Contacts of the helix formed by residues 93 - 107 (chain B) in PDB entry 2YYU
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 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A MET* 3.9 15.3 - - - -
134A GLU* 3.3 11.4 - - - -
135A LEU* 4.6 2.7 - - - -
90B ALA 3.0 12.6 + - - -
91B ALA 3.1 3.0 - - - -
92B GLY* 1.3 78.8 - - - +
94B ARG* 1.3 65.9 + - - -
95B ARG 3.3 2.9 - - - -
96B MET 3.3 2.1 + - - -
97B MET* 3.2 26.8 + - - +
151B LEU* 4.4 2.2 - - - -
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Residues in contact with ARG 94 (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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134A GLU* 2.7 26.5 + - - +
93B GLY* 1.3 71.9 - - - -
95B ARG* 1.3 57.6 + - - +
97B MET* 3.2 1.8 + - - -
98B GLU* 2.9 59.6 + - - +
151B LEU* 4.1 15.2 - - + +
154B GLU* 3.6 43.8 + - - +
155B SER* 3.3 22.5 + - - +
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Residues in contact with ARG 95 (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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129A ARG* 6.2 1.8 - - - +
130A MET* 6.1 3.8 - - - -
134A GLU* 4.6 0.8 + - - -
68B PRO* 3.8 22.1 - - + +
93B GLY* 3.3 0.8 - - - -
94B ARG* 1.3 79.5 - - - +
96B MET* 1.3 56.9 + - - +
98B GLU* 3.4 23.2 + - - +
99B ALA* 3.0 40.6 + - - +
102B GLU* 2.8 35.6 + - - -
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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
----------------------------------------------------------
64B LEU 3.7 16.2 - - - +
65B HIS* 4.1 1.8 - - - -
66B ASP 3.1 39.5 - - - +
68B PRO* 4.0 18.7 - - + +
71B VAL* 3.6 18.6 - - + +
88B VAL* 3.9 18.6 - - + -
89B HIS 3.3 26.5 - - - +
92B GLY* 3.3 32.2 + - - +
93B GLY 3.3 2.0 + - - +
94B ARG 3.2 0.6 - - - -
95B ARG* 1.3 79.3 - - - +
97B MET* 1.3 61.3 + - + +
99B ALA* 3.2 3.8 + - - +
100B ALA* 2.9 26.3 + - - +
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Residues in contact with MET 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 3.4 11.9 - - + -
89B HIS 4.5 1.1 - - - +
90B ALA* 3.3 29.2 - - + +
93B GLY 3.2 16.0 + - - +
94B ARG* 3.2 1.8 + - - +
96B MET* 1.3 84.7 - - + +
98B GLU* 1.3 65.5 + - - +
100B ALA* 3.3 17.1 + - - +
101B ILE* 3.3 18.5 + - - +
119B ALA* 3.0 37.7 - - + -
151B LEU* 4.7 2.9 - - - -
152B ALA* 3.7 23.1 - - - -
155B SER* 3.5 19.3 - - - +
157B LEU* 3.2 19.4 - - + +
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Residues in contact with GLU 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 ARG* 2.9 60.6 + - - +
95B ARG* 3.7 37.7 + - - +
97B MET* 1.3 73.2 - - - +
99B ALA* 1.3 66.0 + - - +
101B ILE* 3.1 6.8 + - - +
102B GLU* 3.0 25.6 + - - +
154B GLU 4.6 1.2 - - - +
155B SER* 3.9 27.9 - - - +
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Residues in contact with ALA 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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68B PRO* 3.4 33.0 - - + +
72B LYS* 3.5 17.3 - - + +
95B ARG* 3.0 30.3 + - - +
96B MET 3.2 8.9 + - - +
98B GLU* 1.3 77.2 - - - +
100B ALA* 1.3 56.2 + - - +
102B GLU* 3.1 8.6 + - - +
103B GLY 2.9 25.3 + - - -
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Residues in contact with ALA 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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71B VAL* 3.8 18.8 - - + +
