Contacts of the helix formed by residues 95 - 109 (chain B) in PDB entry 1YE5
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 ASP 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ARG* 6.2 0.2 - - - -
94B LEU* 1.3 77.7 - - - +
96B MET* 1.3 63.8 + - - +
97B GLU* 3.3 8.8 + - - +
98B ASP* 2.7 46.0 + - - +
99B ILE* 3.2 11.4 + - - +
119B ARG* 5.0 3.3 + - - -
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Residues in contact with MET 96 (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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40A VAL* 3.5 23.6 - - + -
43A TYR* 3.4 40.2 - - + +
44A ARG* 3.4 28.5 - - + +
96A MET* 3.3 38.1 - - + -
97A GLU* 3.6 25.1 - - + +
84B GLU* 5.7 1.3 + - - +
94B LEU 3.9 0.4 + - - -
95B ASP* 1.3 74.2 - - - +
97B GLU* 1.3 64.0 + - - +
99B ILE* 3.2 3.2 + - - +
100B ILE* 3.0 25.8 + - + +
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Residues in contact with GLU 97 (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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96A MET* 4.0 13.4 - - - +
10B ASP* 6.0 2.7 - - + -
11B SER* 2.9 31.9 + - - -
40B VAL* 4.3 12.1 - - + +
41B THR* 4.4 3.5 - - - -
44B ARG* 2.7 57.0 + - - +
95B ASP* 3.2 11.0 + - - +
96B MET* 1.3 78.7 - - - +
98B ASP* 1.3 63.0 + - - +
100B ILE* 4.1 0.9 - - - +
101B THR* 2.7 45.7 + - - +
119B ARG* 5.9 0.4 - - - +
120B TYR* 5.7 1.3 - - - +
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Residues in contact with ASP 98 (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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94B LEU* 4.4 18.0 - - + +
95B ASP* 2.7 41.6 + - - +
97B GLU* 1.3 78.3 - - - +
99B ILE* 1.3 62.3 + - - +
101B THR* 3.9 0.8 - - - -
102B ALA* 2.9 28.8 + - - +
119B ARG* 2.8 52.3 + - - +
120B TYR* 3.7 22.6 + - + -
123B ILE* 4.7 2.2 - - - -
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Residues in contact with ILE 99 (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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43A TYR* 4.1 4.0 - - + +
80B ALA* 3.9 28.7 - - + +
83B ILE* 4.7 3.8 - - + -
84B GLU* 3.3 45.1 - - + +
87B LEU* 4.0 24.5 - - + -
94B LEU* 4.1 19.7 - - + +
95B ASP 3.2 15.1 + - - +
96B MET 3.2 6.0 + - - +
98B ASP* 1.3 77.1 - - - +
100B ILE* 1.3 56.1 + - - +
102B ALA* 4.0 0.9 - - - +
103B THR* 2.6 40.2 + - - +
123B ILE* 4.5 10.9 - - + +
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Residues in contact with ILE 100 (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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43A TYR* 4.0 22.0 - - + +
96A MET* 4.6 6.3 - - + -
38B SER* 3.7 10.8 - - - +
40B VAL* 3.6 28.7 - - + -
72B LEU* 4.0 33.9 - - + -
76B ILE* 4.7 4.7 - - + -
80B ALA* 4.1 18.2 - - + -
96B MET* 3.0 29.1 + - + +
97B GLU 4.2 1.8 - - - +
99B ILE* 1.3 75.3 - - - +
101B THR* 1.3 55.2 + - - +
103B THR* 3.8 3.0 - - - -
104B THR* 2.7 42.7 + - - +
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Residues in contact with THR 101 (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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8B THR* 5.3 3.1 - - + +
9B PHE 4.6 2.2 - - - +
10B ASP* 4.3 15.6 - - + +
38B SER* 4.6 6.4 - - - -
40B VAL* 4.9 4.0 - - - +
41B THR* 3.5 21.9 + - - +
97B GLU* 2.7 34.2 + - - +
98B ASP* 3.9 4.7 - - - -
100B ILE* 1.3 77.7 - - - +
102B ALA* 1.3 58.0 + - - +
104B THR* 3.8 4.9 - - - -
105B ALA* 3.0 26.2 + - - +
112B LEU* 4.1 29.8 - - + -
120B TYR* 4.4 4.0 - - - +
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Residues in contact with ALA 102 (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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98B ASP 2.9 18.7 + - - +
