Contacts of the helix formed by residues 86 - 97 (chain B) in PDB entry 3I7K
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 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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836A VAL* 4.3 15.3 - - + +
837A TYR 3.5 16.9 + - - +
838A PRO* 4.8 10.6 + - + +
840A GLU* 2.8 33.6 + - - +
841A ALA* 3.3 15.9 + - - +
842A GLU 4.4 0.6 - - - +
843A PRO* 4.4 10.6 - - - +
87B PHE* 1.3 69.5 + - - +
88B VAL* 2.7 41.0 + - - +
89B SER* 3.2 16.4 + - - +
90B TRP* 3.0 21.2 + - - +
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Residues in contact with PHE 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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841A ALA* 3.2 17.1 + - - +
842A GLU* 5.0 9.0 - - + -
871A TYR* 3.2 45.8 - + - +
910A MET* 4.7 13.2 - - + -
912A LEU* 4.2 25.4 - - + -
928A ARG* 5.2 7.4 - - - -
86B ASN* 1.3 74.0 + - - +
88B VAL* 1.3 58.3 + - - +
90B TRP* 3.0 39.3 + + - +
91B HIS* 2.8 35.3 + - + +
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Residues in contact with VAL 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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812A TYR* 3.6 32.5 - - + -
814A LEU* 4.3 22.6 - - + +
836A VAL* 4.0 10.8 - - + -
843A PRO* 4.2 15.0 - - + -
869A ALA* 4.8 0.2 - - + -
871A TYR* 3.8 31.2 - - + +
86B ASN* 2.7 24.2 + - - +
87B PHE* 1.3 77.7 - - - +
89B SER* 1.3 56.4 - - - +
91B HIS* 3.4 6.2 + - - +
92B ALA* 3.2 21.6 + - + +
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Residues in contact with SER 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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787A GLU* 4.9 13.0 - - - -
812A TYR* 5.0 6.1 - - - -
836A VAL* 6.1 1.3 - - - -
86B ASN* 3.2 21.9 + - - +
88B VAL* 1.3 80.8 - - - +
90B TRP* 1.3 62.7 + - - +
91B HIS 3.2 0.4 - - - -
92B ALA* 3.7 8.7 - - - +
93B ASN* 2.9 41.1 + - - +
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Residues in contact with TRP 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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912A LEU* 5.2 2.9 - - + -
928A ARG* 5.3 5.2 - - - -
953A TRP* 5.0 20.9 - + - -
970A ASN* 5.8 0.9 - - - -
86B ASN 3.0 13.0 + - - +
87B PHE* 3.2 47.1 - + - +
89B SER* 1.3 78.8 + - - +
91B HIS* 1.3 81.6 + - - +
93B ASN* 3.2 10.9 + - + +
94B ARG* 2.8 70.1 + - - +
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Residues in contact with HIS 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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871A TYR* 6.1 1.8 - + + -
912A LEU* 3.5 36.2 + - + +
913A TYR* 3.2 32.8 + + - -
87B PHE* 2.8 20.7 + - + +
88B VAL* 3.7 9.4 - - - +
89B SER 3.2 0.2 - - - -
90B TRP* 1.3 90.7 - - + +
92B ALA* 1.3 63.1 + - - +
94B ARG* 3.2 22.0 + - - +
95B GLN* 3.3 41.9 + - + +
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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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722A ARG* 3.8 41.8 + - - +
787A GLU* 5.6 1.8 - - - +
88B VAL* 3.2 16.0 + - + +
89B SER* 3.6 7.8 + - - +
91B HIS* 1.3 79.2 - - - +
93B ASN* 1.3 64.9 + - - +
95B GLN* 3.5 11.9 + - - +
96B LEU* 3.5 21.0 + - + +
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Residues in contact with ASN 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 SER* 2.9 31.2 + - - +
90B TRP* 3.4 10.5 - - + +
91B HIS 3.2 0.2 - - - -
92B ALA* 1.3 80.4 - - - +
94B ARG* 1.3 50.8 + - - +
96B LEU* 2.9 18.3 + - - +
97B GLY 2.3 28.6 + - - +
98B MET* 3.3 19.2 + - - +
99B PRO* 2.8 27.7 + - - +
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Residues in contact with ARG 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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912A LEU* 4.9 1.6 - - - +
913A TYR* 2.7 26.9 + - - -
928A ARG* 6.2 0.4 - - - +
953A TRP* 3.5 14.3 + - - +
954A MET 2.7 22.8 + - - -
955A SER* 4.1 7.7 - - - +
970A ASN* 3.3 30.4 - - - +
1003A PHE* 3.9 29.8 - - + -
1033A VAL* 4.3 0.9 - - - +
90B TRP* 2.8 54.4 + - + +
91B HIS* 3.2 18.4 + - - +
93B ASN* 1.3 73.1 - - - +
95B GLN* 1.3 58.7 + - + +
97B GLY* 2.6 32.2 + - - +
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Residues in contact with GLN 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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358A PRO* 3.8 9.0 - - - +
360A VAL* 4.0 31.0 + - + +
722A ARG* 5.0 4.9 - - - +
723A LYS* 5.2 11.5 + - - +
913A TYR* 5.0 3.0 - - - -
955A SER 4.8 6.3 + - - -
1003A PHE* 4.7 1.1 - - + -
1005A ASN* 3.0 60.4 + - - +
1033A VAL* 3.4 9.7 - - - +
91B HIS* 3.3 41.1 + - + +
92B ALA* 4.2 6.8 - - - +
93B ASN 3.2 1.0 - - - -
94B ARG* 1.3 77.9 - - + +
96B LEU* 1.3 57.5 + - - +
97B GLY 3.1 1.6 - - - -
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Residues in contact with LEU 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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327A ARG* 3.0 31.9 + - - -
328A LEU* 3.8 5.5 - - + +
358A PRO* 4.1 13.0 - - + +
360A VAL* 3.8 26.5 - - + -
380A GLY 4.1 2.0 - - - +
381A ALA* 3.5 35.2 - - + -
382A PHE* 4.0 22.0 - - + -
720A SER* 5.6 1.3 - - - +
722A ARG* 5.9 10.3 - - - +
1033A VAL* 4.1 4.6 - - - +
92B ALA* 3.5 15.2 + - + +
93B ASN* 2.9 11.2 + - - +
95B GLN* 1.3 77.9 - - + +
97B GLY* 1.3 56.4 + - - +
99B PRO* 3.7 19.1 - - + +
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Residues in contact with GLY 97 (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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327A ARG* 4.5 3.6 - - - -
1003A PHE* 6.3 0.2 - - - -
1033A VAL* 4.2 15.1 - - - +
93B ASN 2.3 18.2 - - - +
94B ARG* 2.6 29.3 + - - +
95B GLN 3.1 1.8 + - - -
96B LEU* 1.3 76.2 - - - +
98B MET* 1.3 55.2 + - - -
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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