Contacts of the helix formed by residues 98 - 106 (chain B) in PDB entry 6APL
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 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B ASP 4.3 8.3 - - - +
96B LEU* 3.1 14.6 + - - +
97B PHE* 1.3 83.4 - - - +
99B PRO* 1.3 76.0 - - - +
100B ALA* 3.4 11.2 + - - +
101B LEU* 3.0 21.4 + - - +
102B TRP* 2.9 21.7 + - - +
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Residues in contact with PRO 99 (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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97B PHE* 4.9 1.3 - - + +
98B THR* 1.3 86.2 - - - +
100B ALA* 1.3 60.9 + - - +
102B TRP* 3.6 12.6 - - + +
103B ASP* 3.0 33.6 + - - +
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Residues in contact with ALA 100 (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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98B THR* 3.1 10.6 + - - +
99B PRO* 1.3 77.0 - - - +
101B LEU* 1.3 67.0 + - - +
103B ASP* 3.2 8.1 + - - +
104B ARG* 3.1 23.2 + - - +
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Residues in contact with LEU 101 (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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92B LEU* 4.1 18.6 - - + -
96B LEU* 3.5 22.9 - - + +
97B PHE* 4.5 4.0 - - + -
98B THR* 3.0 16.4 + - - +
100B ALA* 1.3 77.9 - - - +
102B TRP* 1.3 58.1 + - - +
104B ARG* 3.5 19.1 - - - +
105B LEU* 2.9 61.6 + - + +
114B TRP* 4.0 13.7 - - + -
276B HIS* 4.5 5.4 - - + +
278B ASP* 3.5 25.1 - - - +
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Residues in contact with TRP 102 (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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97B PHE* 4.2 14.6 - + + -
98B THR 2.9 13.3 + - - +
99B PRO* 3.6 15.5 - - + +
100B ALA 3.2 0.2 - - - -
101B LEU* 1.3 77.0 - - - +
103B ASP* 1.3 72.2 + - - +
106B SER* 3.0 40.2 + - - -
114B TRP* 3.3 38.3 + + - +
117B LEU 3.7 17.7 - - - -
119B HIS* 3.6 56.1 - + + +
122B ILE* 3.7 28.0 - - + -
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Residues in contact with ASP 103 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B PRO* 3.0 24.2 + - - +
100B ALA* 3.2 9.0 + - - +
102B TRP* 1.3 84.9 - - - +
104B ARG* 1.3 66.5 + - - +
106B SER* 3.1 18.9 + - - -
107B GLN* 3.7 15.2 + - - +
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Residues in contact with ARG 104 (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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100B ALA 3.1 13.5 + - - +
101B LEU* 3.5 19.8 - - - +
103B ASP* 1.3 77.1 - - - +
105B LEU* 1.3 72.0 + - - +
106B SER 3.1 1.0 + - - -
107B GLN* 3.1 23.0 + - - +
108B HIS* 3.3 28.8 + - + -
278B ASP* 3.3 37.1 + - - -
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Residues in contact with LEU 105 (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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92B LEU* 5.4 0.2 - - + -
101B LEU* 2.9 41.8 + - + +
104B ARG* 1.3 92.9 - - - +
106B SER* 1.3 58.9 + - - +
107B GLN 3.1 1.2 + - - -
108B HIS* 3.2 10.4 + - - +
112B TYR 4.2 7.4 - - - +
113B GLY* 3.3 16.1 - - - -
114B TRP* 2.8 71.1 + - + +
276B HIS* 4.8 1.1 - - + -
277B PRO* 4.3 18.2 - - + -
278B ASP* 3.7 20.0 - - - +
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Residues in contact with SER 106 (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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102B TRP* 3.0 36.7 + - - -
103B ASP* 3.1 12.3 + - - -
105B LEU* 1.3 76.1 - - - +
107B GLN* 1.3 57.9 + - - +
108B HIS 3.4 2.2 - - - -
114B TRP* 3.9 18.3 + - - -
115B ARG* 3.2 25.9 - - - +
116B GLY 5.0 1.9 + - - -
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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