Contacts of the helix formed by residues 107 - 120 (chain F) 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 ASN 107 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23F TRP* 3.4 25.5 - - - +
24F SER* 5.0 5.3 - - - +
25F THR* 4.5 12.9 - - - +
26F ASP 3.2 28.3 + - - +
27F ASP* 5.0 2.3 - - - +
28F VAL* 3.7 18.0 - - + +
100F ILE* 5.2 1.6 - - - +
105F GLY 4.0 6.6 - - - +
106F GLU* 1.3 89.8 - - - +
108F PRO* 1.3 67.4 - - + +
109F LEU* 3.7 12.8 - - + +
110F GLN* 3.5 14.3 + - - +
111F VAL* 4.0 6.8 + - - +
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Residues in contact with PRO 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F TRP* 3.4 33.7 - - + +
97F PHE* 3.5 46.0 - - + -
100F ILE* 3.7 27.3 - - + +
101F HIS* 5.7 0.4 - - + -
107F ASN* 1.3 82.4 - - + +
109F LEU* 1.3 60.4 + - - +
110F GLN 3.2 1.1 - - - -
111F VAL* 3.2 13.0 - - + +
112F LEU* 2.9 30.6 + - - +
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Residues in contact with LEU 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F THR* 5.3 14.6 - - + -
26F ASP 4.9 7.0 - - - +
27F ASP 5.0 1.3 - - - +
28F VAL* 3.7 24.2 - - + -
41F VAL* 3.6 29.4 - - + -
68F ILE* 3.6 31.4 - - + -
97F PHE* 6.3 0.4 - - - -
107F ASN* 3.1 6.5 - - + +
108F PRO* 1.3 83.0 - - + +
110F GLN* 1.3 56.0 + - - +
112F LEU* 4.1 8.3 - - + -
113F VAL* 2.9 43.9 + - + +
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Residues in contact with GLN 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F VAL* 3.3 43.8 - - + +
29F GLN 4.4 9.5 + - - -
31F ASN* 6.4 0.6 - - - +
106F GLU* 5.3 6.7 - - + -
107F ASN* 3.5 14.4 + - + +
108F PRO 3.2 1.0 - - - -
109F LEU* 1.3 79.2 - - - +
111F VAL* 1.3 62.5 + - + +
113F VAL* 3.9 2.7 - - - +
114F ASN* 2.9 66.9 + - - +
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Residues in contact with VAL 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F ILE* 3.8 31.0 - - + -
103F LEU* 6.6 0.4 - - + -
104F THR* 4.8 15.5 - - + +
105F GLY 5.6 2.2 - - - +
107F ASN 4.0 4.5 + - - +
108F PRO* 3.2 17.7 - - + +
110F GLN* 1.3 79.6 - - + +
112F LEU* 1.3 57.2 + - + +
114F ASN* 3.8 12.5 - - - +
115F ALA* 2.9 27.2 + - - +
177F LEU* 4.0 16.7 - - + +
178F ILE* 5.2 10.8 - - + -
181F ALA* 4.9 13.3 - - + +
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Residues in contact with LEU 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F ILE* 3.7 35.2 - - + +
69F VAL* 5.7 3.6 - - + +
72F LEU* 5.3 14.8 - - + -
97F PHE* 5.6 11.9 - - + -
108F PRO 2.9 20.0 + - - +
109F LEU* 3.6 9.4 - - + +
110F GLN 3.1 0.2 - - - -
111F VAL* 1.3 76.5 - - + +
113F VAL* 1.3 60.9 + - - +
115F ALA* 3.0 5.5 + - - +
116F ILE* 2.9 38.3 + - + +
154F LEU* 4.6 10.3 - - + -
177F LEU* 3.8 35.2 - - + -
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Residues in contact with VAL 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F VAL* 4.2 7.2 - - + -
29F GLN 5.6 4.5 - - - +
30F ILE* 5.5 11.4 - - + -
39F ILE* 4.6 20.9 - - + -
41F VAL* 4.0 20.4 - - + -
68F ILE* 4.7 4.5 - - + -
109F LEU* 2.9 37.6 + - + +
110F GLN* 4.0 4.0 - - - +
112F LEU* 1.3 75.5 - - - +
114F ASN* 1.3 60.5 + - - +
