Contacts of the helix formed by residues 83 - 98 (chain B) in PDB entry 2UYK
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 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 3.8 30.1 - - + +
78B ILE* 6.0 0.2 - - + -
79B THR* 5.2 0.3 + - - -
80B ASP* 2.8 32.6 + - - +
82B ASN* 1.3 77.5 - - - +
84B PHE* 1.3 58.0 + - - +
85B ALA 3.4 1.8 - - - -
86B THR* 3.2 10.7 + - - -
87B ILE* 2.9 44.3 + - + +
118B LYS* 4.0 20.0 + - - +
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Residues in contact with PHE 84 (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 VAL* 5.9 0.7 - - + -
78B ILE* 4.4 5.8 - - + -
80B ASP 4.0 0.8 + - - -
81B LEU* 3.0 39.7 + - + +
82B ASN 3.3 0.4 - - - -
83B ASP* 1.3 77.8 - - - +
85B ALA* 1.3 58.9 + - - +
87B ILE* 3.7 13.0 - - + -
88B ASN* 2.8 63.2 + - - +
105B ARG* 3.5 16.8 - - - -
107B CYS* 3.2 37.7 - - + -
14C ILE* 5.2 12.1 - - + -
114C PRO* 4.5 16.4 - - + -
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Residues in contact with ALA 85 (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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81B LEU 4.7 0.2 + - - -
82B ASN 4.6 4.7 + - - +
83B ASP 3.4 0.6 - - - -
84B PHE* 1.3 78.4 - - - +
86B THR* 1.3 58.8 + - - +
88B ASN* 3.4 8.7 + - - +
89B GLU* 3.0 28.1 + - - +
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Residues in contact with THR 86 (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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46B VAL* 3.7 21.8 - - + -
47B GLN* 3.5 35.7 - - + +
82B ASN 5.4 1.8 + - - -
83B ASP* 3.2 11.3 + - - -
84B PHE 3.2 0.2 - - - -
85B ALA* 1.3 76.9 - - - +
87B ILE* 1.3 66.3 + - - +
89B GLU* 3.2 6.8 + - - +
90B VAL* 3.1 22.7 + - + +
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Residues in contact with ILE 87 (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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46B VAL* 3.8 22.7 - - + +
50B ALA* 4.3 18.0 - - + +
76B VAL* 4.6 12.6 - - + -
78B ILE* 3.9 25.6 - - + -
83B ASP* 2.9 37.7 + - + +
84B PHE* 3.8 11.9 - - + +
86B THR* 1.3 77.8 - - - +
88B ASN* 1.3 58.4 + - - +
90B VAL* 3.3 3.3 + - - +
91B TYR* 2.9 35.9 + - + +
105B ARG* 5.8 1.1 - - - +
118B LYS 4.9 1.6 - - - +
119B LEU* 4.1 26.2 - - + -
121B ILE* 5.9 0.4 - - + -
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Residues in contact with ASN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PHE* 2.8 54.9 + - - +
85B ALA* 3.6 8.0 - - - +
87B ILE* 1.3 72.7 - - - +
89B GLU* 1.3 57.3 + - - +
91B TYR* 3.6 3.4 - - - +
92B LYS* 2.8 33.3 + - - +
105B ARG* 2.7 40.2 + - - +
14C ILE* 6.3 0.6 - - - +
15C GLY* 4.8 7.0 - - - +
16C PRO* 3.6 15.6 - - + +
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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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85B ALA 3.0 17.5 + - - +
86B THR* 3.2 7.4 + - - +
88B ASN* 1.3 77.0 - - - +
90B VAL* 1.3 63.0 + - + +
92B LYS* 3.8 16.9 - - - +
93B GLN* 3.0 34.4 + - + +
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLN* 4.0 35.9 - - + +
50B ALA* 3.9 8.1 - - + -
51B ARG* 3.7 45.5 + - + +
54B LEU* 4.6 3.1 - - + -
86B THR 3.1 14.1 + - - +
87B ILE 3.7 5.6 - - - +
89B GLU* 1.3 77.4 - - + +
91B TYR* 1.3 58.0 + - - +
93B GLN* 3.3 4.5 + - - +
94B PHE* 2.9 27.9 + - - +
