Contacts of the helix formed by residues 84 - 95 (chain B) in PDB entry 3WOO
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 84 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B THR* 1.3 84.7 + - - +
85B HIS* 1.4 53.8 + - - +
86B ALA* 3.7 1.8 - - - +
87B CYS* 3.0 18.0 + - - +
88B ALA* 2.9 30.0 + - - +
224B ASP* 3.1 23.8 + - - +
225B PHE 4.0 2.0 - - - -
226B ALA* 4.0 1.1 - - - -
657B SER* 3.0 31.3 + - - -
658B GLY* 3.1 10.7 + - - +
671B LEU* 3.7 10.6 - - - +
672B ALA 3.1 12.4 - - - +
673B PHE* 3.2 27.1 + - - +
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Residues in contact with HIS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ASN* 1.4 67.7 - - - +
86B ALA* 1.3 54.1 + - - +
88B ALA 3.1 2.1 + - - -
89B TYR* 2.7 66.3 + + - +
92B ILE* 3.8 23.9 - - + +
102B LEU 5.7 0.2 + - - -
103B ILE* 4.6 7.3 + - + -
201B ALA* 4.4 0.6 - - + +
202B PRO* 3.9 30.6 + - + -
204B GLY* 4.1 20.6 - - - -
207B GLY* 3.7 28.8 + - - +
208B LYS* 4.3 7.4 + - + +
224B ASP* 2.8 13.8 + - - +
225B PHE 3.4 22.9 - - - +
226B ALA* 4.0 4.5 - - - -
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Residues in contact with ALA 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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84B ASN* 3.2 4.5 - - + +
85B HIS* 1.3 79.5 + - - +
87B CYS* 1.3 59.7 + - - +
89B TYR* 3.6 19.5 - - - +
90B GLY 5.0 0.2 + - - -
208B LYS* 6.5 1.1 - - + -
224B ASP* 2.9 23.5 + - - +
1D VAL* 4.3 19.7 - - + -
3D ILE* 3.8 29.1 - - + +
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Residues in contact with CYS 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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67B LEU* 4.3 4.8 - - + +
70B CYS* 2.2 52.1 - - + -
83B THR* 3.3 24.7 - - + +
84B ASN* 3.0 11.6 + - - +
86B ALA* 1.3 79.0 - - - +
88B ALA* 1.3 60.4 + - - +
89B TYR 3.6 0.3 + - - -
90B GLY* 4.5 3.6 + - - -
91B ALA 5.3 0.2 + - - -
228B TYR* 3.6 9.7 + - - -
657B SER* 3.5 24.5 - - - -
3D ILE* 4.6 0.2 - - - -
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B THR* 4.4 2.9 - - + +
84B ASN 2.9 14.7 + - - +
85B HIS 3.4 2.7 - - - +
87B CYS* 1.3 74.1 - - - +
89B TYR* 1.3 64.3 + - - +
90B GLY 3.2 3.1 - - - -
91B ALA* 2.9 6.1 + - - +
92B ILE* 2.9 31.1 + - + +
198B LEU* 4.5 2.7 - - + -
226B ALA* 3.8 22.4 - - + -
228B TYR* 3.4 29.6 - - + +
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Residues in contact with TYR 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 HIS* 2.7 41.2 + + - +
86B ALA* 3.6 17.0 - - - +
87B CYS 3.3 1.8 - - - -
88B ALA* 1.3 71.3 - - - +
90B GLY* 1.3 56.7 + - - +
92B ILE* 3.2 7.9 + - - +
93B GLN* 2.8 32.3 + - + +
103B ILE* 3.7 41.1 - - + +
208B LYS* 4.5 22.7 + - + +
322B ALA* 3.6 39.5 + - - +
323B ALA* 3.8 14.8 - - + -
326B ALA* 4.3 13.5 - - + +
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Residues in contact with GLY 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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86B ALA 5.0 0.2 + - - -
87B CYS 4.5 3.2 + - - -
88B ALA 3.2 0.8 - - - -
89B TYR* 1.3 81.0 - - - +
91B ALA* 1.3 54.8 + - - +
93B GLN* 3.3 3.2 + - - +
94B LEU* 2.9 28.3 + - - +
323B ALA* 4.6 7.4 - - - +
447B ARG* 3.0 29.4 + - - -
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Residues in contact with ALA 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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87B CYS 5.3 0.4 + - - -
88B ALA 2.9 9.4 + - - +
90B GLY* 1.3 74.8 - - - +
92B ILE* 1.3 61.8 + - - +
94B LEU* 3.4 2.3 + - - +
95B ASN* 2.9 31.7 + - - +
118B ALA* 3.4 45.8 - - + +
122B ALA* 5.8 0.2 - - + -
198B LEU* 4.9 7.2 - - + -
228B TYR* 3.9 18.8 + - + +
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Residues in contact with ILE 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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85B HIS* 3.8 23.3 - - + +
88B ALA* 2.9 33.0 + - + +
89B TYR* 3.5 9.2 - - - +
91B ALA* 1.3 74.9 - - - +
93B GLN* 1.3 59.9 + - - +
95B ASN* 3.2 12.3 + - - +
96B SER* 2.7 23.7 + - - -
102B LEU* 3.7 16.1 - - + +
103B ILE* 3.7 34.1 - - + +
107B PHE* 6.1 0.2 - - + -
198B LEU* 3.9 27.6 - - + -
201B ALA* 3.7 24.0 - - + -
226B ALA* 5.0 0.2 - - + -
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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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89B TYR* 2.8 20.8 + - + +
90B GLY 3.6 2.2 - - - +
92B ILE* 1.3 75.6 - - - +
94B LEU* 1.3 78.4 + - - +
96B SER* 3.0 25.0 + - - +
103B ILE* 4.0 12.3 - - + +
319B VAL* 2.9 30.3 - - - +
320B LYS* 3.2 7.8 - - - +
322B ALA* 4.1 5.2 - - + -
323B ALA* 4.0 24.5 - - + +
446B ARG* 2.9 23.6 + - - +
447B ARG* 2.9 35.1 - - - +
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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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90B GLY 2.9 18.4 + - - +
91B ALA* 3.7 4.9 - - - +
92B ILE 3.3 0.2 - - - -
93B GLN* 1.3 78.5 - - - +
95B ASN* 1.3 64.1 + - - +
96B SER 3.4 0.9 + - - +
118B ALA 3.6 23.1 - - - +
119B GLY* 4.1 6.1 - - - -
443B GLN* 3.7 52.9 - - + +
446B ARG* 3.5 37.7 + - + +
447B ARG* 3.4 30.1 - - - +
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Residues in contact with ASN 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ALA* 2.9 24.6 + - - +
92B ILE* 3.2 4.4 + - - +
93B GLN 3.1 1.2 - - - -
94B LEU* 1.3 82.2 - - - +
96B SER* 1.3 57.0 + - - -
97B THR* 4.2 2.1 + - - +
100B ASN* 4.3 5.4 + - - +
102B LEU* 3.4 29.4 - - + +
116B VAL* 3.6 28.9 - - + +
117B SER 2.8 28.3 + - - +
118B ALA* 4.4 2.0 - - - +
198B LEU* 5.1 2.6 - - + +
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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