Contacts of the helix formed by residues 88 - 104 (chain B) in PDB entry 2YNU
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 SER 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B SER* 4.5 1.6 + - - -
59B LYS* 4.0 17.3 - - - -
86B PRO* 3.3 1.9 - - - +
87B TRP* 1.3 81.3 - - - +
89B GLU* 1.3 55.6 + - - +
90B GLU* 3.1 17.4 + - - +
91B ASP* 3.0 29.8 + - - +
92B THR* 2.8 37.8 + - - -
119B GLU* 5.6 0.2 - - - -
123B ALA* 4.0 8.5 - - - -
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Residues in contact with GLU 89 (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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88B SER* 1.3 75.1 - - - +
90B GLU* 1.3 66.0 + - + +
92B THR* 4.3 4.7 - - - -
93B LYS* 3.0 45.0 + - - +
123B ALA* 4.6 14.1 + - - +
124B GLY* 5.2 0.2 - - - -
126B LYS* 3.6 35.9 + - - +
127B LEU* 3.6 30.3 + - + +
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Residues in contact with GLU 90 (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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88B SER* 3.1 12.4 + - - +
89B GLU* 1.3 84.2 + - + +
91B ASP* 1.3 65.6 + - - +
93B LYS* 3.2 18.9 + - + +
94B LEU* 3.0 29.2 + - + +
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Residues in contact with ASP 91 (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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40B LYS 4.2 9.5 - - - +
41B PRO* 4.3 4.0 - - - +
42B LEU* 3.3 42.9 + - + +
57B SER* 3.0 18.0 + - - +
58B PHE 4.3 8.1 + - - +
86B PRO* 3.7 19.0 - - + +
88B SER* 3.0 17.2 + - - +
90B GLU* 1.3 74.1 - - - +
92B THR* 1.3 61.3 + - - +
94B LEU* 3.3 14.1 + - - +
95B LEU* 3.0 23.6 + - - +
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Residues in contact with THR 92 (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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82B ILE* 6.0 2.0 - - + -
85B THR* 4.7 2.7 - - - -
86B PRO* 3.6 27.4 - - + +
88B SER 2.8 23.9 + - - -
89B GLU 3.7 5.6 - - - -
91B ASP* 1.3 73.2 - - - +
93B LYS* 1.3 65.9 + - - +
95B LEU* 2.9 14.3 + - + +
96B LEU* 3.0 21.2 + - + +
124B GLY* 3.5 31.7 + - - +
127B LEU* 3.8 16.2 - - + -
128B LEU* 4.6 10.3 - - + -
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Residues in contact with LYS 93 (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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89B GLU* 3.0 35.7 + - - +
90B GLU* 3.2 17.2 + - + +
92B THR* 1.3 75.6 - - - +
94B LEU* 1.3 65.3 + - + +
96B LEU* 3.3 7.7 + - - +
97B SER* 3.1 24.5 + - - -
127B LEU* 3.5 33.9 - - + +
131B LYS* 6.0 2.9 - - - +
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Residues in contact with LEU 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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41B PRO* 4.4 11.9 - - + -
42B LEU* 3.7 24.1 - - + +
90B GLU* 3.0 15.0 + - + +
91B ASP* 3.4 28.7 - - - +
92B THR 3.2 0.2 - - - -
93B LYS* 1.3 74.8 - - + +
95B LEU* 1.3 61.2 + - - +
97B SER* 3.3 10.0 + - - +
98B TRP* 2.9 27.7 + - - +
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Residues in contact with LEU 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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42B LEU* 3.5 16.8 - - + -
44B VAL* 4.0 18.6 - - + -
55B HIS* 3.7 23.8 - - + +
73B VAL* 4.0 19.7 - - + -
82B ILE* 3.7 29.7 - - + +
86B PRO* 3.6 27.8 - - + -
91B ASP 3.0 12.1 + - - +
92B THR* 2.9 11.0 + - + +
94B LEU* 1.3 77.6 - - - +
96B LEU* 1.3 62.8 + - - +
98B TRP* 3.2 10.7 - - + +
99B ALA* 3.1 22.3 + - - +
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Residues in contact with LEU 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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82B ILE* 4.2 14.1 - - + -
