Contacts of the helix formed by residues 100 - 108 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B PRO 3.9 0.4 - - - -
99B ALA* 1.3 79.2 - - - +
101B MET* 1.3 63.2 + - - +
102B ALA* 3.7 3.6 + - - +
103B GLU* 2.9 36.8 + - - +
104B TYR* 3.0 30.4 + - - -
51C ILE* 3.7 8.0 - - - +
112C GLU* 3.4 29.1 + - - -
113C GLU 4.2 7.2 - - - -
114C THR* 5.8 2.4 - - - +
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Residues in contact with MET 101 (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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51B ILE* 3.8 10.8 - - + -
100B SER* 1.3 69.3 - - - +
102B ALA* 1.3 58.2 + - - +
104B TYR* 3.6 2.6 - - - +
105B LEU* 2.8 34.7 + - - +
47C GLY 3.2 37.5 - - - +
48C VAL* 3.6 14.4 - - - +
51C ILE* 3.5 24.6 - - + +
101C MET* 3.8 41.7 - - + +
104C TYR* 3.8 26.9 - - + -
105C LEU* 4.1 10.8 - - + -
112C GLU* 2.5 22.3 + - - +
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Residues in contact with ALA 102 (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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100B SER* 4.0 4.7 - - - +
101B MET* 1.3 77.9 - - - +
103B GLU* 1.3 63.1 + - + +
105B LEU* 3.5 5.0 + - - +
106B ALA* 3.2 21.5 + - - +
105C LEU* 4.0 14.0 - - + +
112C GLU* 2.9 17.1 + - - +
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Residues in contact with GLU 103 (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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40B ARG* 4.7 7.4 + - - -
98B PRO* 3.6 22.3 - - + +
99B ALA 3.1 23.4 + - - -
100B SER* 2.9 30.9 + - - +
102B ALA* 1.3 74.8 - - + +
104B TYR* 1.3 62.9 + - - +
106B ALA* 3.0 7.7 + - - +
107B LEU* 2.9 37.5 + - + +
113C GLU 4.8 2.9 - - - +
114C THR* 5.2 1.8 - - - +
116C LYS* 2.8 31.3 + - - -
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Residues in contact with TYR 104 (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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43B VAL* 3.7 13.5 - - + -
44B ALA* 3.5 30.7 - - + +
47B GLY* 4.6 2.5 - - - -
48B VAL* 4.3 1.3 - - + -
83B PHE* 3.2 32.4 - + - -
98B PRO* 2.7 41.6 + - + -
99B ALA* 3.5 6.8 - - - -
100B SER 3.0 23.0 + - - -
101B MET* 3.2 5.4 + - - +
103B GLU* 1.3 77.5 - - - +
105B LEU* 1.3 56.8 + - - +
108B SER* 2.7 39.3 + - - -
51C ILE* 3.6 29.3 - - + +
58C TRP* 3.7 4.3 - - - -
101C MET* 3.7 29.6 - - + -
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Residues in contact with LEU 105 (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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48B VAL* 4.6 6.3 - - + -
101B MET 2.8 22.8 + - - +
102B ALA* 3.9 5.2 - - - +
104B TYR* 1.3 73.4 - - - +
106B ALA* 1.3 59.9 + - - +
108B SER* 4.2 11.0 + - - +
110B ILE 6.0 0.7 - - - +
112B GLU* 3.6 34.3 - - + +
101C MET* 4.1 11.4 - - + -
102C ALA* 4.0 25.8 - - + +
105C LEU* 4.1 18.8 - - + -
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Residues in contact with ALA 106 (chain B).
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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102B ALA 3.2 12.6 + - - +
103B GLU* 3.0 13.3 + - - +
105B LEU* 1.3 80.8 - - - +
107B LEU* 1.3 65.5 + - + +
108B SER 5.1 0.4 - - - +
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Residues in contact with LEU 107 (chain B).
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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37B GLU* 5.0 8.7 - - - +
40B ARG* 3.8 44.9 - - + +
41B GLN* 3.5 29.1 + - + +
44B ALA* 3.6 13.2 - - + -
98B PRO* 3.9 23.3 - - + -
103B GLU* 2.9 22.4 + - + +
106B ALA* 1.3 84.6 - - + +
108B SER* 1.3 64.4 + - - +
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Residues in contact with SER 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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44B ALA* 3.8 7.1 - - - +
45B ASP* 2.8 20.7 + - - -
48B VAL* 3.4 28.3 - - - +
104B TYR 2.7 22.2 + - - -
105B LEU* 4.2 9.9 + - - +
106B ALA 3.7 0.9 - - - +
107B LEU* 1.3 75.7 - - - +
109B GLY* 1.3 58.3 + - - +
110B ILE* 3.0 23.0 + - - +
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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