Contacts of the helix formed by residues 79 - 94 (chain B) in PDB entry 1W1J
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 ASN 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PRO* 3.4 0.9 - - - +
78B ARG* 1.3 91.2 + - - +
80B VAL* 1.3 65.5 + - - +
81B ALA* 3.2 11.9 - - - +
82B ASP* 2.9 43.7 + - - +
83B VAL* 3.4 13.3 + - - +
127B MET* 3.8 14.7 - - - +
129B ARG* 5.4 7.2 - - - +
229B LYS* 5.4 4.4 + - - -
231B GLU* 5.2 3.4 - - - +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASN* 1.3 73.9 - - - +
81B ALA* 1.3 62.5 + - - +
83B VAL* 3.1 27.2 - - - +
84B GLN* 3.2 8.3 + - - +
127B MET* 3.7 15.8 - - + +
129B ARG* 5.7 2.4 - - - +
143B GLU* 4.7 2.0 - - - +
201B GLU* 3.8 6.3 - - - +
203B VAL* 4.4 9.9 - - + -
209B LEU* 3.9 27.4 - - + -
231B GLU* 3.5 34.9 + - + +
232B ASP* 5.9 1.1 - - - +
263B THR* 4.5 2.5 - - + -
264B LYS* 3.7 26.7 - - - +
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASN* 3.2 9.0 - - - +
80B VAL* 1.3 74.2 - - - +
82B ASP* 1.3 62.8 + - - +
84B GLN* 3.1 15.5 + - - +
85B SER* 2.9 31.1 + - - +
229B LYS* 3.9 20.4 - - + +
231B GLU* 3.3 20.9 + - - +
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Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 3.7 16.8 - - + +
32B VAL* 4.1 7.4 - - + +
77B PRO* 4.0 6.7 - - + -
78B ARG* 2.7 65.0 + - - +
79B ASN* 2.9 22.3 + - - +
81B ALA* 1.3 74.7 - - - +
83B VAL* 1.3 56.7 + - - +
85B SER* 3.5 7.4 + - - -
86B ILE* 2.8 41.9 + - - +
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PRO* 3.9 14.6 - - + +
79B ASN 3.4 16.6 - - - +
80B VAL* 3.1 17.5 - - - +
82B ASP* 1.3 78.1 - - - +
84B GLN* 1.3 59.9 + - - +
86B ILE* 3.7 8.5 - - - +
87B VAL* 3.0 31.6 + - + +
121B LEU* 4.9 4.7 - - + -
123B MET* 4.0 22.2 - - + -
127B MET* 4.2 3.8 - - + -
203B VAL* 3.8 28.0 - - + -
261B ILE* 4.4 17.3 - - + -
263B THR* 4.9 1.3 - - + -
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Residues in contact with GLN 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL 3.2 8.6 + - - +
81B ALA* 3.1 19.0 + - - +
83B VAL* 1.3 75.8 - - - +
85B SER* 1.3 52.4 + - - +
87B VAL* 3.5 5.8 + - - +
88B GLY* 2.8 31.7 + - - -
203B VAL* 4.2 12.8 - - + -
207B GLY* 2.8 31.6 + - - +
208B GLU* 4.1 1.4 - - - +
209B LEU* 3.6 37.9 - - - +
231B GLU* 4.3 10.6 - - - +
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 3.6 27.8 - - - +
81B ALA* 2.9 15.7 + - - +
82B ASP* 3.5 12.5 + - - -
84B GLN* 1.3 72.7 - - - +
86B ILE* 1.3 64.4 + - - +
88B GLY* 3.4 2.3 + - - -
89B LEU* 3.1 28.9 + - - +
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Residues in contact with ILE 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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24B PHE* 4.9 0.8 - - + -
28B ILE* 3.7 25.8 - - + -
31B ILE* 4.8 2.4 - - + +
32B VAL* 4.4 9.4 - - + -
75B VAL* 3.9 19.5 - - + -
77B PRO* 3.9 22.7 - - + -
82B ASP 2.8 30.8 + - - +
83B VAL* 3.7 5.6 - - - +
85B SER* 1.3 71.8 - - - +
87B VAL* 1.3 51.6 + - - +
89B LEU* 2.9 16.3 + - + +
90B ALA* 2.8 31.0 + - - +
97B LEU* 3.9 28.3 - - + -
119B VAL* 5.5 0.7 - - + -
121B LEU* 4.1 19.5 - - + -
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B VAL* 3.0 27.1 + - + +
84B GLN* 3.8 4.9 - - - +
86B ILE* 1.3 72.2 - - + +
88B GLY* 1.3 68.9 + - - +
