Contacts of the helix formed by residues 91 - 96 (chain B) in PDB entry 6JKG
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 LEU 91 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ILE* 4.6 9.0 - - + -
67B PHE* 4.1 30.5 - - + -
85B LEU* 4.1 6.3 - - + +
87B SER 3.3 14.1 + - - +
88B ARG 2.9 6.9 + - - +
90B ASP* 1.3 77.8 - - - +
92B TYR* 1.3 52.9 + - - +
93B PRO* 3.2 2.9 - - - -
94B ALA* 2.6 36.6 + - - +
95B LEU* 3.5 25.7 + - + -
127B ASN* 3.4 26.7 - - - +
128B VAL* 3.9 18.4 - - + -
131B THR* 3.1 24.9 - - - +
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Residues in contact with TYR 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 ARG* 2.8 22.1 + - + +
89B GLN* 5.2 1.1 - - - +
91B LEU* 1.3 72.6 - - - +
93B PRO* 1.3 74.6 - - + +
94B ALA 2.9 1.4 + - - -
95B LEU* 2.9 18.1 + - - +
96B LYS* 3.1 47.7 + - + +
131B THR* 4.5 9.6 + - + -
134B GLU* 4.4 18.8 + - + +
135B ALA* 3.8 35.9 - - + -
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Residues in contact with PRO 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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81B PHE* 3.2 25.9 - - + -
89B GLN 3.3 23.6 - - - +
90B ASP* 4.0 13.9 - - - +
92B TYR* 1.3 101.2 - - + +
94B ALA* 1.3 59.0 + - - +
95B LEU 3.6 0.2 + - - -
96B LYS* 4.4 8.2 + - + +
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Residues in contact with ALA 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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41B THR* 3.4 23.8 + - + +
65B ASN* 4.3 9.8 + - - +
67B PHE* 3.8 24.5 - - + -
81B PHE* 3.5 35.7 - - + -
90B ASP 5.1 0.7 - - - +
91B LEU 2.6 20.3 + - - +
93B PRO* 1.3 75.0 - - - +
95B LEU* 1.3 62.0 + - + +
96B LYS 5.2 1.1 - - - +
98B VAL* 4.5 0.7 - - - +
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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
----------------------------------------------------------
41B THR* 4.3 13.5 - - + -
43B ILE* 4.5 9.6 - - + -
91B LEU* 3.6 36.6 - - + +
92B TYR* 2.9 4.2 + - - +
94B ALA* 1.3 87.5 - - + +
96B LYS* 1.3 66.4 + - - +
97B GLY 3.2 3.1 + - - -
98B VAL* 3.2 24.9 + - + +
101B VAL* 4.5 9.2 - - + -
128B VAL* 4.8 1.6 - - + +
131B THR* 3.1 44.4 - - - +
132B CYS* 3.8 14.4 - - - +
135B ALA* 3.6 16.7 - - + +
137B VAL* 4.0 8.8 - - + +
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Residues in contact with LYS 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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65B ASN* 5.8 1.7 + - - -
92B TYR* 3.1 48.4 + - + +
93B PRO 4.4 7.1 + - - +
94B ALA 3.9 0.9 - - - -
95B LEU* 1.3 75.7 - - - +
97B GLY* 1.3 64.9 + - - +
98B VAL* 4.0 2.9 + - - +
134B GLU 4.8 4.4 + - - +
135B ALA* 3.6 27.1 + - - +
136B GLY* 4.9 3.6 - - - +
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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