Contacts of the helix formed by residues 85 - 95 (chain B) in PDB entry 1B3U
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 VAL 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B THR* 3.3 37.5 - - + +
79B VAL* 4.2 7.0 - - - -
81B GLY 3.2 6.3 + - - +
82B PRO* 3.1 35.2 + - + +
84B TYR* 1.3 77.1 - - - +
86B HIS* 1.3 60.7 + - - +
87B CYS 3.0 1.9 + - - -
88B LEU* 3.2 20.5 + - + +
89B LEU 4.4 0.2 + - - -
114B ILE* 4.1 17.9 - - + +
117B GLU* 4.1 12.8 - - + +
118B HIS* 4.0 23.7 - - + +
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Residues in contact with HIS 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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82B PRO 5.0 1.0 + - - -
83B GLU 4.0 16.2 + - - -
84B TYR* 3.0 11.9 + + - -
85B VAL* 1.3 78.7 - - - +
87B CYS* 1.3 77.0 + - - +
88B LEU 3.0 1.1 - - - -
89B LEU* 3.0 29.1 + - + +
90B PRO* 3.6 3.8 - - - +
118B HIS* 3.8 18.8 + - + +
122B ASP* 5.0 7.9 + - - -
126B HIS* 3.3 60.3 + + + +
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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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47B ARG* 4.0 23.6 - - - +
51B LEU* 3.6 29.5 - - + +
79B VAL* 4.3 6.3 - - + -
84B TYR* 2.9 23.0 + - - +
86B HIS* 1.3 96.6 - - - +
88B LEU* 1.3 60.6 + - - +
89B LEU 3.3 0.2 - - - -
90B PRO* 3.5 13.4 - - - +
91B PRO* 3.7 5.7 - - - +
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Residues in contact with LEU 88 (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 LEU* 4.2 26.5 - - + -
72B LEU* 3.6 31.4 - - + +
75B PHE* 4.0 19.7 - - + +
76B THR* 4.0 26.7 - - - +
79B VAL* 4.7 12.1 - - + -
85B VAL* 3.2 21.7 + - + +
86B HIS 3.0 1.0 - - - -
87B CYS* 1.3 79.1 - - - +
89B LEU* 1.3 64.3 + - - +
90B PRO 3.5 0.7 - - - -
91B PRO* 3.1 17.3 - - + +
92B LEU* 3.4 20.2 + - + +
114B ILE* 4.0 15.3 - - + -
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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
----------------------------------------------------------
86B HIS* 3.0 18.2 + - + +
88B LEU* 1.3 78.4 - - - +
90B PRO* 1.3 65.7 - - + +
92B LEU* 3.3 3.6 + - - +
93B GLU* 2.8 33.9 + - - +
111B LEU* 3.9 14.4 - - + +
114B ILE* 4.1 11.4 - - + -
118B HIS* 4.1 12.3 - - - +
126B HIS* 3.9 41.7 - - + +
127B PHE* 4.0 19.1 - - + +
130B LEU* 3.8 29.3 - - + +
133B ARG* 5.5 4.5 - - - +
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Residues in contact with PRO 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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55B THR* 3.8 24.2 - - + +
86B HIS 3.6 7.0 - - - +
87B CYS* 3.5 16.4 - - - +
89B LEU* 1.3 94.5 - - + +
91B PRO* 1.3 66.9 - - + +
93B GLU* 3.3 12.4 + - + +
94B SER* 3.2 17.7 + - - -
133B ARG* 6.2 1.3 - - - +
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Residues in contact with PRO 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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51B LEU* 4.6 11.0 - - + +
54B LEU* 4.4 11.0 - - + +
55B THR* 3.6 30.9 - - + +
72B LEU* 4.0 28.0 - - + -
87B CYS 3.7 6.5 - - - +
88B LEU* 3.1 27.4 - - + +
90B PRO* 1.3 99.6 - - + +
92B LEU* 1.3 59.2 + - - +
94B SER* 3.4 4.9 + - - -
95B LEU* 3.3 26.0 + - + +
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Residues in contact with LEU 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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69B ALA* 4.1 7.2 - - - +
72B LEU* 3.7 38.1 - - + -
73B GLY* 5.2 0.2 - - - -
88B LEU* 3.6 20.0 - - + +
89B LEU 3.3 1.6 + - - +
91B PRO* 1.3 75.3 - - - +
93B GLU* 1.3 65.7 + - - +
95B LEU* 3.3 4.4 + - + +
96B ALA* 2.9 24.5 + - - +
107B ALA* 3.9 18.6 - - + +
110B SER* 4.0 26.9 - - - -
111B LEU* 3.6 35.7 - - + +
114B ILE* 4.0 17.9 - - + -
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Residues in contact with GLU 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 LEU 2.8 17.1 + - - +
90B PRO* 3.4 12.2 - - - +
92B LEU* 1.3 76.8 - - - +
94B SER* 1.3 65.4 + - - +
96B ALA* 3.2 16.6 + - - +
97B THR* 3.3 15.2 + - - +
111B LEU* 5.1 2.2 - - - +
130B LEU* 3.4 25.5 - - + +
133B ARG* 3.1 45.1 + - - +
134B LEU* 4.0 16.4 - - + +
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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
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54B LEU 5.7 0.9 - - - -
55B THR* 3.5 26.0 + - - -
90B PRO 3.2 8.9 + - - -
91B PRO* 3.5 10.3 - - - -
92B LEU 3.2 0.2 - - - -
93B GLU* 1.3 79.6 - - - +
95B LEU* 1.3 59.1 + - - +
97B THR* 2.9 27.6 + - - -
98B VAL* 3.5 9.7 + - - +
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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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54B LEU 6.0 1.1 - - - +
58B ILE* 5.7 1.1 - - + -
65B LEU* 4.0 40.4 - - + +
68B LEU* 4.0 14.8 - - + -
69B ALA* 3.9 22.7 - - + +
72B LEU* 3.6 31.0 - - + -
91B PRO 3.3 8.4 + - - +
92B LEU* 3.3 8.5 + - + +
94B SER* 1.3 79.4 - - - +
96B ALA* 1.3 59.4 + - - +
97B THR 3.2 1.6 + - - -
98B VAL* 3.7 21.3 + - + +
103B VAL* 3.8 12.8 - - + +
104B ARG* 3.8 14.6 - - - -
107B ALA* 4.0 11.2 - - + -
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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