99B ILE 4.0 0.2 - - - +
101B THR* 1.3 75.5 - - - +
103B THR* 1.3 66.3 + - - +
105B ALA* 3.1 7.5 + - - +
106B ILE* 2.9 29.7 + - - +
112B LEU* 4.6 1.6 - - - -
120B TYR* 4.4 5.8 - - + -
123B ILE* 3.4 30.5 - - + -
128B LEU* 3.9 21.4 - - + +
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Residues in contact with THR 103 (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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76B ILE* 3.5 33.0 - - + +
79B LYS* 3.5 29.1 - - + +
80B ALA* 3.6 21.2 - - - +
83B ILE* 3.9 8.7 - - + +
99B ILE* 2.6 29.0 + - - +
100B ILE* 3.8 4.3 - - - -
102B ALA* 1.3 75.1 - - - +
104B THR* 1.3 58.2 + - - +
106B ILE* 3.3 11.6 + - - +
107B TYR* 2.9 26.7 + - - +
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Residues in contact with THR 104 (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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36B ASN 5.2 3.6 - - - +
37B LEU 5.1 0.2 - - - -
38B SER* 3.7 29.4 + - - +
70B VAL* 3.9 35.9 - - + -
71B PRO 5.2 0.5 + - - -
72B LEU* 6.1 0.2 - - - -
76B ILE* 3.8 19.8 - - + +
100B ILE* 2.7 23.1 + - - +
101B THR 3.8 3.8 - - - -
102B ALA 3.2 0.2 - - - -
103B THR* 1.3 75.9 - - - +
105B ALA* 1.3 60.0 + - - +
107B TYR* 3.3 5.5 + - - +
108B THR* 2.9 36.9 + - + +
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Residues in contact with ALA 105 (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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8B THR* 4.0 18.4 - - + -
36B ASN 6.2 0.2 - - - -
101B THR 3.0 15.8 + - - +
102B ALA* 3.1 8.3 + - - +
104B THR* 1.3 77.4 - - - +
106B ILE* 1.3 56.1 + - - +
108B THR* 3.4 5.3 + - - -
109B ASN* 2.9 24.6 + - - -
110B SER* 2.9 30.3 + - - +
112B LEU* 4.4 3.1 - - + -
128B LEU* 3.8 17.0 - - + -
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Residues in contact with ILE 106 (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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79B LYS* 4.2 20.2 - - + +
83B ILE* 4.1 13.2 - - + -
102B ALA 2.9 18.8 + - - +
103B THR* 3.6 6.7 - - - +
105B ALA* 1.3 77.4 - - - +
107B TYR* 1.3 62.9 + - - +
109B ASN* 3.2 13.4 + - - +
123B ILE* 3.9 23.1 - - + -
126B PHE* 3.8 29.4 - - + +
127B GLY* 4.0 7.4 - - - +
128B LEU* 3.7 28.7 - - + +
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Residues in contact with TYR 107 (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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70B VAL* 5.1 1.6 - - + -
73B LEU* 3.6 28.6 - - + +
75B ASP* 3.7 38.6 + - + -
76B ILE* 4.0 24.0 - - + -
79B LYS* 5.0 15.9 - - + +
103B THR 2.9 17.0 + - - +
104B THR 3.3 5.6 + - - +
106B ILE* 1.3 80.0 - - - +
108B THR* 1.3 71.0 + - + +
109B ASN* 3.5 1.4 + - - +
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Residues in contact with THR 108 (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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6B ASP* 4.5 6.2 - - - +
36B ASN* 4.1 18.2 + - + +
68B ASN* 5.5 0.7 - - - +
70B VAL* 3.9 27.8 - - + -
104B THR* 2.9 29.5 + - + +
105B ALA* 3.4 2.3 + - - -
107B TYR* 1.3 88.1 - - + +
109B ASN* 1.3 70.4 + - - +
110B SER* 2.6 31.8 + - - -
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Residues in contact with ASN 109 (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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6B ASP* 3.6 21.4 + - - +
105B ALA 2.9 7.5 + - - -
106B ILE* 3.2 11.6 + - - +
107B TYR 3.2 2.2 - - - +
108B THR* 1.3 81.2 - - - +
110B SER* 1.3 57.9 + - - +
111B LEU 4.3 0.3 + - - -
129B ASP* 5.4 3.5 - - - +
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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