Contacts of the helix formed by residues 87 - 94 (chain B) in PDB entry 3RIG
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 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B GLN 3.3 23.1 - - - +
84B ASP* 3.4 10.0 + - - +
85B LEU 2.8 7.9 + - - +
86B ALA* 1.3 74.4 - - - +
88B PRO* 1.3 75.2 - - - +
89B LEU* 4.0 9.5 - - - +
90B ALA* 3.1 25.1 + - - +
91B PHE* 3.1 15.9 + - - +
222B TRP* 3.7 10.3 - - - -
223B PHE* 3.8 16.6 - - + +
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Residues in contact with PRO 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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87B THR* 1.3 85.1 - - - +
89B LEU* 1.3 60.8 + - + +
91B PHE* 3.3 2.5 + - + +
92B ALA* 2.8 29.3 + - - +
217B ARG* 5.2 0.7 - - - +
222B TRP* 3.5 26.7 - - + -
223B PHE 3.4 17.9 - - - +
224B GLY* 5.2 3.6 - - - -
225B GLU* 3.6 27.6 - - + +
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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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87B THR* 3.3 7.6 + - - +
88B PRO* 1.3 77.7 - - + +
90B ALA* 1.3 65.7 + - - +
92B ALA* 4.4 5.8 - - + -
93B HIS* 3.0 51.4 + - + +
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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
----------------------------------------------------------
84B ASP 3.5 16.2 - - - +
85B LEU* 3.7 6.5 - - + +
87B THR* 3.1 25.0 + - - +
89B LEU* 1.3 77.1 - - - +
91B PHE* 1.3 57.6 + - - +
93B HIS* 5.1 1.3 - - - -
94B ASN* 2.8 38.0 + - - +
98B VAL* 3.5 17.4 - - + +
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Residues in contact with PHE 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 THR 3.1 4.7 + - - +
88B PRO 3.3 4.0 + - - +
89B LEU 3.2 0.2 - - - -
90B ALA* 1.3 77.7 - - - +
92B ALA* 1.3 66.4 + - - +
95B PRO* 3.2 36.8 - - + +
98B VAL* 3.5 28.7 - - + +
99B TRP* 3.7 27.1 - + - -
167B THR* 4.2 12.3 - - + -
215B LEU* 3.8 26.5 - - + -
216B LEU 3.6 20.6 - - - -
217B ARG* 3.8 18.6 - - + -
218B PRO* 4.7 0.4 - - + -
222B TRP* 3.5 33.4 - + + -
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Residues in contact with ALA 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 PRO 2.8 20.1 + - - +
89B LEU* 3.4 9.6 + - + +
91B PHE* 1.3 76.3 - - - +
93B HIS* 1.3 73.8 + - + +
95B PRO* 4.2 5.0 - - - +
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Residues in contact with HIS 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* 3.0 45.0 + - + +
90B ALA* 4.3 1.8 - - - +
92B ALA* 1.3 89.5 + - + +
94B ASN* 1.3 64.2 + - + +
95B PRO* 3.8 3.4 - - - +
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Residues in contact with ASN 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 ALA* 2.8 21.0 + - - +
93B HIS* 1.3 77.1 - - + +
95B PRO* 1.4 67.2 - - - +
96B SER* 4.0 8.7 - - - +
97B ARG* 3.2 58.9 + - + +
98B VAL* 3.1 18.2 + - + +
196B ASP* 4.9 4.1 + - - +
198B SER* 6.0 1.4 - - - +
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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