Contacts of the helix formed by residues 100 - 108 (chain M) in PDB entry 2FJC
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 100 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98M PRO 3.9 0.2 - - - -
99M ALA* 1.3 79.5 - - - +
101M MET* 1.3 64.0 + - - +
102M ALA* 3.7 3.6 + - - +
103M GLU* 2.8 37.3 + - - +
104M TYR* 3.0 30.6 + - - -
51N ILE* 3.7 8.0 - - - +
112N GLU* 3.4 29.6 + - - -
113N GLU 4.2 6.5 - - - -
114N THR* 5.8 2.6 - - - +
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Residues in contact with MET 101 (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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51M ILE* 3.9 13.7 - - + -
100M SER* 1.3 69.3 - - - +
102M ALA* 1.3 59.0 + - - +
104M TYR* 3.7 1.7 - - - +
105M LEU* 2.8 35.2 + - - +
47N GLY 3.2 38.6 - - - +
48N VAL* 3.6 12.3 - - - +
51N ILE* 3.6 19.5 - - + +
101N MET* 3.8 35.9 - - + +
104N TYR* 3.7 31.9 - - + -
105N LEU* 4.1 11.0 - - + -
112N GLU* 2.5 24.3 + - - +
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Residues in contact with ALA 102 (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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100M SER* 4.0 4.3 - - - +
101M MET* 1.3 78.8 - - - +
103M GLU* 1.3 64.0 + - + +
105M LEU* 3.5 5.1 + - - +
106M ALA* 3.2 21.7 + - - +
105N LEU* 4.0 13.8 - - + +
112N GLU* 2.9 16.9 + - - +
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Residues in contact with GLU 103 (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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98M PRO* 3.6 20.9 - - + +
99M ALA 3.0 17.1 + - - -
100M SER* 2.8 30.7 + - - +
102M ALA* 1.3 76.5 - - + +
104M TYR* 1.3 59.7 + - - +
106M ALA* 3.0 8.1 + - - +
107M LEU* 2.9 36.6 + - + +
113N GLU 4.8 1.0 - - - +
114N THR* 5.6 1.1 - - - -
116N LYS* 2.7 34.5 + - - -
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Residues in contact with TYR 104 (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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43M VAL* 3.7 11.6 - - + +
44M ALA* 3.5 31.9 - - + +
47M GLY* 4.6 2.7 - - - -
48M VAL* 4.3 1.6 - - + -
83M PHE* 3.2 31.9 - + - -
98M PRO* 2.7 43.9 + - + -
99M ALA* 3.5 6.2 - - - -
100M SER 3.0 21.3 + - - -
101M MET* 3.2 4.9 + - - +
103M GLU* 1.3 77.9 - - - +
105M LEU* 1.3 55.0 + - - +
108M SER* 2.7 38.9 + - - -
51N ILE* 3.5 31.2 - - + +
58N TRP* 3.7 4.7 - - - -
101N MET* 3.7 28.7 - - + -
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Residues in contact with LEU 105 (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 VAL* 4.7 5.2 - - + -
101M MET 2.8 15.8 + - - +
102M ALA* 3.9 4.9 - - - +
104M TYR* 1.3 77.0 - - - +
106M ALA* 1.3 60.1 + - - +
107M LEU 3.7 0.2 + - - -
108M SER* 4.3 10.6 + - - +
110M ILE 6.1 0.4 - - - +
112M GLU* 3.6 35.9 - - + +
101N MET* 4.1 10.1 - - + -
102N ALA* 4.0 23.1 - - + +
105N LEU* 3.9 27.1 - - + -
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Residues in contact with ALA 106 (chain M).
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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102M ALA 3.2 12.8 + - - +
103M GLU* 3.0 12.9 + - - +
105M LEU* 1.3 79.4 - - - +
107M LEU* 1.3 64.2 + - + +
108M SER 5.1 0.2 - - - +
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Residues in contact with LEU 107 (chain M).
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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37M GLU* 4.9 12.6 - - - +
40M ARG* 4.1 25.6 - - + +
41M GLN* 3.5 29.0 + - + +
44M ALA* 3.6 13.5 - - + -
98M PRO* 4.0 27.1 - - + -
103M GLU* 2.9 21.5 + - + +
106M ALA* 1.3 84.8 - - + +
108M SER* 1.3 64.0 + - - +
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Residues in contact with SER 108 (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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44M ALA* 3.9 7.3 - - - +
45M ASP* 2.8 19.4 + - - -
48M VAL* 3.4 24.2 - - - +
104M TYR 2.7 22.7 + - - -
105M LEU* 4.3 8.7 + - - +
106M ALA 3.7 1.1 - - - +
107M LEU* 1.3 75.1 - - - +
109M GLY* 1.3 58.7 + - - +
110M ILE* 2.9 26.3 + - - +
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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