Contacts of the helix formed by residues 119 - 127 (chain S) in PDB entry 5FLX
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 ALA 119 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118P GLU* 3.3 37.9 - - + +
114S LEU* 3.4 28.1 + - + +
117S ILE* 3.1 5.5 - - + -
118S ARG* 1.3 76.0 - - - +
120S HIS* 1.3 53.4 + - - +
121S ARG* 4.3 3.8 - - + +
122S GLY* 2.8 14.3 + - - +
123S LEU* 2.4 36.2 + - - +
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Residues in contact with HIS 120 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16211 U 2.9 44.8 + - + +
16221 U 3.0 62.9 + - + +
81P ARG* 5.3 2.7 - - - +
117P GLY 3.2 15.4 + - - +
118P GLU* 3.2 34.4 + - + +
120P SER 4.9 5.4 - - - +
118S ARG 3.3 3.0 + - - -
119S ALA* 1.3 70.8 - - - +
121S ARG* 1.3 67.3 + - + +
123S LEU* 3.5 14.9 - - + +
124S ARG* 2.9 33.4 + - - +
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Residues in contact with ARG 121 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16101 G 2.7 42.9 + - - +
16111 G 3.4 26.7 + - - -
16211 U 5.6 0.2 - - - +
16221 U 4.3 14.3 + - - +
118P GLU* 5.6 4.0 - - - +
114S LEU* 5.6 10.0 - - + +
119S ALA* 3.1 5.1 - - + +
120S HIS* 1.3 87.3 + - + +
122S GLY* 1.3 57.9 + - - +
124S ARG* 3.3 1.8 + - - +
125S HIS* 2.9 28.8 + - - +
131S VAL* 3.7 34.5 - - + +
132S ARG* 4.4 29.6 - - - +
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Residues in contact with GLY 122 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111S LEU* 5.7 4.0 - - - -
114S LEU* 4.7 22.4 - - - +
115S LYS* 5.5 7.6 - - - +
118S ARG 5.8 0.2 - - - -
119S ALA* 2.8 19.4 + - - +
121S ARG* 1.3 75.0 - - - +
123S LEU* 1.3 60.0 + - - +
125S HIS* 4.0 7.5 - - - +
126S PHE* 2.9 28.3 + - - +
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Residues in contact with LEU 123 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16221 U 4.2 17.0 - - + +
118P GLU 5.2 0.2 - - - +
119P PHE 5.8 0.7 - - - +
120P SER 5.4 1.1 - - - +
121P ILE* 4.4 22.2 - - + -
118S ARG* 3.3 33.0 - - + +
119S ALA 2.4 24.9 + - - +
120S HIS* 3.5 16.4 - - + +
122S GLY* 1.3 71.9 - - - +
124S ARG* 1.3 55.1 + - - +
126S PHE* 3.0 9.3 + - + +
127S TRP* 2.6 56.8 + - + +
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Residues in contact with ARG 124 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15201 G 5.1 12.3 - - - -
16221 U 3.4 46.6 + - + -
123P TYR* 3.9 8.9 + - - -
120S HIS 2.9 18.9 + - - +
123S LEU* 1.3 74.6 - - - +
125S HIS* 1.3 57.8 + - - +
127S TRP* 2.9 23.2 - - - +
129S LEU* 2.8 63.1 + - + +
130S ARG 2.4 34.1 + - - +
131S VAL* 3.7 23.4 + - + +
134S GLN 4.6 4.2 + - - -
136S THR* 3.9 16.6 + - - -
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Residues in contact with HIS 125 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16091 C 3.9 42.8 + - - -
16101 G 4.8 7.0 - - - +
111S LEU* 3.4 45.7 - - + +
121S ARG 2.9 17.6 + - - +
122S GLY* 4.0 7.2 - - - +
124S ARG* 1.3 74.1 - - - +
126S PHE* 1.3 63.7 + - - +
127S TRP 3.0 11.5 - - - +
129S LEU 4.6 2.2 - - - -
131S VAL* 4.3 6.2 - - + +
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Residues in contact with PHE 126 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115S LYS* 4.8 25.1 - - + +
122S GLY 2.9 20.7 + - - +
123S LEU* 3.3 11.7 - - + +
125S HIS* 1.3 78.0 - - - +
127S TRP* 1.3 86.6 + + - +
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Residues in contact with TRP 127 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15221 A 5.8 3.8 - - - -
125P PRO* 3.5 31.6 - - + +
126P VAL* 3.8 35.0 - - + -
123S LEU* 2.6 48.4 + - + +
124S ARG* 2.9 16.9 - - - +
125S HIS* 3.0 12.3 - - - +
126S PHE* 1.3 96.3 - + - +
128S GLY* 1.3 61.3 + - - +
129S LEU* 3.2 19.4 + - + +
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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