Contacts of the helix formed by residues 69 - 83 (chain A) in PDB entry 2YY9
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 PHE 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A VAL* 5.1 2.9 - - + -
65A LEU* 5.0 4.0 - - + -
66A PRO* 3.0 43.9 + - + +
67A ALA 3.0 1.4 - - - -
68A GLY* 1.3 86.9 - - - +
70A ALA* 1.3 64.9 + - - +
71A GLU 3.3 2.9 - - - -
72A ILE* 3.0 15.4 + - + +
73A PHE* 2.8 36.1 + + + +
94A GLN 5.6 1.1 - - - -
97A LEU* 4.7 14.6 - - + -
98A ALA* 3.9 33.4 - - + -
101A GLU* 4.2 16.6 - - + -
102A LEU* 3.5 35.4 - - + -
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Residues in contact with ALA 70 (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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32A VAL* 3.3 26.7 - - + +
33A GLY* 4.3 11.7 - - - -
34A GLY 5.3 0.2 - - - +
35A LEU* 3.8 27.0 - - + +
37A PHE* 5.5 0.3 - - - -
67A ALA 3.2 15.5 + - - +
68A GLY 3.5 0.2 - - - -
69A PHE* 1.3 77.2 - - - +
71A GLU* 1.3 64.3 + - - +
72A ILE 3.2 1.0 + - - -
73A PHE* 3.5 7.8 + - - +
74A GLY 4.7 2.1 + - - -
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Residues in contact with GLU 71 (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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67A ALA 5.0 0.4 + - - -
68A GLY 5.0 3.0 + - - +
69A PHE 3.1 1.2 + - - -
70A ALA* 1.3 78.9 - - - +
72A ILE* 1.3 64.2 + - + +
74A GLY 5.3 0.9 + - - -
75A LEU* 5.3 2.4 - - - +
94A GLN* 3.2 34.7 + - - +
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Residues in contact with ILE 72 (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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68A GLY 5.5 0.4 - - - +
69A PHE* 3.0 14.5 + - + +
71A GLU* 1.3 84.8 - - + +
73A PHE* 1.3 71.6 + - + +
74A GLY 3.3 2.7 - - - -
75A LEU* 3.2 32.3 + - + +
76A LEU* 3.3 14.6 + - + -
91A ASN* 4.1 20.9 - - + -
94A GLN* 4.2 31.0 - - + +
95A VAL* 4.0 21.7 - - + +
98A ALA* 3.7 29.8 - - + -
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Residues in contact with PHE 73 (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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30A LEU* 3.4 34.1 - - + -
32A VAL* 3.6 30.5 - - + -
37A PHE* 3.5 38.8 - + + -
51A PHE* 4.7 7.0 - + - -
65A LEU* 4.8 9.0 - - + -
69A PHE* 2.8 29.2 + + + +
70A ALA 3.5 5.3 + - - +
72A ILE* 1.3 76.9 - - + +
74A GLY* 1.3 63.0 + - - +
76A LEU* 3.3 15.4 + - + +
77A LEU* 2.9 34.8 + - + +
80A PHE* 6.5 0.2 - + - -
98A ALA* 6.5 0.4 - - + -
102A LEU* 4.1 25.4 - - + -
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Residues in contact with GLY 74 (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 ARG* 6.1 0.7 - - - -
37A PHE* 4.0 25.9 - - - -
70A ALA 4.7 2.0 + - - -
71A GLU 5.3 0.6 + - - -
72A ILE 3.3 1.0 - - - -
73A PHE* 1.3 78.1 - - - +
75A LEU* 1.3 56.6 + - - +
77A LEU* 3.3 2.7 + - - +
78A ASP* 2.8 41.4 + - - +
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Residues in contact with LEU 75 (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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71A GLU 5.3 2.2 - - - +
72A ILE* 3.2 30.9 + - + +
74A GLY* 1.3 76.0 - - - +
76A LEU* 1.3 64.4 + - - +
78A ASP* 3.1 12.8 + - - +
79A PHE* 2.9 24.3 + - - +
84A HIS 4.4 2.9 - - - +
85A LEU* 4.4 14.4 - - + +
86A ALA* 3.2 34.8 - - + +
91A ASN* 3.3 27.4 - - - +
95A VAL* 4.3 6.1 - - + -
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Residues in contact with LEU 76 (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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51A PHE* 5.5 0.2 - - + -
72A ILE* 3.3 12.0 + - + +
73A PHE* 3.3 21.1 + - + +
