Contacts of the helix formed by residues 109 - 122 (chain O) in PDB entry 5FLX
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 GLY 109 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35O ALA* 3.5 11.4 - - - +
36O SER* 4.2 21.7 - - - +
37O PHE* 4.9 8.0 - - - -
107O THR 3.9 0.8 + - - -
108O PRO* 1.3 80.4 - - - +
110O PRO* 1.3 75.9 - - - +
111O GLY 3.2 3.4 + - - -
112O ALA* 3.5 14.3 + - - +
113O GLN* 4.2 8.3 + - - +
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Residues in contact with PRO 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O SER 5.4 1.6 - - - +
37O PHE* 4.7 18.2 - - + -
71O PRO* 4.3 13.8 - - + +
108O PRO 3.9 2.2 - - - +
109O GLY* 1.3 83.9 - - - +
111O GLY* 1.3 61.9 + - - +
113O GLN* 3.7 13.7 + - + +
114O SER* 4.0 6.6 + - - -
334z C 3.7 22.7 + - - +
335z G 4.6 14.4 - - - +
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Residues in contact with GLY 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O SER 5.4 2.1 + - - -
40O THR* 4.1 14.4 - - - -
69O SER 5.0 0.2 - - - -
70O SER* 4.6 0.9 - - - -
71O PRO* 3.7 27.5 - - - +
74O ALA* 3.2 24.8 - - - +
109O GLY* 3.2 1.4 - - - -
110O PRO* 1.3 84.0 - - - +
112O ALA* 1.3 63.4 + - - +
113O GLN 3.3 0.5 + - - -
114O SER* 3.5 6.6 + - - -
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Residues in contact with ALA 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O ILE* 4.0 18.7 - - + +
34O PHE 4.0 7.9 - - - +
35O ALA* 3.7 37.5 - - + -
36O SER 5.2 1.2 + - - +
40O THR* 3.7 15.1 + - + +
97O LEU* 4.7 4.9 - - + -
109O GLY 3.5 6.9 + - - +
110O PRO 3.4 0.8 - - - -
111O GLY* 1.3 78.0 - - - +
113O GLN* 1.3 64.5 + - - +
115O ALA* 3.4 17.3 - - - +
116O LEU* 3.9 4.7 + - - +
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Residues in contact with GLN 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97O LEU* 3.3 39.2 - - - +
108O PRO* 4.5 13.0 - - + +
109O GLY 4.3 10.3 - - - +
110O PRO* 3.7 8.9 + - + +
111O GLY 3.2 0.8 - - - -
112O ALA* 1.3 75.3 - - - +
114O SER* 1.3 60.4 + - - +
115O ALA 3.0 2.0 - - - -
116O LEU* 3.0 23.9 + - - +
117O ARG* 2.9 25.1 + - - +
44a ILE* 5.0 0.4 - - - +
45a VAL* 1.6 61.9 - - + +
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Residues in contact with SER 114 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71O PRO* 3.3 44.0 + - - +
74O ALA* 4.4 2.1 - - - +
75O MET* 4.3 10.7 + - - +
110O PRO 4.0 4.5 + - - -
111O GLY 3.5 3.9 + - - -
112O ALA 3.4 0.4 - - - -
113O GLN* 1.3 76.6 - - - +
115O ALA* 1.3 57.2 + - - +
117O ARG* 3.5 21.0 - - - +
118O ALA* 2.9 28.1 + - - +
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Residues in contact with ALA 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O ILE* 4.8 7.2 - - + -
40O THR* 5.2 0.9 - - + -
42O VAL* 3.7 30.1 - - + -
74O ALA* 3.9 23.7 - - + +
78O ALA* 3.9 1.8 - - + -
111O GLY 3.9 2.8 + - - -
112O ALA* 3.4 15.4 + - - +
113O GLN 3.0 0.8 - - - -
114O SER* 1.3 75.7 - - - +
116O LEU* 1.3 59.6 + - - +
118O ALA* 3.1 1.6 + - - +
119O LEU* 2.9 38.0 + - + +
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Residues in contact with LEU 116 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31O CYS* 5.7 0.7 - - - -
33O ILE* 3.5 28.5 - - + -
