Contacts of the helix formed by residues 120 - 129 (chain M) 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 120 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119M GLN* 1.3 84.5 - - + +
121M LYS* 1.3 65.8 + - - +
122M ASP* 3.1 16.4 + - - +
123M VAL* 3.4 13.3 + - + +
124M ILE* 3.1 23.2 + - + +
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Residues in contact with LYS 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114M TYR* 3.5 40.4 - - + +
115M GLY 4.4 3.4 - - - -
116M LYS* 4.5 9.9 + - - +
118M SER 4.0 14.3 + - - +
119M GLN* 3.4 3.0 - - - +
120M ALA* 1.3 78.2 - - - +
122M ASP* 1.3 64.0 + - - +
124M ILE* 3.1 12.6 + - - +
125M GLU* 3.0 27.2 + - - +
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Residues in contact with ASP 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120M ALA* 3.3 18.3 - - - +
121M LYS* 1.3 73.0 - - - +
123M VAL* 1.3 85.1 + - - +
125M GLU* 3.1 20.0 - - - +
126M GLU* 2.8 36.9 + - + +
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Residues in contact with VAL 123 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M ASP* 3.5 36.6 - - + +
17M ALA* 5.4 6.2 - - + +
120M ALA* 3.4 13.6 + - + +
121M LYS 3.4 0.2 - - - -
122M ASP* 1.3 92.2 + - - +
124M ILE* 1.3 67.5 + - + +
126M GLU* 2.9 21.8 + - + -
127M TYR* 3.0 17.3 + - + +
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Residues in contact with ILE 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M ALA* 3.5 42.0 - - + +
20M GLU* 5.7 4.3 - - + -
21M VAL* 4.8 11.4 - - + +
49M LEU* 4.9 13.5 - - + -
114M TYR* 3.5 34.5 - - + +
119M GLN 4.6 3.8 - - - +
120M ALA* 3.1 18.2 - - + +
121M LYS* 3.1 8.5 + - - +
123M VAL* 1.3 77.2 - - + +
125M GLU* 1.3 52.6 + - - +
127M TYR* 4.8 1.0 - - - +
128M PHE* 2.6 41.5 + - + +
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Residues in contact with GLU 125 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121M LYS* 3.0 14.5 + - - +
122M ASP* 3.1 24.7 + - - +
124M ILE* 1.3 76.0 - - + +
126M GLU* 1.3 64.8 + - - +
128M PHE* 3.6 13.9 - - + -
129M LYS 2.7 37.8 + - - +
130M CYS 3.3 1.4 - - - +
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Residues in contact with GLU 126 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122M ASP* 2.8 30.2 + - + +
123M VAL* 2.9 17.7 + - + +
125M GLU* 1.3 85.3 - - - +
127M TYR* 1.3 61.0 + - - +
130M CYS* 3.0 39.7 + - - +
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Residues in contact with TYR 127 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13M ASP* 4.9 15.7 - - - +
14M VAL* 3.4 60.6 - - + +
17M ALA* 6.2 2.0 - - + -
77M ILE* 3.8 26.1 - - + +
78M LYS 5.7 1.4 + - - -
123M VAL* 3.0 13.0 + - + +
124M ILE* 4.8 1.1 - - - +
126M GLU* 1.3 75.6 - - - +
128M PHE* 1.3 69.3 + - - +
129M LYS* 4.5 0.2 - - - -
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Residues in contact with PHE 128 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48M HIS 5.6 0.2 - - - -
49M LEU* 3.5 36.1 - - + -
50M CYS 4.5 0.2 - - - -
75M ASN* 3.3 35.2 - - + -
76M LEU* 3.4 29.6 - - - +
77M ILE* 3.5 55.6 - - + +
124M ILE* 2.6 25.7 + - + +
125M GLU* 3.6 12.8 - - + -
127M TYR* 1.3 82.2 - - - +
129M LYS* 1.3 79.7 + - + +
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Residues in contact with LYS 129 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75M ASN* 5.7 7.0 - - + +
76M LEU 5.0 5.6 - - - +
125M GLU* 2.7 24.3 + - - +
126M GLU 3.9 0.2 - - - -
127M TYR 4.5 0.2 - - - -
128M PHE* 1.3 93.9 - - + +
130M CYS* 1.3 92.0 + - - +
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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