Contacts of the helix formed by residues 97 - 108 (chain c) in PDB entry 5JPQ
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 97 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14652 C 3.8 15.0 - - - -
14662 G 4.2 5.6 - - - -
16032 U 2.3 32.8 + - - -
95c ASP 3.7 0.6 + - - -
96c PRO* 1.3 70.9 - - - +
98c SER* 1.3 58.9 + - - +
99c ARG* 3.4 3.1 - - - -
100c LEU* 3.4 9.2 + - - +
101c MET* 2.9 23.9 + - - +
144c GLU* 6.0 0.9 - - - -
130x GLY 2.5 3.3 + - - +
138x PHE* 1.9 22.6 - - - +
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Residues in contact with SER 98 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14652 C 2.4 22.7 - - - -
14662 G 2.8 7.1 + - - -
97c SER* 1.3 72.3 - - - +
99c ARG* 1.3 57.1 + - - +
101c MET* 3.2 0.7 + - - +
102c ALA 2.9 8.8 + - - -
138x PHE* 2.2 12.1 - - - +
139x GLN 1.6 53.8 - - - +
140x LYS* 1.8 31.7 + - - +
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Residues in contact with ARG 99 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14642 G 5.7 0.7 - - - +
14652 C 3.8 27.4 + - - +
97c SER* 3.4 1.5 - - - -
98c SER* 1.3 79.4 - - - +
100c LEU* 1.3 62.2 + - - +
102c ALA* 3.3 13.3 + - - +
103c PHE* 3.3 11.8 + - - +
140x LYS* 3.2 8.3 - - - +
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Residues in contact with LEU 100 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16042 U 5.2 4.0 - - - +
96c PRO* 5.0 1.3 - - + -
97c SER* 3.4 19.1 + - - +
98c SER 3.3 0.4 - - - -
99c ARG* 1.3 79.3 - - - +
101c MET* 1.3 58.1 + - - +
103c PHE* 3.2 10.9 + - - +
104c SER* 3.1 24.3 + - - -
142c LEU* 5.3 8.3 - - + +
143c HIS 5.7 1.1 - - - +
144c GLU* 5.4 6.7 - - + -
150c THR* 5.1 18.4 - - - -
130x GLY* 4.2 7.4 - - - +
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Residues in contact with MET 101 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15802 C 5.9 2.0 - - - -
97c SER 2.9 15.5 + - - +
98c SER 3.6 0.7 - - - +
100c LEU* 1.3 76.0 - - - +
102c ALA* 1.3 58.0 + - - +
104c SER* 3.2 9.8 + - - -
105c LYS* 3.0 28.1 + - - +
130x GLY* 4.6 6.9 + - - -
137x ARG* 3.7 12.6 - - + -
138x PHE 2.8 40.8 - - - +
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Residues in contact with ALA 102 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15802 C 6.0 1.8 - - - -
98c SER 2.9 5.1 + - - -
99c ARG 3.4 6.1 - - - +
100c LEU 3.3 0.2 - - - -
101c MET* 1.3 76.0 - - - +
103c PHE* 1.3 61.8 + - - +
105c LYS* 3.5 6.9 + - - +
106c GLU* 3.1 24.8 + - - +
140x LYS* 2.7 38.8 - - + +
141x SER 4.4 0.9 - - - +
142x TYR* 4.8 14.4 - - + +
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Residues in contact with PHE 103 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99c ARG 3.3 8.3 + - - +
100c LEU* 3.2 14.3 + - - +
102c ALA* 1.3 77.9 - - - +
104c SER* 1.3 62.6 + - - +
106c GLU* 3.6 4.1 + - - +
107c ILE* 3.1 27.3 + - - +
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Residues in contact with SER 104 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11592 C 5.7 0.4 - - - -
90c VAL* 5.2 13.0 - - - -
100c LEU 3.1 11.5 + - - -
101c MET* 3.2 13.4 + - - -
103c PHE* 1.3 75.2 - - - +
105c LYS* 1.3 55.3 + - - +
107c ILE* 3.3 3.9 + - - +
108c ARG* 2.8 40.3 + - - +
142c LEU* 5.6 2.0 - - - -
129x PHE 4.9 11.9 - - - -
130x GLY* 5.8 0.7 - - - -
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Residues in contact with LYS 105 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11592 C 1.9 65.6 - - + +
15802 C 4.7 5.6 - - - +
15812 C 6.0 0.4 - - - +
101c MET 3.0 15.9 + - - +
102c ALA* 3.7 8.1 - - - +
104c SER* 1.3 77.9 - - - +
106c GLU* 1.3 55.7 + - - +
108c ARG 2.2 15.1 - - - +
109c LEU* 4.4 1.4 - - - +
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Residues in contact with GLU 106 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11592 C 4.3 0.4 - - - -
102c ALA 3.1 14.7 + - - +
103c PHE* 4.2 3.8 - - - +
105c LYS* 1.3 80.0 - - - +
107c ILE* 1.3 61.5 + - - +
108c ARG 3.7 1.2 + - - +
109c LEU* 5.2 3.5 - - - +
259c PRO* 4.3 23.1 - - + +
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Residues in contact with ILE 107 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103c PHE 3.1 19.3 + - - +
104c SER* 4.0 3.1 - - - +
106c GLU* 1.3 78.4 - - - +
108c ARG* 1.3 59.3 + - + +
109c LEU 4.4 0.2 + - - -
259c PRO* 5.3 6.2 - - + +
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Residues in contact with ARG 108 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11592 C 2.8 18.3 - - - +
88c VAL* 6.5 0.9 - - + -
90c VAL* 4.8 16.6 - - + -
104c SER* 2.8 16.2 + - - +
105c LYS 2.2 29.5 - - - +
106c GLU 4.6 0.2 - - - -
107c ILE* 1.3 79.8 - - + +
109c LEU* 1.3 61.9 + - - +
114c ALA* 5.0 9.6 - - + -
115c ILE 6.1 0.4 - - - +
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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