Contacts of the helix formed by residues 89 - 103 (chain B) in PDB entry 2HKU
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 THR 89 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ALA* 3.9 0.3 - - - +
88B GLU* 1.3 89.1 - - + +
90B VAL* 1.3 54.5 + - - +
92B ASP* 3.0 23.9 + - - +
93B TYR* 2.8 34.5 + - - +
206B ARG 3.4 13.6 + - - -
207B ASN* 3.3 24.4 + - - +
208B THR 3.3 10.3 - - - +
209B SER* 4.1 7.2 - - - +
210B ILE* 3.7 6.8 - - - +
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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
----------------------------------------------------------
89B THR* 1.3 72.9 - - - +
91B GLY* 1.3 58.9 + - - +
93B TYR* 3.3 3.2 + - - +
94B THR* 2.9 38.4 + - - +
147B THR* 4.0 25.1 - - + +
148B LEU* 4.1 19.3 - - + -
151B THR* 3.8 25.1 - - + -
196B PHE* 5.4 1.3 - - + -
201B ILE* 4.5 17.7 - - + -
205B VAL 3.5 22.0 - - - +
206B ARG* 3.6 5.6 + - - -
208B THR 3.1 7.3 + - - +
210B ILE* 3.8 10.7 - - + +
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Residues in contact with GLY 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B VAL* 1.3 70.0 - - - +
92B ASP* 1.3 63.8 + - - +
94B THR* 3.4 2.6 + - - -
95B GLU* 3.0 34.7 + - - +
196B PHE* 3.8 21.7 - - - -
206B ARG* 2.8 28.7 + - - -
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Residues in contact with ASP 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B THR 4.4 0.2 - - - +
87B ALA* 3.1 11.7 - - + -
88B GLU* 2.9 30.1 + - + +
89B THR* 3.0 27.2 + - + +
91B GLY* 1.3 75.7 - - - +
93B TYR* 1.3 62.0 + - - +
95B GLU* 3.1 11.4 + - - +
96B LYS* 3.0 47.0 + - - +
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Residues in contact with TYR 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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81B GLU* 5.1 5.7 + - - +
84B ALA* 3.3 40.0 - - + +
85B ALA* 4.9 2.7 - - - -
87B ALA* 3.2 14.9 - - + +
89B THR 2.8 20.2 + - - +
90B VAL 3.4 4.7 - - - +
92B ASP* 1.3 72.2 - - - +
94B THR* 1.3 65.5 + - - +
95B GLU 3.3 0.2 + - - -
96B LYS 3.4 0.2 + - - -
97B LEU* 2.8 64.0 + - + +
143B ALA* 3.4 26.6 - - - +
144B LEU* 6.0 0.4 - - - -
147B THR* 3.3 35.2 + - + -
210B ILE* 3.6 15.0 - - + -
214B PG4 5.0 4.3 - - - -
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B VAL* 2.9 22.4 + - - +
91B GLY 3.7 5.2 - - - -
92B ASP 3.4 0.2 - - - -
93B TYR* 1.3 83.7 - - - +
95B GLU* 1.3 56.8 + - - +
97B LEU* 4.4 4.9 - - + -
98B VAL* 2.9 42.1 + - + +
166B PHE* 6.0 1.1 - - + -
192B VAL* 4.1 9.6 - - + -
195B ILE* 4.1 24.5 - - + -
196B PHE* 3.7 29.3 - - + -
201B ILE* 5.2 3.8 - - + +
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLY* 3.0 24.4 + - - +
92B ASP* 3.1 10.0 + - - +
94B THR* 1.3 75.7 - - - +
96B LYS* 1.3 60.5 + - + +
98B VAL* 4.3 0.2 - - - +
99B GLY* 2.8 28.1 + - - -
192B VAL* 3.8 31.3 - - + +
196B PHE* 5.0 5.2 - - - -
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Residues in contact with LYS 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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83B ASP* 3.1 27.3 - - + +
84B ALA* 3.8 16.8 - - + -
86B THR* 4.0 17.3 - - - +
87B ALA* 4.4 7.2 - - + +
92B ASP* 3.0 40.5 + - - +
93B TYR 3.7 3.4 - - - +
95B GLU* 1.3 74.9 - - + +
97B LEU* 1.4 65.3 + - - +
99B GLY* 4.5 1.3 - - - +
100B SER* 2.9 24.8 + - - -
