Contacts of the helix formed by residues 105 - 113 (chain B) in PDB entry 3SL3
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 HIS 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B GLU* 4.4 13.8 + - - +
98B ASP* 5.8 0.6 + - - -
103B GLY 3.4 3.8 + - - +
104B LEU* 1.3 75.4 - - - +
106B VAL* 1.3 57.7 + - - +
107B PHE* 3.2 36.5 + + + -
108B ARG* 2.9 36.7 + - + +
109B ILE* 3.1 31.6 + - - +
111B GLU* 5.8 0.9 - - - -
327B GLN* 5.0 8.2 - - + +
328B LEU* 3.7 19.0 - - + +
331B GLN* 3.9 10.6 + - - -
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Residues in contact with VAL 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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104B LEU* 3.2 13.0 + - + +
105B HIS* 1.3 71.3 + - - +
107B PHE* 1.3 64.8 + - + +
109B ILE* 3.4 11.4 + - + +
110B ALA* 2.7 32.4 + - - +
117B PRO* 4.3 4.0 - - + -
121B ILE* 4.1 22.0 - - + -
163B ILE* 3.8 28.3 - - + +
166B ALA* 4.2 7.9 - - + -
167B ASP* 4.2 17.0 - - + +
328B LEU* 5.5 2.7 - - + -
332B TRP* 4.0 26.2 - - + +
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Residues in contact with PHE 107 (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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105B HIS* 3.2 14.5 + + + -
106B VAL* 1.3 75.8 - - + +
108B ARG* 1.3 67.1 + - - +
110B ALA* 2.9 18.2 + - - +
111B GLU* 2.9 21.3 + - + +
163B ILE* 3.9 13.5 - - + -
328B LEU* 3.9 11.7 - - + -
331B GLN* 3.4 52.7 - - + +
332B TRP* 3.5 56.1 - + - -
335B ARG* 3.4 34.5 - - - -
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Residues in contact with ARG 108 (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* 4.0 15.0 - - - +
95B GLU* 3.1 28.3 + - - -
105B HIS* 2.9 37.5 + - + +
107B PHE* 1.3 70.8 - - - +
109B ILE* 1.3 64.8 + - - +
111B GLU* 3.1 19.0 + - - +
112B LEU* 2.9 55.1 + - + +
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Residues in contact with ILE 109 (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 5.8 0.2 - - - +
95B GLU* 4.1 22.4 - - + +
96B LEU* 4.0 20.6 - - + -
104B LEU* 3.7 39.3 - - + -
105B HIS 3.1 20.3 + - - +
106B VAL* 3.4 10.8 - - - +
107B PHE 3.1 0.2 - - - -
108B ARG* 1.3 75.6 - - - +
110B ALA* 1.3 53.0 + - - +
112B LEU* 3.2 9.7 + - + +
113B SER* 2.7 41.1 + - - -
117B PRO* 4.4 7.6 - - + -
120B VAL* 4.0 26.7 - - + -
121B ILE* 4.3 6.7 - - + -
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Residues in contact with ALA 110 (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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106B VAL 2.7 18.3 + - - +
107B PHE* 2.9 17.5 - - + +
109B ILE* 1.3 74.8 - - - +
111B GLU* 1.3 59.6 + - + +
113B SER* 3.2 2.4 + - - -
115B ASN* 2.8 32.4 + - - +
117B PRO* 3.5 28.7 - - + -
163B ILE* 4.3 16.8 - - + -
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Residues in contact with GLU 111 (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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105B HIS* 5.8 0.9 - - - -
107B PHE* 2.9 16.3 + - - +
108B ARG* 3.4 23.2 + - - +
110B ALA* 1.3 74.4 - - + +
112B LEU* 1.3 55.7 + - + +
113B SER 2.7 11.3 + - - -
114B GLY* 2.8 16.8 + - - -
115B ASN 5.1 0.2 - - - +
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Residues in contact with LEU 112 (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* 3.6 46.1 + - + +
95B GLU* 3.9 8.5 - - + -
108B ARG* 2.9 60.2 + - + +
109B ILE* 3.7 5.8 - - - +
111B GLU* 1.3 73.6 - - + +
113B SER* 1.3 57.9 + - - +
114B GLY 3.4 1.0 + - - -
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Residues in contact with SER 113 (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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109B ILE* 2.7 29.6 + - - -
110B ALA 3.6 4.7 - - - -
111B GLU 2.7 0.6 + - - -
112B LEU* 1.3 74.3 - - - +
114B GLY* 1.3 63.5 + - - +
116B ARG* 3.2 44.4 + - - +
117B PRO 4.2 0.7 - - - -
120B VAL* 3.4 15.4 - - - +
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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