72B LYS* 4.8 0.4 - - - +
75B MET* 3.5 21.1 - - + +
88B VAL* 4.2 15.7 - - + -
96B MET 2.9 12.3 + - - +
97B MET* 3.3 14.8 - - - +
99B ALA* 1.3 77.1 - - - +
101B ILE* 1.3 60.6 + - - +
103B GLY 3.4 1.0 + - - -
104B LEU* 3.1 29.5 + - - +
117B CYS* 4.5 7.2 - - - -
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Residues in contact with ILE 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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97B MET 3.4 13.0 - - - +
98B GLU* 3.1 8.0 + - - +
100B ALA* 1.3 73.6 - - - +
102B GLU* 1.3 65.4 + - + +
104B LEU* 3.3 7.0 + - + +
105B ASP* 3.1 30.9 + - - +
114B ARG* 3.8 29.6 - - - +
117B CYS* 3.9 25.4 - - + -
155B SER 4.1 11.4 - - - +
156B GLY* 4.0 14.6 - - - +
157B LEU* 3.6 25.1 - - + -
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Residues in contact with GLU 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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72B LYS* 2.9 34.5 + - - +
95B ARG* 2.8 33.9 + - - -
98B GLU* 3.0 16.6 + - - +
99B ALA* 3.1 9.1 + - - +
101B ILE* 1.3 77.1 - - + +
103B GLY* 1.3 56.6 + - - +
105B ASP* 3.4 7.1 + - - +
106B ALA* 3.0 28.8 + - - +
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Residues in contact with GLY 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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72B LYS* 3.3 30.4 - - - +
75B MET* 4.1 0.2 - - - -
76B LYS* 3.2 25.6 - - - +
99B ALA 2.9 11.5 + - - -
100B ALA 3.4 3.1 + - - -
102B GLU* 1.3 77.8 - - - +
104B LEU* 1.3 55.6 + - - +
106B ALA* 3.2 1.3 + - - -
107B GLY 2.9 24.3 + - - -
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Residues in contact with LEU 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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75B MET* 3.7 33.7 - - + +
78B LEU* 5.1 0.4 - - + -
79B ALA* 3.7 15.0 - - + +
86B VAL* 4.2 12.1 - - + -
100B ALA 3.1 16.6 + - - +
101B ILE* 3.6 12.8 - - + +
102B GLU 3.3 0.2 - - - -
103B GLY* 1.3 75.8 - - - +
105B ASP* 1.3 57.5 + - - +
107B GLY 3.2 3.1 + - - -
108B THR* 2.5 33.1 + - - -
114B ARG* 4.0 14.4 - - + +
115B PRO* 3.8 23.3 - - + +
117B CYS* 3.6 36.3 - - + -
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Residues in contact with ASP 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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101B ILE* 3.1 31.2 + - - +
102B GLU* 3.8 6.1 - - - +
104B LEU* 1.3 76.5 - - - +
106B ALA* 1.3 62.8 + - - +
108B THR* 3.2 25.4 + - - +
114B ARG* 3.4 25.1 + - - +
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Residues in contact with ALA 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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72B LYS* 5.3 2.0 - - - -
76B LYS* 3.5 30.6 - - + +
80B ARG* 5.1 2.1 + - - -
102B GLU 3.0 17.3 + - - +
103B GLY 3.4 6.1 - - - +
105B ASP* 1.3 78.2 - - - +
107B GLY* 1.3 56.6 + - - +
108B THR 3.3 2.9 + - - +
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Residues in contact with GLY 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LYS* 3.7 21.9 - - - +
79B ALA* 3.4 23.5 - - - +
80B ARG* 3.8 19.0 + - - +
103B GLY 2.9 11.4 + - - -
104B LEU 3.2 2.8 + - - -
106B ALA* 1.3 75.7 - - - +
108B THR* 1.3 60.4 + - - +
109B PRO* 4.1 4.9 - - - +
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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