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Residues in contact with TYR 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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50B ALA* 6.2 0.2 - - + -
54B LEU* 3.8 26.9 - - + +
74B MET* 3.4 36.3 - - - +
76B VAL* 3.9 13.7 - - + -
87B ILE* 2.9 24.3 + - + +
88B ASN* 3.6 6.5 - - - +
90B VAL* 1.3 76.7 - - - +
92B LYS* 1.3 61.3 + - - +
94B PHE* 3.2 2.1 + - - +
95B PHE* 3.1 49.6 + + - -
103B PRO* 3.7 11.5 + - + +
105B ARG* 3.2 38.3 - - - +
121B ILE* 4.8 4.0 - - + -
16C PRO* 3.2 36.1 + - + -
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Residues in contact with LYS 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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88B ASN 2.8 22.7 + - - +
89B GLU* 3.8 19.1 - - - +
91B TYR* 1.3 70.4 - - - +
93B GLN* 1.3 59.5 + - - +
95B PHE* 3.2 3.3 + - - +
96B ASP* 2.9 43.7 + - - +
102B TYR* 2.9 39.7 + - - +
15C GLY 5.9 0.6 - - - -
16C PRO* 3.7 25.4 - - + +
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Residues in contact with GLN 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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51B ARG* 5.8 2.0 - - - +
89B GLU* 3.0 28.2 + - + +
90B VAL* 3.9 4.5 - - - +
92B LYS* 1.3 78.2 - - - +
94B PHE* 1.3 52.2 + - - +
96B ASP* 3.6 15.6 - - - +
97B GLU* 2.8 75.6 + - - +
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Residues in contact with PHE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ARG* 3.7 30.7 - - - +
54B LEU* 3.8 50.5 - - + -
55B GLU* 3.6 21.5 - - - -
57B VAL* 6.5 0.4 - - + -
58B LYS* 4.0 7.0 - - + -
68B VAL* 3.8 31.0 - - + -
71B ILE* 5.5 3.1 - - + -
90B VAL 2.9 17.7 + - - +
91B TYR 3.2 5.4 + - - +
93B GLN* 1.3 78.4 - - - +
95B PHE* 1.3 79.5 + + - +
97B GLU* 3.4 4.5 + - - +
98B HIS* 2.8 48.5 + + - -
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Residues in contact with PHE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 4.5 1.8 - - + -
68B VAL* 3.6 36.1 - - + -
71B ILE* 4.5 9.9 - - + -
74B MET* 3.8 15.5 - - + -
91B TYR* 3.1 55.3 + + - -
92B LYS 4.0 0.9 - - - +
94B PHE* 1.3 93.1 - + - +
96B ASP* 1.3 64.2 + - - +
98B HIS* 3.1 7.7 + - - -
100B ALA* 3.0 39.5 + - + +
101B THR 4.1 4.0 - - - -
102B TYR* 3.7 26.5 - + + -
103B PRO* 3.6 31.9 - - + -
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Residues in contact with ASP 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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92B LYS* 2.9 34.2 + - - +
93B GLN* 3.6 20.8 - - - +
95B PHE* 1.3 75.5 - - - +
97B GLU* 1.3 56.5 + - - +
99B GLN* 3.0 23.8 + - - +
100B ALA 5.0 2.4 - - - +
102B TYR* 2.6 34.8 + - - -
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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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51B ARG* 3.4 32.4 + - - -
93B GLN* 2.8 55.2 + - - +
94B PHE 3.7 5.2 - - - +
96B ASP* 1.3 71.8 - - - +
98B HIS* 1.3 65.4 + - + +
99B GLN* 3.3 5.2 + - - +
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Residues in contact with HIS 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ARG* 5.0 5.2 - - - -
55B GLU* 5.0 2.2 - - - -
58B LYS* 2.7 35.4 + - + +
68B VAL* 3.6 34.2 - - + +
69B GLY* 5.3 2.8 + - - +
94B PHE* 2.8 51.2 + + - +
95B PHE 3.1 8.2 + - - +
97B GLU* 1.3 84.2 - - + +
99B GLN* 1.3 70.1 + - - +
100B ALA* 3.1 4.1 + - + +
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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