Contacts of the helix formed by residues 100 - 108 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A PRO 3.9 0.8 - - - -
99A ALA* 1.3 78.4 - - - +
101A MET* 1.3 64.6 + - - +
102A ALA* 3.7 4.1 + - - +
103A GLU* 2.8 38.2 + - - +
104A TYR* 3.0 27.9 + - - -
51D ILE* 3.7 7.4 - - - +
112D GLU* 3.4 28.7 + - - -
113D GLU 4.2 6.5 - - - -
114D THR* 5.8 2.5 - - - -
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Residues in contact with MET 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ILE* 3.8 10.3 - - + -
100A SER* 1.3 69.0 - - - +
102A ALA* 1.3 57.7 + - - +
104A TYR* 4.0 1.8 - - - -
105A LEU* 2.8 35.7 + - - +
47D GLY 3.2 36.3 - - - +
48D VAL* 3.7 14.1 - - - +
51D ILE* 3.5 24.6 - - + +
101D MET* 3.7 36.8 - - + +
104D TYR* 3.8 32.3 - - + -
105D LEU* 4.0 11.7 - - + -
112D GLU* 2.6 22.5 + - - +
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A SER* 3.1 4.7 - - - +
101A MET* 1.3 78.6 - - - +
103A GLU* 1.3 62.9 + - + +
105A LEU* 3.4 5.1 + - - +
106A ALA* 3.1 21.8 + - - +
105D LEU* 4.0 14.5 - - + +
112D GLU* 2.9 15.5 + - - +
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Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG* 4.5 9.7 + - - -
98A PRO* 3.5 23.5 - - + +
99A ALA 3.2 15.5 + - - -
100A SER* 2.8 30.5 + - - +
102A ALA* 1.3 75.4 - - + +
104A TYR* 1.3 60.2 + - - +
106A ALA* 3.0 9.1 + - - +
107A LEU* 2.9 36.9 + - + +
113D GLU 4.7 0.5 - - - +
114D THR* 5.5 1.0 - - - -
116D LYS* 2.6 34.7 + - - -
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Residues in contact with TYR 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL* 3.7 14.1 - - + +
44A ALA* 3.4 31.6 - - + +
47A GLY* 4.6 2.2 - - - -
48A VAL* 4.3 1.1 - - + -
83A PHE* 3.2 32.5 - + - -
98A PRO* 2.6 44.4 + - + -
99A ALA* 3.5 6.6 - - - -
100A SER 3.0 22.5 + - - -
101A MET* 3.2 4.9 + - - +
103A GLU* 1.3 76.1 - - - +
105A LEU* 1.3 55.1 + - - +
108A SER* 2.7 39.6 + - - -
51D ILE* 3.7 27.1 - - + +
58D TRP* 3.7 4.2 - - - -
101D MET* 3.7 29.8 - - + -
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 4.7 5.2 - - + -
101A MET 2.8 19.4 + - - +
102A ALA* 3.8 4.3 - - - +
104A TYR* 1.3 72.8 - - - +
106A ALA* 1.3 60.3 + - - +
108A SER* 4.2 11.1 + - - +
110A ILE 6.1 0.4 - - - +
112A GLU* 3.5 36.1 - - + +
101D MET* 4.0 11.9 - - + -
102D ALA* 4.0 22.9 - - + +
105D LEU* 3.9 27.8 - - + -
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Residues in contact with ALA 106 (chain A).
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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102A ALA 3.1 12.6 + - - +
103A GLU* 3.0 12.2 + - - +
105A LEU* 1.3 79.3 - - - +
107A LEU* 1.3 64.9 + - + +
108A SER 5.0 0.5 - - - +
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Residues in contact with LEU 107 (chain A).
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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37A GLU* 4.9 11.9 - - - +
40A ARG* 3.7 44.2 - - + +
41A GLN* 3.9 25.3 + - + +
44A ALA* 3.6 13.2 - - + -
98A PRO* 4.0 20.4 - - + -
103A GLU* 2.9 20.7 + - + +
106A ALA* 1.3 84.8 - - + +
108A SER* 1.3 63.7 + - - +
109A GLY 3.6 1.4 + - - -
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Residues in contact with SER 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA* 3.8 8.2 - - - +
45A ASP* 2.8 18.7 + - - -
48A VAL* 3.4 24.3 - - - +
104A TYR 2.7 23.3 + - - -
105A LEU* 4.4 9.1 - - - +
106A ALA 3.7 1.1 - - - +
107A LEU* 1.3 75.5 - - - +
109A GLY* 1.3 58.0 + - - +
110A ILE* 2.9 26.5 + - - +
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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