Contacts of the helix formed by residues 141 - 156 (chain F) in PDB entry 4S0H
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 THR 141 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135F ALA* 4.0 1.8 - - - -
140F LEU* 1.3 75.6 - - - +
142F SER* 1.3 63.8 + - - +
143F THR* 3.6 10.3 + - - -
144F GLN* 2.9 45.2 + - - +
145F VAL* 3.4 13.5 + - - +
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Residues in contact with SER 142 (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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131F ARG* 3.8 14.7 - - - +
132F ASP* 2.8 37.7 + - - -
135F ALA* 4.1 10.0 - - - +
141F THR* 1.3 73.0 - - - +
143F THR* 1.3 57.9 + - - +
145F VAL* 3.2 5.3 + - - +
146F LYS* 2.9 30.2 + - - +
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Residues in contact with THR 143 (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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141F THR* 3.2 9.6 + - - -
142F SER* 1.3 80.3 - - - +
144F GLN* 1.3 57.4 + - + +
146F LYS* 3.8 21.0 + - - +
147F ILE* 2.9 41.2 + - + +
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Residues in contact with GLN 144 (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 PHE* 3.9 27.9 - - + -
140F LEU* 3.6 19.6 - - + +
141F THR* 2.9 47.4 + - - +
142F SER 3.2 0.2 - - - -
143F THR* 1.3 79.1 - - + +
145F VAL* 1.3 58.3 + - - +
147F ILE* 3.7 1.5 - - - +
148F TRP* 2.8 29.9 + - - +
15G A 3.1 39.7 + - - +
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Residues in contact with VAL 145 (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 LEU* 4.2 8.7 - - + -
126F LEU* 4.5 0.4 - - + -
131F ARG* 4.1 20.9 - - + +
134F LEU* 3.9 26.5 - - + -
135F ALA* 4.3 17.9 - - + +
138F LEU* 5.2 0.4 - - + -
140F LEU* 4.2 23.6 - - + -
141F THR 3.5 13.2 - - - +
142F SER* 3.2 7.8 + - - +
144F GLN* 1.3 75.6 - - - +
146F LYS* 1.3 65.6 + - - +
147F ILE 3.2 0.2 - - - -
148F TRP* 3.3 5.4 + - - +
149F PHE* 3.1 37.3 + - + -
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Residues in contact with LYS 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131F ARG* 3.4 45.1 - - - +
142F SER 2.9 12.5 + - - +
143F THR* 3.8 23.8 + - - +
145F VAL* 1.3 75.5 - - - +
147F ILE* 1.3 69.8 + - + +
149F PHE* 3.7 5.4 + - - +
150F GLN* 3.1 27.2 + - - +
153F ARG* 4.4 4.6 + - - +
1H C 6.2 3.8 - - + -
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Residues in contact with ILE 147 (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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143F THR* 2.9 33.0 + - + +
144F GLN* 4.0 4.3 - - - +
146F LYS* 1.3 87.3 - - + +
148F TRP* 1.3 60.2 + - - +
149F PHE 3.2 0.4 - - - -
150F GLN* 3.5 29.7 - - - +
151F ASN* 2.7 51.4 + - - +
14G A 4.9 1.3 - - + -
15G A 3.9 29.4 - - + +
16G G 6.4 0.4 - - - +
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Residues in contact with TRP 148 (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 PHE* 3.9 10.9 - + + -
113F VAL* 4.7 10.7 - - + +
116F LEU* 3.2 66.8 - - + +
117F GLU* 3.8 28.3 - - + -
120F PHE* 3.9 10.1 - + + -
144F GLN 2.8 21.8 + - - +
145F VAL* 3.3 6.5 + - - +
147F ILE* 1.3 72.7 - - - +
149F PHE* 1.3 71.6 + + - +
151F ASN* 3.6 4.5 - - - +
152F ARG* 2.8 65.1 + - + +
155F LYS* 5.9 2.0 - - - +
14G A 3.6 36.5 + - - -
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Residues in contact with PHE 149 (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 LEU* 4.2 7.9 - - + -
119F ARG* 4.0 20.4 - - + -
120F PHE* 3.7 26.0 - + + -
123F GLN 3.6 21.3 - - - -
124F ARG 3.6 17.3 - - - -
