +
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 5.3 4.3 - - - -
56A PRO* 3.2 7.2 - - + +
57A GLU* 1.3 80.9 - - - +
59A SER* 1.3 59.7 + - - +
61A ALA* 3.4 3.3 + - - +
62A LEU* 3.2 13.3 + - - +
83A GLU 5.7 0.4 - - - +
84A ILE* 3.0 40.7 - - + +
85A GLY 5.4 2.0 - - - +
90A ALA* 4.4 7.4 - - + -
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 3.5 10.2 - - - +
56A PRO* 3.3 31.5 + - - +
57A GLU 3.4 0.2 - - - -
58A ALA* 1.3 74.5 - - - +
60A GLN* 1.3 68.4 + - - +
61A ALA 3.1 1.6 - - - -
62A LEU* 3.2 4.1 + - - +
63A LEU* 3.0 23.7 + - - +
90A ALA* 3.0 34.1 - - - -
93A PRO* 4.1 8.2 - - - +
94A LEU* 3.8 12.0 - - - +
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.4 19.5 - - + +
27A ARG* 2.7 33.6 + - - +
52A PHE* 2.9 53.1 + - + +
53A ALA* 3.3 23.4 + - - +
55A LEU* 3.6 23.9 + - + +
56A PRO 3.0 15.9 + - - +
57A GLU* 4.1 2.2 - - - +
59A SER* 1.3 77.6 + - - +
61A ALA* 1.3 61.8 + - - +
63A LEU* 3.4 2.8 + - - +
64A VAL* 3.2 27.2 + - - +
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 3.6 20.0 - - + -
22A TYR* 3.1 38.4 - - + +
23A LEU* 3.8 6.9 - - + +
57A GLU 3.2 17.6 + - - +
58A ALA 3.4 6.1 - - - +
59A SER 3.1 0.8 - - - -
60A GLN* 1.3 75.7 - - - +
62A LEU* 1.3 65.8 + - - +
64A VAL 3.3 1.7 + - - -
65A ARG* 3.1 19.4 + - - +
84A ILE* 3.8 6.5 - - + -
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ALA 3.2 6.6 + - - +
59A SER* 3.2 10.8 + - - +
61A ALA* 1.3 75.1 - - - +
63A LEU* 1.3 67.7 + - - +
65A ARG* 2.9 14.8 + - + +
66A MET* 3.0 33.1 + - + +
79A LEU* 4.1 31.9 - - + +
81A TYR* 4.4 12.1 - - + -
84A ILE* 3.3 21.4 - - + +
87A THR* 4.1 27.6 - - + +
90A ALA* 4.2 10.3 - - + -
91A VAL* 4.1 16.6 - - + +
94A LEU* 4.7 4.5 - - + -
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 5.9 2.0 - - + -
48A PHE* 4.7 7.9 - - + -
52A PHE* 3.7 30.7 - - + -
55A LEU* 4.2 2.2 - - + -
59A SER 3.0 15.9 + - - +
60A GLN 3.7 5.8 - - - +
62A LEU* 1.3 75.3 - - - +
64A VAL* 1.3 57.4 + - - +
66A MET* 3.3 6.9 + - - +
67A VAL* 2.9 51.6 + - + +
94A LEU* 3.8 34.0 - - + +
99A TRP* 4.3 14.8 - - + -
100A VAL* 5.7 0.7 - - + -
166A LEU* 3.9 23.3 - - + -
172A CYS* 5.4 3.1 - - - -
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A TYR* 3.4 36.3 - - + +
23A LEU* 3.9 9.2 - - + -
26A PHE* 3.4 46.0 - - + -
52A PHE* 4.4 2.7 - - + -
60A GLN 3.2 13.5 + - - +
61A ALA 3.8 7.2 - - - +
62A LEU 3.2 0.6 - - - -
63A LEU* 1.3 73.8 - - + +
65A ARG* 1.3 61.3 + - - +
67A VAL* 3.8 6.5 - - + +
68A MET* 2.9 43.3 + - + +
187A TRP* 5.7 1.8 - - + -
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Residues in contact with ARG 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PRO 4.9 1.4 + - - -
21A TYR* 4.4 11.5 + - - -
22A TYR* 3.2 39.8 + - - +
61A ALA 3.1 15.3 + - - +
62A LEU* 2.9 11.8 + - + +
64A VAL* 1.3 76.6 - - - +
66A MET* 1.3 62.7 + - + +
68A MET* 3.2 24.0 + - - +
69A ARG* 3.0 29.5 + - - +
79A LEU* 5.6 0.7 - - + -
81A TYR* 3.2 58.8 - - + -
83A GLU* 2.8 33.1 + - - -
84A ILE* 4.6 0.4 - - + -
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Residues in contact with MET 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 3.0 39.0 + - + +
63A LEU* 3.9 7.0 - - - +
65A ARG* 1.3 72.9 - - - +
67A VAL* 1.3 67.1 + - - +
69A ARG* 3.3 17.1 + - - +
71A GLY 4.1 2.8 - - - +
74A PHE* 3.8 36.9 - - + -
79A LEU* 3.4 41.5 - - + -
91A VAL* 4.6 7.6 - - + -
94A LEU* 5.5 0.9 - - + -
100A VAL* 4.1 23.3 - - + -
164A TYR* 4.5 14.8 - - + -
166A LEU* 3.5 22.4 - - + +
169A MET* 5.1 0.7 - - - +
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Residues in contact with VAL 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 5.5 7.2 - - + -
63A LEU* 2.9 39.2 + - + +
64A VAL* 4.0 6.7 - - - +
66A MET* 1.3 77.5 - - - +
68A MET* 1.3 60.9 + - - +
69A ARG 3.6 4.9 + - - +
166A LEU* 3.7 12.6 - - + -
169A MET* 4.0 17.1 - - - +
172A CYS* 3.8 37.0 - - + -
173A ASP* 5.8 1.8 - - - +
187A TRP* 3.9 23.0 + - + +
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Residues in contact with MET 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TYR* 5.6 3.4 - - + +
22A TYR* 4.4 16.4 - - + -
64A VAL* 2.9 34.7 + - + +
65A ARG* 3.8 33.9 - - - +
66A MET 3.1 0.2 - - - -
67A VAL* 1.3 76.0 - - - +
69A ARG* 1.3 62.5 + - + +
186A ASP* 5.1 7.1 - - - +
187A TRP* 3.6 39.7 - - + -
188A SER* 5.5 3.8 - - - +
191A VAL* 6.3 2.9 - - - -
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Residues in contact with ARG 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG 3.0 16.8 + - - +
66A MET* 3.3 11.4 + - - +
67A VAL 3.8 4.5 - - - +
68A MET* 1.3 83.7 - - + +
70A LYS* 1.3 69.7 + - - +
71A GLY 3.4 4.0 + - - +
74A PHE* 3.9 31.0 - - + -
78A LYS* 2.5 55.7 + - - +
79A LEU* 4.1 6.5 - - - +
81A TYR* 3.2 35.8 + - - +
169A MET* 5.7 1.9 - - - +
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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
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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