Contacts of the helix formed by residues 100 - 110 (chain F) in PDB entry 4DHZ
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 GLN 100 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A PRO* 4.7 9.7 - - - +
130A TRP* 2.6 36.6 + - + +
131A THR* 4.4 6.9 - - + +
7F ARG* 3.5 13.2 - - - +
11F GLU* 3.2 12.3 - - + +
62F TYR* 4.1 1.6 - - - -
67F PRO* 5.5 0.2 - - - -
95F TRP* 3.8 6.4 - - - -
98F ALA 4.4 9.7 + - - -
99F LEU* 1.3 75.3 - - - +
101F ILE* 1.3 65.6 + - - +
102F ARG* 3.5 30.6 + - + +
103F THR* 2.8 33.6 + - - +
104F VAL* 3.3 14.2 + - - +
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Residues in contact with ILE 101 (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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11F GLU* 2.6 36.7 + - + +
15F LEU* 4.2 18.6 - - + -
25F ALA* 5.9 0.7 - - + -
35F PHE* 4.4 18.2 - - + -
56F LEU* 3.7 38.6 - - + -
58F LEU* 3.9 27.4 - - + -
62F TYR* 4.1 2.4 + - - +
67F PRO* 4.7 2.9 - - + -
100F GLN* 1.3 70.0 - - - +
102F ARG* 1.3 59.6 + - - +
104F VAL* 2.8 25.9 + - - +
105F LEU* 3.0 34.4 + - + +
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Residues in contact with ARG 102 (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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130A TRP* 3.7 29.0 - - - +
11F GLU* 5.3 0.6 + - - +
14F ARG* 3.5 30.1 + - - +
15F LEU* 3.7 30.8 - - + +
18F GLU* 2.7 48.6 + - - +
20F VAL* 4.8 15.3 - - + -
100F GLN* 3.3 20.9 + - + +
101F ILE* 1.3 77.9 - - - +
103F THR* 1.3 59.8 + - - +
105F LEU* 3.9 6.5 - - - +
106F LEU* 3.2 43.9 + - + +
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Residues in contact with THR 103 (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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90F ILE* 3.9 12.7 - - + +
99F LEU* 3.7 26.2 - - + -
100F GLN* 2.8 41.9 + - - +
102F ARG* 1.3 73.4 - - - +
104F VAL* 1.3 66.6 + - - +
106F LEU* 3.8 6.4 + - - +
107F SER* 3.2 26.3 + - - -
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Residues in contact with VAL 104 (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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56F LEU* 4.3 8.3 - - + -
67F PRO* 4.0 24.2 - - + -
69F VAL* 3.8 12.3 - - + -
88F LEU* 4.7 0.6 - - + +
90F ILE* 4.3 10.1 - - + -
91F LEU* 3.7 26.0 - - + -
95F TRP* 4.1 13.5 - - + -
100F GLN 3.3 15.5 - - - +
101F ILE* 2.8 8.9 + - - +
103F THR* 1.3 76.8 - - - +
105F LEU* 1.3 65.7 + - + +
107F SER* 3.6 1.7 - - - -
108F ILE* 3.0 48.1 + - + +
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Residues in contact with LEU 105 (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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15F LEU* 4.8 4.3 - - + -
20F VAL* 4.2 12.1 - - + -
23F ILE* 4.0 36.0 - - + +
25F ALA* 4.0 15.5 - - + -
37F VAL* 4.0 28.3 - - + -
39F ILE* 5.0 6.0 - - + +
54F LEU* 6.0 1.3 - - + -
56F LEU* 4.5 10.3 - - + -
69F VAL* 6.0 1.1 - - + -
101F ILE* 3.0 39.4 + - + +
102F ARG* 3.9 7.2 - - - +
104F VAL* 1.3 76.6 - - + +
106F LEU* 1.3 52.2 - - + +
108F ILE* 3.1 13.7 + - + +
109F GLN* 2.8 34.5 + - - +
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Residues in contact with LEU 106 (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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20F VAL* 4.1 19.7 - - + -
21F PRO* 6.3 1.1 - - + -
23F ILE* 4.6 0.4 - - - +
102F ARG* 3.2 30.8 + - + +
103F THR* 4.1 5.8 - - - +
105F LEU* 1.3 78.2 - - - +
107F SER* 1.3 53.5 + - - +
109F GLN* 3.5 26.4 + - - +
110F ALA* 2.8 35.2 + - - +
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Residues in contact with SER 107 (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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88F LEU* 3.5 19.6 - - - +
89F ASP* 5.0 1.2 + - - -
90F ILE* 3.7 19.5 - - - +
103F THR* 3.2 18.6 + - - -
104F VAL 3.6 3.6 - - - -
106F LEU* 1.3 76.1 - - - +
108F ILE* 1.3 66.5 + - - +
110F ALA* 3.4 8.0 + - - +
111F LEU* 3.2 25.0 + - - +
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Residues in contact with ILE 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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39F ILE* 3.9 20.4 - - + -
54F LEU* 4.1 4.3 - - + -
69F VAL* 3.9 22.7 - - + -
71F PHE* 4.0 25.4 - - + -
86F ILE* 3.9 15.9 - - + -
88F LEU* 4.1 14.6 - - + -
91F LEU* 5.0 0.9 - - + -
104F VAL* 3.0 39.0 + - + +
105F LEU* 3.5 11.7 - - + +
107F SER* 1.3 72.4 - - - +
109F GLN* 1.3 61.7 + - - +
111F LEU* 2.9 38.4 + - + +
112F LEU* 3.7 7.5 + - + +
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Residues in contact with GLN 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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21F PRO 3.4 20.4 + - - +
22F GLY* 4.1 6.2 - - - +
23F ILE* 3.3 28.9 - - + +
39F ILE* 4.5 14.0 - - + +
40F ALA 5.3 2.5 - - - +
42F PRO* 5.4 5.4 - - + -
105F LEU 2.8 19.6 + - - +
106F LEU* 3.5 29.3 + - - +
108F ILE* 1.3 74.5 - - - +
110F ALA* 1.3 49.7 + - - +
112F LEU* 2.8 18.4 + - + +
113F SER* 2.7 47.9 + - - +
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Residues in contact with ALA 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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106F LEU 2.8 21.7 + - - +
107F SER* 3.6 9.2 - - - +
108F ILE 3.3 0.4 - - - -
109F GLN* 1.3 72.9 - - - +
111F LEU* 1.3 54.6 + - - +
112F LEU 3.2 0.7 - - - -
113F SER* 3.6 12.3 - - - -
114F ALA* 2.7 30.7 - - + +
116F ASN* 3.8 5.9 - - - +
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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