116F ILE* 3.2 8.0 + - + +
117F ILE* 2.9 48.2 + - + +
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Residues in contact with ASN 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F ASN* 4.8 12.1 + - - -
110F GLN* 2.9 56.3 + - - +
111F VAL* 3.9 11.0 - - - +
113F VAL* 1.3 78.2 - - - +
115F ALA* 1.3 57.2 + - - +
117F ILE* 4.5 7.9 - - - +
118F ASN* 2.3 48.7 + - - +
180F ALA 4.8 0.7 - - - -
181F ALA* 4.7 11.2 - - + +
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Residues in contact with ALA 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F VAL 2.9 19.2 + - - +
112F LEU* 3.0 9.4 + - - +
114F ASN* 1.3 74.1 - - - +
116F ILE* 1.3 55.7 + - - +
118F ASN 3.8 0.3 - - - -
119F SER* 2.6 38.9 + - - -
154F LEU* 4.7 7.6 - - + -
177F LEU* 4.0 31.2 - - + +
180F ALA* 4.2 20.5 - - + +
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Residues in contact with ILE 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F LEU* 5.9 0.9 - - + -
39F ILE* 4.2 16.2 - - + -
68F ILE* 6.2 3.6 - - + -
112F LEU* 2.9 27.9 + - + +
113F VAL* 3.2 9.6 + - + +
115F ALA* 1.3 77.7 - - - +
117F ILE* 1.3 63.4 + - + +
119F SER* 3.4 17.3 + - - -
120F GLY* 3.7 4.2 + - - -
146F ARG* 4.9 7.9 + - - +
147F VAL* 4.0 34.8 - - + -
150F ALA* 4.2 10.2 - - + +
151F ILE* 3.9 22.0 - - + -
154F LEU* 3.6 29.2 - - + -
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Residues in contact with ILE 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ILE* 5.1 8.1 - - + -
31F ASN* 3.4 31.2 - - - +
32F ASP* 4.1 21.1 - - - +
39F ILE* 5.7 3.4 - - + -
113F VAL* 2.9 38.9 + - + +
114F ASN* 4.2 8.3 - - - +
116F ILE* 1.3 78.5 - - + +
118F ASN* 1.3 65.6 + - - +
119F SER 3.3 0.5 + - - -
120F GLY* 3.4 14.6 + - - -
146F ARG* 5.0 21.8 + - - +
193F LYS* 5.1 1.4 + - - -
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Residues in contact with ASN 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F ASN* 2.3 46.2 + - - +
115F ALA 4.2 0.2 - - - +
117F ILE* 1.3 76.4 - - - +
119F SER* 1.3 65.9 + - - +
180F ALA 3.2 17.0 - - - +
181F ALA 2.8 24.6 + - - +
182F LYS 5.3 0.9 - - - -
183F GLY* 5.0 2.8 + - - +
190F ILE* 3.4 12.3 - - + +
193F LYS* 3.2 28.7 + - - +
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Residues in contact with SER 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F ALA 2.6 26.1 + - - -
116F ILE* 3.4 7.6 - - - -
117F ILE 3.2 0.4 - - - -
118F ASN* 1.3 75.0 - - - +
120F GLY* 1.3 66.3 + - - +
121F PRO* 3.4 7.8 - - - +
150F ALA* 3.7 28.2 + - - +
153F LEU* 5.0 3.1 - - - +
154F LEU* 4.7 5.4 - - - +
180F ALA* 5.5 1.3 - - - +
189F ALA* 3.9 27.5 - - - +
190F ILE* 5.0 0.9 - - - -
193F LYS* 3.1 26.8 - - - +
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Residues in contact with GLY 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F ILE 3.7 3.4 + - - -
117F ILE 3.4 13.2 + - - -
118F ASN 4.5 0.4 - - - -
119F SER* 1.3 78.4 - - - +
121F PRO* 1.3 61.9 - - - +
122F ARG* 2.7 27.1 + - - +
146F ARG* 3.7 17.9 - - - -
193F LYS* 4.2 16.8 - - - +
197F GLU* 5.2 1.7 - - - +
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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