Contacts of the helix formed by residues 100 - 108 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51J ILE* 3.6 7.8 - - - +
112J GLU* 3.5 28.4 + - - -
113J GLU 4.2 6.7 - - - -
114J THR* 5.9 2.2 - - - -
98K PRO 3.9 0.6 - - - -
99K ALA* 1.3 79.1 - - - +
101K MET* 1.3 64.9 + - - +
102K ALA* 3.7 3.2 + - - +
103K GLU* 2.8 38.2 + - - +
104K TYR* 3.0 28.0 + - - -
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Residues in contact with MET 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47J GLY 3.2 37.9 - - - +
48J VAL* 3.6 11.0 - - - +
51J ILE* 3.5 25.3 - - + +
101J MET* 3.7 41.5 - - + +
104J TYR* 3.8 26.0 - - + -
105J LEU* 4.2 10.8 - - + -
112J GLU* 2.6 23.4 + - - +
51K ILE* 3.8 10.5 - - + -
100K SER* 1.3 70.1 - - - +
102K ALA* 1.3 57.9 + - - +
104K TYR* 3.6 1.9 - - - +
105K LEU* 2.8 35.0 + - - +
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Residues in contact with ALA 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105J LEU* 4.1 14.3 - - + +
112J GLU* 3.0 16.6 + - - +
100K SER* 4.1 4.3 - - - +
101K MET* 1.3 78.0 - - - +
103K GLU* 1.3 62.4 + - + +
105K LEU* 3.5 5.0 + - - +
106K ALA* 3.2 21.7 + - - +
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Residues in contact with GLU 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J GLU 4.9 2.4 - - - +
114J THR* 5.6 1.4 - - - -
116J LYS* 2.8 33.9 + - - -
40K ARG* 4.1 10.4 + - - -
98K PRO* 3.7 21.3 - - + +
99K ALA 3.1 18.7 + - - -
100K SER* 2.8 29.6 + - - +
102K ALA* 1.3 74.5 - - + +
104K TYR* 1.3 62.1 + - - +
106K ALA* 3.0 7.7 + - - +
107K LEU* 2.9 37.0 + - + +
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Residues in contact with TYR 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J ILE* 3.6 28.9 - - + +
58J TRP* 3.6 4.5 - - - -
101J MET* 3.8 29.6 - - + -
43K VAL* 3.7 13.6 - - + +
44K ALA* 3.5 30.5 - - + +
47K GLY* 4.6 2.9 - - - -
48K VAL* 4.4 1.1 - - + -
83K PHE* 3.2 33.5 - + - -
98K PRO* 2.6 42.9 + - + -
99K ALA* 3.6 5.9 - - - -
100K SER 3.0 16.4 + - - -
101K MET* 3.6 4.9 - - - +
103K GLU* 1.3 77.7 - - - +
105K LEU* 1.3 55.0 + - - +
108K SER* 2.7 39.3 + - - -
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Residues in contact with LEU 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101J MET* 4.1 13.5 - - + -
102J ALA* 4.0 24.9 - - + +
105J LEU* 4.1 16.8 - - + -
48K VAL* 4.6 4.9 - - + -
101K MET 2.8 19.6 + - - +
102K ALA* 3.9 4.7 - - - +
104K TYR* 1.3 76.8 - - - +
106K ALA* 1.3 60.0 + - - +
108K SER* 4.3 10.6 + - - +
110K ILE 6.1 0.4 - - - +
112K GLU* 3.5 35.9 - - + +
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Residues in contact with ALA 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102K ALA 3.2 13.5 + - - +
103K GLU* 3.0 12.8 + - - +
105K LEU* 1.3 79.8 - - - +
107K LEU* 1.3 64.5 + - + +
108K SER 5.1 0.7 - - - +
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Residues in contact with LEU 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K GLU* 5.0 11.7 - - - +
40K ARG* 3.8 44.2 - - + +
41K GLN* 3.8 26.2 + - + +
44K ALA* 3.6 13.5 - - + -
98K PRO* 4.0 19.1 - - + -
103K GLU* 2.9 20.7 + - + +
106K ALA* 1.3 84.2 - - + +
108K SER* 1.3 64.4 + - - +
109K GLY* 3.6 1.6 + - - -
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Residues in contact with SER 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44K ALA* 3.8 7.1 - - - +
45K ASP* 2.7 21.8 + - - -
48K VAL* 3.5 24.1 - - - +
104K TYR 2.7 23.0 + - - -
105K LEU* 4.4 9.8 - - - +
106K ALA 3.7 1.1 - - - +
107K LEU* 1.3 75.3 - - - +
109K GLY* 1.3 58.3 + - - +
110K ILE* 3.0 25.8 + - - +
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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