Contacts of the helix formed by residues 92 - 104 (chain B) in PDB entry 3ESF
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 SER 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B GLU 5.3 0.7 - - - -
91B PRO* 1.3 75.0 - - - +
93B GLY* 1.3 70.1 + - - +
94B LYS 3.5 1.4 + - - -
95B LEU 3.8 2.4 + - - -
96B ALA* 3.5 13.9 + - - -
192B GLU* 3.4 23.2 + - - +
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Residues in contact with GLY 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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92B SER* 1.3 76.7 - - - +
94B LYS* 1.3 63.7 + - - -
96B ALA* 3.3 4.0 + - - +
97B GLU* 3.1 27.4 + - - +
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Residues in contact with LYS 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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92B SER 3.5 0.6 + - - -
93B GLY* 1.3 71.7 - - - +
95B LEU* 1.3 58.2 + - - +
97B GLU* 3.5 6.2 + - - +
98B ALA* 3.0 28.2 + - - +
195B PHE* 3.8 18.4 - - + -
196B THR* 4.2 22.6 - - + +
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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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91B PRO* 4.2 3.6 - - + -
92B SER 3.8 2.3 + - - +
93B GLY 3.4 0.4 - - - -
94B LYS* 1.3 76.9 - - - +
96B ALA* 1.3 60.4 + - - +
98B ALA* 3.3 0.9 + - - -
99B ILE* 2.8 49.2 + - + +
128B LEU* 4.7 1.3 - - + -
137B LEU* 4.1 13.9 - - + -
157B ILE* 4.5 10.5 - - + -
188B TRP* 3.8 19.1 - - + -
191B ALA* 3.4 32.8 - - + -
192B GLU* 3.7 32.4 - - + +
195B PHE* 4.2 29.7 - - + -
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Residues in contact with ALA 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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91B PRO* 3.4 38.2 - - + +
92B SER* 3.5 12.4 + - - -
93B GLY 3.3 9.9 + - - +
95B LEU* 1.3 75.8 - - - +
97B GLU* 1.3 67.8 + - - +
99B ILE* 3.5 4.7 + - - +
100B ARG* 3.2 28.6 + - - +
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Residues in contact with GLU 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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93B GLY 3.1 16.8 + - - +
94B LYS* 3.8 9.4 - - - +
96B ALA* 1.3 81.0 - - - +
98B ALA* 1.3 56.3 + - - +
100B ARG* 3.2 26.9 + - - +
101B ALA* 2.9 28.3 + - - +
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Residues in contact with ALA 98 (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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94B LYS 3.0 12.0 + - - +
95B LEU 3.3 3.8 + - - +
97B GLU* 1.3 71.5 - - - +
99B ILE* 1.3 60.9 + - - +
101B ALA* 3.7 8.8 - - - +
102B SER* 2.9 34.4 + - - +
135B LYS 5.8 1.6 - - - +
137B LEU* 3.8 9.9 - - + -
195B PHE* 3.4 38.1 - - + -
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Residues in contact with ILE 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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91B PRO* 4.0 24.9 - - + -
95B LEU* 2.8 31.8 + - + +
96B ALA* 3.7 6.3 - - - +
98B ALA* 1.3 72.4 - - - +
100B ARG* 1.3 54.0 + - - +
102B SER 3.2 0.5 + - - -
103B PHE* 2.8 43.9 + - + +
105B SER 4.0 0.9 - - - +
106B PHE* 3.9 24.0 - - + +
109B PHE* 3.7 47.3 - - + -
128B LEU* 4.4 7.0 - - + -
137B LEU* 3.7 19.5 - - + -
188B TRP* 4.3 6.7 - - + -
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Residues in contact with ARG 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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96B ALA* 3.2 16.2 + - - +
97B GLU* 3.2 30.6 + - - +
99B ILE* 1.3 74.8 - - + +
101B ALA* 1.3 59.1 + - - +
104B GLY* 2.9 40.9 + - - +
105B SER* 4.1 27.3 - - - +
106B PHE* 4.5 6.4 - - + +
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Residues in contact with ALA 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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97B GLU 2.9 16.8 + - - +
98B ALA* 3.8 9.2 - - - +
99B ILE 3.3 0.4 - - - -
100B ARG* 1.3 75.6 - - - +
102B SER* 1.3 58.9 + - - +
136B LYS* 5.4 3.1 - - - +
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Residues in contact with SER 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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98B ALA* 2.9 17.1 + - - +
101B ALA* 1.3 80.2 + - - +
103B PHE* 1.3 67.1 + - - +
104B GLY 3.8 0.4 - - - -
135B LYS 4.8 0.3 + - - -
136B LYS* 3.6 27.4 + - - +
137B LEU* 2.8 50.2 + - - +
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Residues in contact with PHE 103 (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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99B ILE* 2.8 27.3 + - + +
102B SER* 1.3 77.4 - - - +
104B GLY* 1.3 55.7 + - - +
105B SER 3.2 17.9 + - - +
108B LYS* 3.5 21.9 - - + +
109B PHE* 3.7 42.8 - + + +
112B GLU* 3.2 27.1 - - - -
128B LEU* 3.8 15.5 - - + -
137B LEU* 3.6 41.7 - - + -
138B LYS* 3.8 4.7 - - - -
139B VAL* 3.9 14.6 - - + -
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Residues in contact with GLY 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 ARG* 2.9 34.3 + - - +
101B ALA 4.9 0.2 - - - -
102B SER 3.8 0.8 - - - -
103B PHE* 1.3 76.1 - - - +
105B SER* 1.3 61.1 + - - +
108B LYS* 5.2 0.2 - - - -
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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