Contacts of the helix formed by residues 106 - 122 (chain F) in PDB entry 6DVD
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 GLU 106 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1049C TYR* 4.6 0.6 - - - -
1054C GLN* 5.4 1.2 + - - -
1096C THR* 4.6 5.9 - - - +
1099C ARG* 3.2 32.6 + - - -
1100C VAL* 3.3 32.4 - - + +
104F PRO 4.8 4.9 - - - +
105F ASP* 1.3 81.1 - - - +
107F VAL* 1.3 55.0 + - - +
108F ASN 3.5 1.8 - - - -
109F ALA* 3.8 15.0 - - + -
110F ALA* 2.7 37.0 + - + +
113F ARG* 5.2 4.5 - - - +
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Residues in contact with VAL 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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1046C THR* 3.3 28.9 - - + +
1103C TYR* 3.6 45.5 - - + +
473D LYS* 3.7 23.8 - - + -
105F ASP* 3.2 22.2 + - + +
106F GLU* 1.3 77.4 - - - +
108F ASN* 1.3 68.3 + - - +
110F ALA* 3.2 4.8 + - - +
111F LEU* 3.0 30.6 + - + +
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Residues in contact with ASN 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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470D LYS* 4.3 14.6 - - - +
473D LYS* 3.2 37.9 + - - +
105F ASP* 4.9 7.8 + - - +
106F GLU 3.5 0.2 - - - -
107F VAL* 1.3 83.3 - - - +
109F ALA* 1.3 61.7 + - - +
111F LEU* 3.7 3.7 + - - +
112F ASP* 3.1 33.4 + - - +
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Residues in contact with ALA 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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815C THR* 6.0 7.2 - - + +
817C GLU* 5.9 0.7 - - - +
105F ASP 5.5 0.2 + - - -
106F GLU* 3.4 18.4 + - + +
107F VAL 3.2 0.6 - - - -
108F ASN* 1.3 77.7 - - - +
110F ALA* 1.3 64.2 + - - +
112F ASP* 3.5 7.1 + - - +
113F ARG* 3.1 28.5 + - - +
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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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1100C VAL* 4.4 9.9 - - + +
1103C TYR* 5.7 6.5 - - + -
1104C GLU* 4.0 17.2 - - + +
106F GLU 2.7 23.8 + - - +
107F VAL* 3.8 4.3 - - - +
109F ALA* 1.3 72.8 - - - +
111F LEU* 1.3 61.7 + - + +
113F ARG* 3.4 27.3 + - - +
114F LEU* 3.0 33.7 + - - +
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Residues in contact with LEU 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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1103C TYR* 4.6 8.5 - - + -
1107C VAL* 4.4 13.2 - - + -
457D MET* 4.7 4.3 - - + -
469D ILE* 3.9 48.2 - - + +
470D LYS* 4.6 13.2 - - + -
473D LYS* 3.9 34.1 - - + -
107F VAL* 3.0 24.4 + - + +
108F ASN 4.1 3.6 - - - +
110F ALA* 1.3 74.9 - - + +
112F ASP* 1.3 67.0 + - - +
114F LEU* 3.2 19.3 + - + +
115F LEU* 3.0 27.9 + - - +
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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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817C GLU* 5.5 5.6 - - + -
821C LEU* 4.2 25.9 - - + +
470D LYS* 3.0 37.2 + - - +
108F ASN* 3.1 20.4 + - - +
109F ALA* 3.9 6.9 - - - +
110F ALA 3.4 0.2 - - - -
111F LEU* 1.3 77.0 - - - +
113F ARG* 1.3 56.9 + - - +
115F LEU* 3.2 7.8 + - - +
116F ILE* 2.8 37.2 + - + +
175F VAL* 6.0 1.2 - - - +
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Residues in contact with ARG 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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817C GLU* 4.0 37.5 + - + +
1100C VAL* 3.9 15.4 - - - +
1104C GLU* 2.5 30.5 + - - +
106F GLU* 5.0 5.9 + - - +
109F ALA* 3.1 17.6 + - - +
110F ALA* 3.6 27.6 - - - +
111F LEU 3.3 0.2 - - - -
112F ASP* 1.3 77.4 - - - +
114F LEU* 1.3 65.1 + - + +
116F ILE* 4.0 1.5 - - - +
117F ALA* 3.1 24.6 + - + +
136F TYR* 5.4 1.7 + - - +
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Residues in contact with LEU 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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1104C GLU* 4.0 31.9 - - + +