95O ILE* 3.7 46.7 - - + -
97O LEU* 5.6 7.0 - - + -
112O ALA 4.6 3.1 - - - +
113O GLN* 3.0 36.5 + - - +
115O ALA* 1.3 78.3 - - - +
117O ARG* 1.3 62.7 + - - +
119O LEU* 3.8 11.7 - - + +
120O ALA* 2.9 25.9 + - - +
126O ILE* 5.4 2.3 - - + +
129O ILE* 6.0 1.6 - - + -
44a ILE 5.8 0.7 - - - +
45a VAL* 4.6 3.1 - - + -
53a ILE* 4.5 16.6 - - + +
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Residues in contact with ARG 117 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F ARG* 5.7 2.2 + - - -
75O MET* 6.2 3.1 - - - -
113O GLN 2.9 13.1 + - - +
114O SER* 3.5 21.9 + - - +
116O LEU* 1.3 75.3 - - - +
118O ALA* 1.3 57.1 + - - +
120O ALA* 3.1 8.1 + - - +
121O ARG* 2.9 37.1 + - + +
45a VAL* 5.6 2.4 - - - +
46a GLU 3.4 23.6 + - - -
47a ALA 4.4 3.8 + - - -
48a ALA 4.1 4.9 + - - -
49a ALA* 3.6 33.5 - - + +
52a ASP* 3.4 27.6 + - + +
53a ILE* 5.3 1.5 - - - +
63c ARG* 5.1 10.9 - - - +
333z C 4.4 9.7 + - - -
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Residues in contact with ALA 118 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75O MET* 3.6 26.0 - - - +
78O ALA* 3.5 24.0 - - + -
79O GLN* 3.5 18.4 - - - +
82O ALA* 5.6 0.3 - - - +
114O SER 2.9 18.4 + - - +
115O ALA 3.1 0.2 + - - -
117O ARG* 1.3 73.1 - - - +
119O LEU* 1.3 66.8 + - - +
121O ARG* 3.0 27.9 + - - +
122O SER* 3.8 4.0 + - - -
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Residues in contact with LEU 119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31O CYS* 4.5 15.9 - - - -
33O ILE* 5.5 0.9 - - + -
42O VAL* 4.9 5.8 - - + -
78O ALA* 3.6 33.9 - - + +
81O VAL* 4.9 13.7 - - + -
82O ALA* 5.0 8.1 - - + -
93O LEU* 3.8 28.7 - - + -
115O ALA* 2.9 27.7 + - + +
116O LEU* 4.0 13.7 - - + +
118O ALA* 1.3 76.6 - - - +
120O ALA* 1.3 57.2 + - - +
121O ARG 3.5 0.3 + - - -
122O SER 3.6 5.3 - - - +
123O GLY 3.2 18.7 - - - +
124O MET* 3.3 24.5 - - + +
126O ILE* 6.2 0.4 - - - -
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Residues in contact with ALA 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116O LEU 2.9 19.2 + - - +
117O ARG 3.4 5.8 - - - +
118O ALA 3.1 0.2 - - - -
119O LEU* 1.3 76.6 - - - +
121O ARG* 1.3 63.2 + - - +
122O SER 3.6 0.2 - - - -
123O GLY 4.6 5.6 - - - +
124O MET 5.1 1.8 - - - -
126O ILE* 4.3 8.5 - - + +
52a ASP* 3.0 44.4 - - + +
53a ILE* 3.8 14.8 - - + -
56a ALA* 5.1 4.9 - - - +
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Residues in contact with ARG 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201F LYS 5.6 2.6 + - - -
204F ARG* 3.6 42.7 + - - +
75O MET* 4.8 15.9 - - + +
79O GLN* 5.0 3.6 - - - +
117O ARG* 2.9 24.1 + - + +
118O ALA* 3.0 17.8 + - - +
120O ALA* 1.3 79.6 - - - +
122O SER* 1.3 63.4 + - - +
123O GLY 4.2 1.1 + - - -
52a ASP* 3.3 34.1 + - - -
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Residues in contact with SER 122 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79O GLN* 4.3 19.4 + - - -
82O ALA* 5.0 7.1 - - - +
86O LYS* 3.3 24.2 + - - -
118O ALA 3.8 2.4 + - - +
119O LEU 3.6 6.6 - - - +
121O ARG* 1.3 79.9 - - - +
123O GLY* 1.3 67.4 + - - +
124O MET* 3.7 3.5 + - - +
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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