Contacts of the helix formed by residues 110 - 123 (chain F) in PDB entry 3F0D
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 HIS 110 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25F VAL* 4.1 23.1 - - + +
26F THR 5.0 2.5 - - - -
27F ILE* 3.7 32.7 - - + +
28F PRO* 4.5 10.7 - - + +
106F LYS 3.5 22.0 + - - -
107F LEU* 2.8 9.9 + - - +
109F PRO* 1.3 94.9 - - + +
111F ILE* 1.3 64.8 + - - +
112F ASP 3.4 2.9 - - - -
113F ALA* 3.3 10.2 + - - +
114F MET* 3.2 37.9 + - + +
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Residues in contact with ILE 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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58E ASP* 5.6 2.5 - - - +
100F ILE* 4.3 4.3 - - + -
107F LEU* 3.3 15.4 + - + +
108F ALA* 3.4 18.2 + - - +
110F HIS* 1.3 77.6 - - - +
112F ASP* 1.3 68.0 + - - +
114F MET* 3.2 15.2 + - + +
115F ARG* 3.0 35.1 + - - +
131F VAL* 3.4 48.5 - - + +
133F ALA* 4.2 22.0 - - + +
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Residues in contact with ASP 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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108F ALA 4.8 1.2 + - - -
109F PRO 5.0 3.0 + - - +
110F HIS 3.4 1.2 - - - -
111F ILE* 1.3 81.9 - - - +
113F ALA* 1.3 62.9 + - - +
115F ARG* 3.4 31.3 + - - +
116F ALA* 3.1 22.9 + - - +
126F LEU* 5.3 0.9 - - - +
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Residues in contact with ALA 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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25F VAL* 3.7 20.2 - - + -
109F PRO 5.5 1.0 + - - +
110F HIS* 3.3 12.7 + - - +
111F ILE 3.2 0.6 - - - -
112F ASP* 1.3 79.0 - - - +
114F MET* 1.3 62.8 + - - +
116F ALA* 3.3 6.9 + - - +
117F ASN* 3.0 29.4 + - - +
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Residues in contact with MET 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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22F ILE* 3.5 40.6 - - + +
23F GLY* 3.6 16.4 - - - +
25F VAL* 3.6 5.2 - - + -
27F ILE* 3.9 21.1 - - + -
42F LEU* 3.8 15.7 - - + -
100F ILE* 3.7 26.5 - - + -
107F LEU* 4.6 6.5 - - + +
110F HIS* 3.2 24.2 + - + +
111F ILE* 3.2 13.8 + - + +
113F ALA* 1.3 76.4 - - - +
115F ARG* 1.3 61.9 + - - +
117F ASN* 3.2 2.6 + - - +
118F ILE* 3.0 30.5 + - - +
131F VAL* 4.2 9.4 - - + -
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Residues in contact with ARG 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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55E ALA 4.7 10.0 + - - -
111F ILE* 3.0 25.4 + - + +
112F ASP* 3.6 29.5 + - - +
114F MET* 1.3 75.9 - - - +
116F ALA* 1.3 56.2 + - - +
118F ILE* 3.4 2.6 + - - +
119F ALA* 3.0 30.7 + - - +
126F LEU* 2.7 50.6 + - + +
127F ASP* 4.5 3.8 - - - +
129F VAL* 3.0 31.0 + - + +
130F ASN* 4.3 6.7 + - - +
131F VAL* 3.9 24.0 - - + +
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Residues in contact with ALA 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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112F ASP 3.1 14.0 + - - +
113F ALA* 3.6 10.5 - - - +
115F ARG* 1.3 77.0 - - - +
117F ASN* 1.3 65.2 + - - +
119F ALA* 3.5 1.2 + - - +
120F ALA* 3.0 26.2 + - - +
126F LEU* 3.8 18.3 - - + +
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Residues in contact with ASN 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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23F GLY 3.0 24.8 + - - +
24F GLY* 3.6 20.4 + - - -
25F VAL* 3.6 7.1 - - - +
43F LEU* 6.2 0.7 - - + -
76F ARG* 3.4 35.0 + - - +
113F ALA* 3.0 18.6 + - - +
114F MET 3.2 7.6 + - - +
116F ALA* 1.3 78.0 - - - +
118F ILE* 1.3 62.2 + - + +
120F ALA* 3.4 1.7 + - - -
121F ASP* 3.0 31.5 + - - +
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Residues in contact with ILE 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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23F GLY 5.0 0.9 - - - +
42F LEU* 3.9 13.2 - - + -
43F LEU* 3.7 22.0 - - + -
46F ILE* 3.6 31.2 - - + -
79F LEU* 4.6 9.4 - - + -
96F VAL* 5.2 1.8 - - + -
114F MET* 3.0 20.7 + - + +
115F ARG 3.8 2.7 - - - +
117F ASN* 1.3 75.2 - - + +
119F ALA* 1.3 66.3 + - - +
121F ASP* 3.2 1.2 + - - +
122F LEU* 2.9 45.2 + - + +
129F VAL* 3.7 19.3 - - + -
131F VAL* 3.8 23.3 - - + -
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Residues in contact with ALA 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 ARG 3.0 18.1 + - - +
116F ALA 3.8 3.4 - - - +
118F ILE* 1.3 77.8 - - - +
120F ALA* 1.3 57.8 + - - +
123F ASP* 2.9 26.0 + - - -
124F LEU* 2.9 32.7 + - - +
126F LEU* 4.1 20.9 - - + +
129F VAL* 4.0 18.8 - - + -
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Residues in contact with ALA 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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76F ARG* 4.3 11.0 - - - +
116F ALA 3.0 18.7 + - - +
117F ASN* 3.7 4.3 - - - +
119F ALA* 1.3 76.6 - - - +
121F ASP* 1.3 64.0 + - - +
123F ASP* 3.3 12.2 + - - +
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Residues in contact with ASP 121 (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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43F LEU* 5.1 0.5 - - - +
76F ARG* 2.8 51.7 + - - +
79F LEU* 3.9 20.6 - - + +
80F ARG* 3.0 54.2 + - + +
83F ALA* 4.3 4.7 - - - +
117F ASN 3.0 14.3 + - - +
118F ILE 3.2 3.6 + - - +
120F ALA* 1.3 78.7 - - - +
122F LEU* 1.3 62.9 + - - +
123F ASP* 3.3 1.3 - - - +
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Residues in contact with LEU 122 (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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46F ILE* 4.5 3.8 - - + -
50F LEU* 3.9 16.4 - - + -
79F LEU* 3.8 27.1 - - + -
83F ALA* 3.8 27.3 - - + +
93F ILE* 3.9 15.0 - - + +
96F VAL* 3.8 29.2 - - + -
118F ILE* 2.9 33.5 + - + +
119F ALA 4.3 0.2 - - - +
121F ASP* 1.3 75.9 - - - +
123F ASP* 1.3 71.0 + - - +
124F LEU* 3.4 25.8 + - + +
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Residues in contact with ASP 123 (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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119F ALA 2.9 8.7 + - - -
120F ALA* 3.3 10.3 + - - +
121F ASP 3.3 1.5 - - - +
122F LEU* 1.3 81.1 - - - +
124F LEU* 1.3 57.9 + - - +
125F PRO* 4.7 0.7 - - - +
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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