75A LEU* 1.3 80.2 - - - +
77A LEU* 1.3 60.5 + - - +
79A PHE* 3.3 12.1 - - + +
80A PHE* 3.0 61.7 - - + -
85A LEU* 4.6 5.8 - - + +
95A VAL* 4.9 11.4 - - + -
98A ALA* 5.3 9.0 - - + -
99A ALA* 4.7 9.4 - - + +
102A LEU* 3.9 27.1 - - + -
104A VAL* 4.5 7.0 - - + -
107A ALA* 4.2 22.9 - - + -
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Residues in contact with LEU 77 (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 ARG* 3.4 29.8 - - - +
30A LEU* 4.7 0.7 - - + -
37A PHE* 3.8 31.0 - - + -
38A LYS 4.3 9.6 - - - +
39A ALA* 4.5 5.8 - - + -
44A LEU* 3.8 29.6 - - + -
73A PHE* 2.9 31.8 + - + +
74A GLY* 3.8 4.7 - - - +
76A LEU* 1.3 75.6 - - + +
78A ASP* 1.3 66.3 + - - +
80A PHE* 2.9 29.9 + - + +
81A TYR* 3.3 17.8 + - + -
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Residues in contact with ASP 78 (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 ARG* 2.8 26.4 + - - +
21A GLU* 5.4 0.9 - - - +
74A GLY* 2.8 34.0 + - - +
75A LEU* 3.5 13.3 - - + +
77A LEU* 1.3 70.8 - - - +
79A PHE* 1.3 53.7 + - - +
81A TYR 3.0 4.3 + - - -
82A THR* 2.7 47.9 + - + +
84A HIS 4.5 6.1 - - - +
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Residues in contact with PHE 79 (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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47A CYS* 5.1 5.2 - - + -
75A LEU 2.9 12.3 + - - +
76A LEU* 3.3 11.2 - - + +
78A ASP* 1.3 76.2 - - - +
80A PHE* 1.3 76.2 + + - +
83A GLY* 2.7 50.5 + - - -
84A HIS 3.5 15.4 + - - +
85A LEU* 3.6 24.5 - - + -
104A VAL* 4.4 8.3 - - + -
106A GLU* 3.9 36.6 - - + -
107A ALA* 4.4 15.0 - - + -
110A LEU* 3.4 24.7 - - + -
8B HIS* 3.3 13.1 + + - -
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Residues in contact with PHE 80 (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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13A LEU* 4.3 3.1 - - - +
43A VAL* 4.3 14.3 - - + +
44A LEU* 3.6 43.1 - - + -
47A CYS* 4.1 17.3 - - + -
48A SER* 4.3 11.4 - - - -
51A PHE* 4.3 10.3 - + - -
76A LEU* 3.0 47.6 - - + -
77A LEU* 2.9 17.3 + - + +
79A PHE* 1.3 86.5 - + - +
81A TYR* 1.3 64.9 + - + +
104A VAL* 3.7 34.8 - - + -
8B HIS* 2.7 25.4 + - - -
12B VAL* 4.3 5.0 - - - +
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Residues in contact with TYR 81 (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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13A LEU* 3.3 33.4 - - + +
14A GLN* 5.3 0.9 - - - -
16A LEU* 3.8 10.3 - - + -
17A ASN* 3.5 42.5 - - - +
20A ARG* 3.8 27.4 - - + +
39A ALA* 3.6 5.5 - - + +
40A HIS* 2.6 54.5 + + - +
43A VAL* 3.7 27.5 - - + +
44A LEU* 5.6 1.1 - - + -
77A LEU* 3.6 28.7 - - + +
78A ASP 3.0 6.2 + - - +
80A PHE* 1.3 84.3 - + + +
82A THR* 1.3 60.6 + - - +
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Residues in contact with THR 82 (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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13A LEU* 5.0 0.7 - - - -
17A ASN* 3.5 21.1 - - - +
20A ARG* 5.9 0.2 - - - +
78A ASP* 2.7 32.4 + - + +
81A TYR* 1.3 80.2 - - - +
83A GLY* 1.3 62.0 + - - +
84A HIS* 3.2 20.7 + - - +
8B HIS* 3.7 10.2 - - - +
9B SER* 5.4 2.7 + - - -
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Residues in contact with GLY 83 (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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79A PHE* 2.7 38.4 + - - -
82A THR* 1.3 73.8 - - - +
84A HIS* 1.3 58.8 + - - +
85A LEU 4.1 0.3 + - - -
110A LEU* 5.3 1.6 - - - +
8B HIS* 3.3 30.1 - - - +
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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