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ALA* 3.7 34.3 - - + +
81B GLU* 4.0 9.6 - - + +
84B ALA* 4.2 4.5 - - + -
93B TYR* 2.8 50.7 + - + +
94B THR* 3.2 6.7 + - + +
96B LYS* 1.4 76.8 - - - +
98B VAL* 1.3 62.1 + - + +
100B SER* 3.2 3.3 + - - -
101B LEU* 3.2 23.9 + - + +
166B PHE* 3.7 22.9 - - + -
214B PG4 3.6 39.5 - - - +
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Residues in contact with VAL 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 THR* 2.9 27.0 + - + +
97B LEU* 1.3 72.7 - - + +
99B GLY* 1.3 65.5 + - - +
100B SER 3.1 0.3 + - - -
101B LEU* 3.1 6.3 + - - +
102B LEU* 2.9 51.1 + - + +
166B PHE* 4.2 16.2 - - + -
170B ILE* 4.2 6.7 - - + -
188B LEU* 4.9 1.3 - - - +
191B ALA* 4.1 9.6 - - + -
192B VAL* 3.8 22.2 - - + +
195B ILE* 3.9 22.9 - - + -
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Residues in contact with GLY 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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95B GLU 2.8 23.7 + - - -
96B LYS* 3.9 1.1 - - - -
98B VAL* 1.3 73.1 - - - +
100B SER* 1.3 57.5 + - - +
102B LEU 3.9 0.2 - - - -
103B GLY* 3.0 26.2 + - - -
104B PRO* 4.0 2.9 - - - +
188B LEU* 4.1 28.6 - - - +
192B VAL* 5.2 0.6 - - - +
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Residues in contact with SER 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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76B ALA 4.7 1.2 + - - -
79B ARG* 4.0 3.8 - - - +
80B ALA* 3.4 24.8 + - - +
83B ASP* 2.7 27.3 + - - -
96B LYS 2.9 18.7 + - - -
97B LEU 3.4 4.7 - - - -
98B VAL 3.1 0.2 - - - -
99B GLY* 1.3 75.2 - - - +
101B LEU* 1.4 63.6 + - - +
103B GLY 3.2 5.0 + - - -
104B PRO* 3.5 13.4 - - - +
105B GLY* 2.9 28.0 + - - -
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Residues in contact with LEU 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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73B VAL* 5.7 0.7 - - + +
76B ALA* 3.9 19.5 - - + +
77B GLY* 4.2 7.2 - - - -
80B ALA* 3.7 21.5 - - + -
97B LEU* 3.2 15.1 + - + +
98B VAL 3.1 5.8 + - - +
100B SER* 1.4 75.3 - - - +
102B LEU* 1.3 64.6 + - + +
103B GLY 3.3 0.2 - - - -
105B GLY* 3.2 4.8 - - - +
106B ALA* 2.8 30.7 + - - -
109B VAL* 3.9 19.0 - - + +
166B PHE* 3.6 37.7 - - + -
167B TRP* 4.1 15.9 - - + -
170B ILE* 4.1 17.3 - - + -
174B VAL* 4.3 1.4 - - - +
214B PG4 5.7 1.1 - - - +
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Residues in contact with LEU 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 VAL* 2.9 23.5 + - + +
99B GLY 3.9 1.3 - - - +
101B LEU* 1.3 81.0 - - + +
103B GLY* 1.3 58.3 + - - +
106B ALA* 3.4 16.6 - - - +
170B ILE* 3.9 26.7 - - + +
173B LEU* 4.7 4.9 - - + -
174B VAL* 3.8 23.1 - - + -
177B LYS* 4.3 28.6 - - + +
188B LEU* 4.9 20.6 - - + +
191B ALA* 3.1 36.3 - - + -
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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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99B GLY 3.0 13.1 + - - -
100B SER 3.2 1.0 + - - -
102B LEU* 1.3 77.7 - - - +
104B PRO* 1.3 74.4 - - - +
105B GLY 3.1 0.4 - - - -
106B ALA* 3.2 15.4 + - - +
107B PRO* 3.9 4.9 - - - +
188B LEU* 6.1 2.9 - - - -
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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