125F TYR* 5.1 0.7 - - - -
126F LEU* 3.7 36.1 - - + +
131F ARG* 5.9 0.9 - - + -
134F LEU* 4.3 6.1 - - + -
145F VAL* 3.1 36.1 + - + +
146F LYS* 4.0 3.4 - - - +
148F TRP* 1.3 86.8 - + - +
150F GLN* 1.3 62.0 + - - +
152F ARG* 4.2 1.6 - - - -
153F ARG* 2.8 52.0 + - - +
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Residues in contact with GLN 150 (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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146F LYS* 3.1 18.5 + - - +
147F ILE* 3.2 29.8 + - - +
149F PHE* 1.3 78.7 - - - +
151F ASN* 1.3 67.1 + - - +
152F ARG 3.1 0.9 + - - -
153F ARG* 3.3 19.0 + - - +
154F TYR* 3.3 21.7 + - + +
16G G 4.5 3.4 + - - -
17G T 4.5 3.8 + - - -
1H C 4.3 11.6 + - - -
2H C 3.1 46.5 + - + +
3H A 3.6 18.8 + - - +
4H C 5.0 2.5 - - - +
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Residues in contact with ASN 151 (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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147F ILE* 2.7 33.1 + - - +
148F TRP* 3.9 2.9 - - - +
150F GLN* 1.3 76.6 + - - +
152F ARG* 1.3 57.2 + - - +
154F TYR* 4.1 7.5 - - - +
155F LYS* 3.2 35.3 + - - +
14G A 3.3 28.3 + - - +
15G A 2.5 52.6 + - - +
16G G 4.4 1.6 - - - +
4H C 3.7 11.3 + - - +
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Residues in contact with ARG 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F GLU* 3.3 33.0 + - - -
120F PHE* 3.6 32.4 - - + -
121F LYS* 5.1 7.7 - - - +
148F TRP* 2.8 49.2 + - + +
149F PHE* 3.8 3.8 - - - +
151F ASN* 1.3 75.4 - - - +
153F ARG* 1.3 63.0 + - - +
154F TYR 3.1 1.8 - - - -
155F LYS* 3.3 19.8 + - - +
156F SER* 2.9 60.7 + - - +
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Residues in contact with ARG 153 (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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120F PHE* 3.8 13.0 - - + -
124F ARG* 2.8 46.9 + - + +
125F TYR* 3.3 43.5 - - - +
126F LEU 5.7 0.8 - - - +
131F ARG* 5.8 3.6 - - - +
146F LYS* 4.4 4.6 + - - +
149F PHE* 2.8 45.2 + - - +
150F GLN* 3.6 20.6 - - - +
152F ARG* 1.3 72.3 - - - +
154F TYR* 1.3 61.2 + - - +
156F SER* 3.6 19.8 - - - -
157F LYS* 4.5 9.0 + - - +
1H C 4.0 11.9 + - - -
2H C 2.2 40.2 + - - +
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Residues in contact with TYR 154 (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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150F GLN* 3.3 15.2 + - + +
151F ASN* 4.1 7.2 - - - +
152F ARG 3.1 0.4 - - - -
153F ARG* 1.3 78.7 - - - +
155F LYS* 1.3 68.1 + - + +
157F LYS* 2.9 45.2 + - + +
2H C 5.5 0.4 - - - -
3H A 3.2 43.1 - + + +
4H C 3.5 63.1 + + + +
5H T 4.1 15.6 - - + +
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Residues in contact with LYS 155 (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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148F TRP* 5.9 2.2 - - - +
151F ASN* 3.2 29.6 + - - +
152F ARG* 3.3 23.5 + - - +
154F TYR* 1.3 80.9 - - + +
156F SER* 1.3 54.7 + - - +
157F LYS* 2.6 25.3 + - - +
13G G 3.7 44.5 + - + +
14G A 4.7 4.7 + - - -
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Residues in contact with SER 156 (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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120F PHE* 3.3 15.8 - - - -
124F ARG* 3.4 22.4 + - - -
152F ARG* 2.9 34.8 + - - +
153F ARG 3.6 8.7 - - - -
154F TYR 3.2 1.0 - - - -
155F LYS* 1.3 74.9 - - - +
157F LYS* 1.3 58.0 + - - +
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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