90B ALA* 3.2 8.5 + - - +
91B ASN* 2.9 25.2 + - - +
97B LEU* 4.0 12.3 - - + -
121B LEU* 5.3 1.3 - - + -
203B VAL* 4.5 3.8 - - + -
204B LEU 4.0 11.2 - - - +
205B ALA* 3.4 26.7 - - - +
207B GLY* 4.0 11.7 - - - +
261B ILE* 3.8 28.9 - - + -
540B ILE* 4.5 5.8 - - + -
541B ILE* 4.6 0.4 - - + -
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Residues in contact with GLY 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLN 2.8 20.7 + - - -
85B SER* 3.8 2.9 - - - -
87B VAL* 1.3 74.0 - - - +
89B LEU* 1.3 57.4 + - - +
91B ASN* 3.3 8.8 + - - +
92B LYS* 3.0 25.9 + - - +
206B ASN 6.1 0.4 - - - -
207B GLY* 5.5 2.6 - - - -
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Residues in contact with LEU 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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24B PHE* 3.7 14.8 - - + -
27B ASP* 3.8 32.1 - - + +
28B ILE* 4.1 26.5 - - + -
31B ILE* 3.7 24.7 - - + -
85B SER 3.1 20.3 + - - +
86B ILE 2.9 6.9 + - - +
88B GLY* 1.3 72.9 - - - +
90B ALA* 1.3 66.2 + - - +
92B LYS* 3.0 12.1 + - + +
93B PHE* 2.8 40.2 + - + -
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Residues in contact with ALA 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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24B PHE* 3.7 12.0 - - + -
86B ILE 2.8 13.4 + - - +
87B VAL 3.6 5.6 - - - +
89B LEU* 1.3 71.2 - - - +
91B ASN* 1.3 52.8 + - - +
94B SER* 2.7 32.7 + - - -
95B PHE* 2.9 30.4 + - + +
97B LEU* 3.6 32.3 - - + -
540B ILE* 3.8 7.9 - - + +
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Residues in contact with ASN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B VAL* 2.9 15.0 + - - +
88B GLY* 3.4 11.4 - - - +
90B ALA* 1.3 74.8 - - - +
92B LYS* 1.3 63.4 + - - +
93B PHE 3.0 1.4 + - - -
94B SER* 3.1 15.6 + - - -
205B ALA 3.0 25.9 + - - +
206B ASN* 4.1 12.7 + - - +
536B ASP* 4.7 2.1 - - - +
537B PRO* 5.8 1.6 - - - +
538B ASN* 3.1 30.4 + - - +
540B ILE* 3.3 22.9 - - - +
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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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23B GLU* 5.5 4.6 + - - -
88B GLY 3.0 12.6 + - - +
89B LEU* 3.0 17.3 + - + +
91B ASN* 1.3 75.3 - - - +
93B PHE* 1.3 83.2 + - + +
94B SER* 3.5 0.4 + - - -
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Residues in contact with PHE 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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16B LEU* 3.3 23.2 - - + +
20B ASP* 3.9 45.8 - - + -
23B GLU* 4.1 36.6 - - - -
24B PHE* 3.4 32.1 - + + -
27B ASP* 4.4 5.6 - - - -
89B LEU* 2.8 33.6 + - + +
92B LYS* 1.3 104.2 - - + +
94B SER* 1.3 71.6 + - - +
95B PHE* 4.3 5.4 - - + -
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Residues in contact with SER 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO* 5.5 0.9 - - - +
14B PRO 5.0 6.6 - - - +
16B LEU* 4.9 5.1 - - - +
90B ALA 2.7 10.5 + - - -
91B ASN 3.1 10.7 + - - -
92B LYS 3.5 0.4 + - - -
93B PHE* 1.3 82.0 - - - +
95B PHE* 1.3 57.0 + - - +
96B PRO* 3.6 9.3 - - - +
538B ASN* 4.2 18.8 + - - +
540B ILE* 3.8 13.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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