Contacts of the helix formed by residues 100 - 108 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98I PRO 3.9 0.4 - - - -
99I ALA* 1.3 79.1 - - - +
101I MET* 1.3 64.5 + - - +
102I ALA* 3.7 3.8 + - - +
103I GLU* 2.9 38.1 + - - +
104I TYR* 3.0 28.2 + - - -
51L ILE* 3.8 7.6 - - - +
112L GLU* 3.5 27.6 - - - -
113L GLU 4.2 6.3 - - - -
114L THR* 5.9 2.9 - - - -
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Residues in contact with MET 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51I ILE* 3.9 9.6 - - + -
100I SER* 1.3 70.2 - - - +
102I ALA* 1.3 57.8 + - - +
104I TYR* 3.7 1.9 - - - +
105I LEU* 2.8 34.7 + - - +
47L GLY 3.2 37.5 - - - +
48L VAL* 3.6 14.6 - - + +
51L ILE* 3.5 24.2 - - + -
101L MET* 3.6 45.8 - - + +
104L TYR* 3.8 25.4 - - + -
105L LEU* 4.0 10.8 - - + -
112L GLU* 2.6 20.1 + - - +
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Residues in contact with ALA 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I SER* 4.0 4.5 - - - +
101I MET* 1.3 78.8 - - - +
103I GLU* 1.3 62.9 + - + +
105I LEU* 3.4 4.3 + - - +
106I ALA* 3.1 22.3 + - - +
105L LEU* 4.0 12.9 - - + +
112L GLU* 3.0 16.2 + - - +
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Residues in contact with GLU 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40I ARG* 5.1 6.2 + - - -
98I PRO* 3.6 23.3 - - + +
99I ALA 3.1 18.8 + - - +
100I SER* 2.9 29.1 + - - +
102I ALA* 1.3 79.0 - - + +
104I TYR* 1.3 58.9 + - - +
106I ALA* 3.0 7.4 + - - +
107I LEU* 2.9 38.1 + - + +
113L GLU 4.9 1.4 - - - +
114L THR* 5.6 0.7 - - - -
116L LYS* 2.9 32.8 + - - -
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Residues in contact with TYR 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I VAL* 3.7 14.4 - - + -
44I ALA* 3.5 31.9 - - + +
47I GLY* 4.7 2.2 - - - -
48I VAL* 4.4 1.6 - - + -
83I PHE* 3.3 31.2 - + - -
98I PRO* 2.7 42.7 + - + -
99I ALA* 3.5 6.9 - - - -
100I SER 3.0 20.8 + - - -
101I MET* 3.2 4.7 + - - +
103I GLU* 1.3 76.8 - - - +
105I LEU* 1.3 54.3 + - - +
108I SER* 2.7 38.5 + - - -
51L ILE* 3.6 26.4 - - + +
58L TRP* 3.7 4.3 - - - -
101L MET* 3.8 28.7 - - + -
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Residues in contact with LEU 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I VAL* 4.6 5.6 - - + -
101I MET 2.8 23.2 + - - +
102I ALA* 3.8 4.9 - - - +
104I TYR* 1.3 72.7 - - - +
106I ALA* 1.3 61.2 + - - +
108I SER* 4.2 10.2 + - - +
110I ILE 6.0 0.7 - - - +
112I GLU* 3.5 35.2 - - + +
101L MET* 4.1 11.0 - - + -
102L ALA* 4.0 26.5 - - + +
105L LEU* 4.0 18.8 - - + -
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Residues in contact with ALA 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I ALA 3.1 11.9 + - - +
103I GLU* 3.0 13.3 + - - +
105I LEU* 1.3 80.6 - - - +
107I LEU* 1.3 63.7 + - + +
108I SER 5.1 0.3 - - - +
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Residues in contact with LEU 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I GLU* 5.0 9.0 - - - +
40I ARG* 3.9 42.4 - - + +
41I GLN* 4.1 22.6 + - + +
44I ALA* 3.6 13.5 - - + -
98I PRO* 3.9 24.2 - - + -
103I GLU* 2.9 21.7 + - + +
106I ALA* 1.3 84.2 - - + +
108I SER* 1.3 64.9 + - - +
109I GLY* 3.6 1.7 + - - -
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Residues in contact with SER 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I ALA* 3.8 7.8 - - - +
45I ASP* 2.8 22.4 + - - -
48I VAL* 3.4 23.8 - - - +
104I TYR 2.7 22.7 + - - -
105I LEU* 4.2 9.1 + - - +
106I ALA 3.7 1.1 - - - +
107I LEU* 1.3 75.1 - - - +
109I GLY* 1.3 58.3 + - - +
110I ILE* 3.0 26.0 + - - +
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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