92B THR* 3.0 13.7 + - + +
93B LYS* 3.4 9.9 - - - +
95B LEU* 1.3 78.8 - - - +
97B SER* 1.3 56.8 + - - +
99B ALA* 3.4 3.0 + - - +
100B THR* 3.0 36.5 + - + +
109B VAL* 4.1 22.0 - - + -
127B LEU* 4.3 18.2 - - + -
128B LEU* 3.5 36.1 - - + -
131B LYS* 3.9 31.0 - - + +
134B ILE* 4.1 8.3 - - + -
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Residues in contact with SER 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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93B LYS 3.1 14.3 + - - -
94B LEU* 3.7 14.3 - - - +
95B LEU 3.3 0.2 - - - -
96B LEU* 1.3 72.7 - - - +
98B TRP* 1.3 68.3 + - - +
100B THR* 3.6 7.9 - - - -
102B ASP* 2.8 40.7 + - - +
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Residues in contact with TRP 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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42B LEU* 5.6 0.2 - - + -
44B VAL* 3.6 34.8 + - + +
53B TYR* 3.4 53.2 - + - -
73B VAL* 4.3 21.1 - - + -
94B LEU 2.9 14.2 + - - +
95B LEU* 3.2 24.2 - - + +
97B SER* 1.3 78.6 - - - +
99B ALA* 1.3 77.9 + - + +
102B ASP* 4.9 0.4 - - - -
104B ARG* 2.9 75.7 + - - +
106B TYR* 3.8 26.0 - + - -
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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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73B VAL* 5.7 2.2 - - + -
80B ALA* 4.9 4.5 - - + -
82B ILE* 6.2 1.6 - - + -
95B LEU 3.1 12.3 + - - +
96B LEU 3.8 1.3 - - - +
97B SER 3.1 1.0 - - - -
98B TRP* 1.3 91.7 - - + +
100B THR* 1.3 63.0 + - - +
104B ARG 3.3 5.7 + - - -
106B TYR* 3.0 43.8 + - + +
109B VAL* 3.7 28.5 - - + -
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Residues in contact with THR 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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96B LEU* 3.0 23.8 + - + +
97B SER* 3.4 9.4 + - - -
99B ALA* 1.3 73.3 - - + +
102B ASP* 1.3 65.0 + - - +
104B ARG 3.0 5.2 - - - -
105B GLY* 2.9 18.4 + - - -
106B TYR 3.9 13.2 - - - +
109B VAL* 5.2 6.7 - - + +
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Residues in contact with ASP 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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97B SER* 2.8 33.0 + - - +
98B TRP* 4.0 4.0 - - - +
100B THR* 1.3 81.5 + - - +
104B ARG* 1.3 68.6 + - - +
105B GLY 3.5 0.7 + - - -
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Residues in contact with ARG 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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53B TYR* 6.0 0.4 - - - -
98B TRP* 2.9 77.2 + - - +
99B ALA 3.3 3.7 + - - +
100B THR 3.0 0.8 - - - -
102B ASP* 1.3 88.1 - - - +
105B GLY* 1.3 55.6 + - - +
106B TYR* 3.1 49.2 - - + +
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Residues in contact with GLY 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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78B ASN* 3.0 25.8 + - - +
100B THR* 2.9 14.5 + - - -
102B ASP 3.5 1.4 + - - -
104B ARG* 1.3 77.3 - - - +
106B TYR* 1.3 61.5 + - - +
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Residues in contact with TYR 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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53B TYR* 4.2 10.0 + - - -
75B LEU* 3.9 38.5 - - + +
77B ASN 5.0 0.7 - - - -
78B ASN* 3.1 25.8 - - + +
80B ALA* 4.1 14.4 - - + -
98B TRP* 3.8 30.1 - + - -
99B ALA* 3.0 27.5 + - + +
100B THR* 3.9 14.9 - - - +
104B ARG* 3.1 39.7 - - + +
105B GLY* 1.3 80.8 - - - +
107B GLN* 1.3 61.7 + - - +
109B VAL 3.7 2.1 + - - -
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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