1107C VAL* 3.8 29.4 - - + -
1108C LYS* 3.6 33.2 - - + +
469D ILE* 5.5 3.6 - - + -
110F ALA 3.0 19.6 + - - +
111F LEU* 3.4 19.1 - - + +
112F ASP 3.2 0.2 - - - -
113F ARG* 1.3 79.8 - - + +
115F LEU* 1.3 66.9 + - + +
117F ALA* 3.3 8.3 + - + +
118F ASP* 3.2 26.3 + - - +
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Residues in contact with LEU 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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468D ASN* 3.7 36.8 - - + +
469D ILE* 3.9 18.6 - - + +
470D LYS* 3.9 20.0 - - + +
111F LEU 3.0 20.5 + - - +
112F ASP* 3.9 6.5 - - - +
114F LEU* 1.3 74.9 - - + +
116F ILE* 1.3 67.6 + - + +
118F ASP* 3.3 15.2 + - + +
119F ALA* 3.1 22.9 + - - +
170F LEU* 4.1 13.8 - - + +
173F LEU* 5.1 12.3 - - + -
175F VAL* 4.3 11.2 - - + -
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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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817C GLU* 4.6 12.8 - - + +
820C LEU* 3.9 24.5 - - + -
821C LEU* 4.5 18.6 - - + -
824C ILE* 3.9 28.9 - - + -
112F ASP 2.8 27.4 + - - +
113F ARG* 4.0 6.7 - - - +
115F LEU* 1.3 73.0 - - + +
117F ALA* 1.3 58.0 + - - +
119F ALA* 3.5 4.1 + - + +
120F LEU* 3.0 35.6 + - + +
136F TYR* 3.5 24.2 - - - +
166F LEU* 5.8 2.0 - - + -
170F LEU* 4.3 12.6 - - + -
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Residues in contact with ALA 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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113F ARG* 3.1 21.0 + - + +
114F LEU* 3.6 8.7 - - + +
115F LEU 3.2 0.2 - - - -
116F ILE* 1.3 78.9 - - - +
118F ASP* 1.3 63.8 + - - +
120F LEU* 3.5 11.3 + - - +
121F ALA* 3.4 19.6 + - - +
136F TYR* 5.6 1.6 - - - +
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Residues in contact with ASP 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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1108C LYS* 6.2 0.2 - - - -
114F LEU 3.2 14.7 + - - +
115F LEU* 3.7 19.1 - - + +
116F ILE 3.3 0.2 - - - -
117F ALA* 1.3 76.7 - - - +
119F ALA* 1.3 65.2 + - - +
121F ALA* 3.1 18.9 + - - +
122F GLN* 3.6 11.8 + - - +
169F THR* 5.5 0.7 - - - -
173F LEU* 5.8 7.8 - - + +
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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 LEU 3.1 13.5 + - - +
116F ILE* 4.0 5.4 - - + +
118F ASP* 1.3 78.9 - - - +
120F LEU* 1.3 61.2 + - - +
121F ALA 3.5 0.2 + - - -
122F GLN* 3.5 10.7 + - - +
123F LEU* 3.6 9.7 - - - +
166F LEU* 3.3 29.4 - - + +
169F THR* 3.9 32.7 + - + -
170F LEU* 4.1 14.4 - - + -
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Residues in contact with LEU 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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820C LEU* 4.5 2.7 - - + -
116F ILE* 3.0 34.7 + - + +
117F ALA* 3.7 9.4 - - - +
118F ASP 3.1 0.2 - - - -
119F ALA* 1.3 80.0 - - - +
121F ALA* 1.3 61.6 + - - +
123F LEU* 3.4 14.8 + - + +
128F ARG* 3.3 30.5 + - + +
131F ILE* 3.6 33.0 - - + -
132F GLN* 5.5 2.5 - - + +
136F TYR* 4.0 31.4 - - + +
166F LEU* 3.8 26.9 - - + -
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Residues in contact with ALA 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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117F ALA 3.4 9.2 + - - +
118F ASP* 3.1 13.4 + - - +
120F LEU* 1.3 80.6 - - - +
122F GLN* 1.3 59.1 + - + +
123F LEU 3.1 10.7 + - - +
128F ARG* 3.8 10.8 + - - +
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Residues in contact with GLN 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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118F ASP 3.6 10.0 + - - +
119F ALA 3.5 8.8 + - - +
120F LEU 3.3 0.8 - - - -
121F ALA* 1.3 77.0 - - + +
123F LEU* 1.3 65.2 + - - +
169F THR* 3.4 29.4 + - - +
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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