Contacts of the helix formed by residues 131 - 144 (chain F) in PDB entry 3ECS
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 SER 131 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127F THR* 5.5 1.3 - - - -
128F HIS 5.2 4.5 - - - -
129F ALA 4.0 0.8 + - - -
130F TYR* 1.3 82.0 - - - +
132F ARG* 1.3 56.1 + - - +
134F VAL* 3.1 36.2 + - - +
135F LEU* 2.9 30.0 + - - +
164F MSE 3.6 9.0 - - - +
196F GLY* 3.6 15.7 - - - -
506F SO4 3.0 20.8 + - - -
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Residues in contact with ARG 132 (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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14F MSE 5.0 6.3 - - - +
18F PRO 4.0 9.8 + - - -
19F ASP* 3.7 31.6 - - - +
20F MSE 3.5 19.7 + - - -
21F ALA* 4.6 5.8 - - - +
22F SER* 4.4 13.9 + - - +
108F ARG* 3.7 22.7 - - - +
130F TYR* 3.9 21.9 - - + -
131F SER* 1.3 71.2 - - - +
133F VAL* 1.3 63.7 + - + +
135F LEU* 3.3 6.6 + - - +
136F ARG* 3.0 27.0 + - - +
506F SO4 2.7 53.6 + - - +
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Residues in contact with VAL 133 (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 ARG* 4.4 19.1 - - + +
111F ILE* 3.7 33.9 - - + -
131F SER* 4.1 0.9 - - - +
132F ARG* 1.3 74.9 - - + +
134F VAL* 1.3 68.3 + - - +
136F ARG* 3.1 3.1 + - - +
137F VAL* 3.0 22.3 + - + +
229F VAL* 3.8 26.9 - - + +
230F ALA 4.6 0.4 - - - +
231F GLU* 3.5 37.0 - - + +
234F LYS* 4.6 0.7 - - - +
506F SO4 2.9 22.7 + - - +
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Residues in contact with VAL 134 (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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125F ILE* 6.2 0.4 - - + -
127F THR* 3.9 18.8 - - - +
131F SER* 3.1 28.5 + - - +
133F VAL* 1.3 76.0 - - - +
135F LEU* 1.3 63.4 + - - +
137F VAL* 3.1 6.2 + - - +
138F LEU* 3.0 35.1 + - + +
164F MSE 4.0 12.6 - - + -
194F ILE* 4.0 18.8 - - + +
195F VAL* 3.7 8.3 - - - -
196F GLY 3.5 19.7 - - - +
229F VAL* 3.7 16.6 - - + -
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Residues in contact with LEU 135 (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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19F ASP* 5.3 5.8 - - - +
130F TYR* 3.2 30.7 - - + +
131F SER 2.9 17.8 + - - +
132F ARG* 3.4 7.2 - - - +
134F VAL* 1.3 72.7 - - - +
136F ARG* 1.3 67.0 + - + +
137F VAL 3.2 0.2 + - - -
138F LEU* 3.3 5.6 + - - +
139F GLU* 2.9 50.3 + - - +
164F MSE 3.7 18.8 - - + +
167F ALA* 4.1 20.0 - - + -
168F LEU* 4.9 5.6 - - + -
171F LEU* 3.7 19.1 - - + -
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Residues in contact with ARG 136 (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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19F ASP* 2.7 28.6 + - - -
108F ARG* 2.8 58.9 - - + +
109F ASN* 4.2 19.0 + - - +
112F ALA* 3.7 19.4 - - + +
132F ARG 3.0 12.3 + - - +
133F VAL 3.1 6.9 + - - +
135F LEU* 1.3 75.8 - - - +
137F VAL* 1.3 63.2 + - - +
139F GLU* 3.1 34.2 + - - +
140F ALA* 3.1 17.3 + - - +
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Residues in contact with VAL 137 (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 ILE* 4.1 12.8 - - + +
112F ALA* 3.8 24.7 - - - +
115F CYS* 4.1 26.0 - - + -
116F HIS* 3.9 6.7 - - - +
119F ILE* 4.0 20.9 - - + -
133F VAL 3.0 18.5 + - - +
134F VAL* 3.3 11.2 - - + +
135F LEU 3.1 0.2 - - - -
136F ARG* 1.3 74.6 - - - +
138F LEU* 1.3 68.2 + - + +
140F ALA* 3.0 15.6 + - - +
141F ALA* 3.1 9.2 + - - +
194F ILE* 4.8 6.7 - - + -
229F VAL* 4.3 13.9 - - + -
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Residues in contact with LEU 138 (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 ILE* 4.0 9.0 - - + -
125F ILE* 4.0 23.8 - - + -
127F THR* 5.7 1.3 - - + -
134F VAL* 3.0 29.8 + - + +
135F LEU 3.9 2.9 - - - +
137F VAL* 1.3 78.1 - - + +
139F GLU* 1.3 63.7 + - - +
141F ALA* 2.8 17.0 + - - +
142F VAL* 3.1 19.6 + - + +
148F PHE* 3.7 25.1 - - + -
150F VAL* 4.5 11.2 - - + -
164F MSE 4.2 6.1 - - + -
168F LEU* 3.5 40.6 - - + -
171F LEU* 5.2 0.7 - - + -
173F VAL* 5.5 0.2 - - + -
194F ILE* 4.7 5.6 - - + -
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Residues in contact with GLU 139 (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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135F LEU* 2.9 36.2 + - - +
136F ARG* 3.1 39.9 + - - +
137F VAL 3.2 0.2 - - - -
138F LEU* 1.3 75.9 - - - +
140F ALA* 1.3 62.9 + - - +
142F VAL* 3.2 8.7 + - - +
143F ALA* 3.0 24.5 + - - +
171F LEU* 3.3 40.6 - - + +
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Residues in contact with ALA 140 (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 ALA* 3.8 18.4 - - + +
113F ASP* 4.9 2.9 - - + +
116F HIS* 3.3 23.7 + - + +
136F ARG 3.1 7.8 + - - +
137F VAL 3.0 10.6 + - - +
139F GLU* 1.3 80.3 - - - +
141F ALA* 1.3 57.4 + - - +
143F ALA* 3.4 8.1 + - - +
144F ALA* 2.9 28.9 + - - +
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Residues in contact with ALA 141 (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 HIS* 3.8 11.4 - - + +
119F ILE* 3.8 28.5 - - + -
137F VAL 3.1 5.1 + - - +
138F LEU 2.8 11.5 + - - +
140F ALA* 1.3 76.5 - - - +
142F VAL* 1.3 61.6 + - - +
144F ALA* 3.2 8.7 + - - +
145F LYS 3.3 0.2 + - - -
146F LYS* 2.8 34.0 + - + +
148F PHE* 3.5 20.9 - - + -
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Residues in contact with VAL 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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138F LEU 3.1 17.0 + - - +
139F GLU* 3.9 9.9 - - - +
141F ALA* 1.3 72.8 - - - +
143F ALA* 1.3 65.3 + - + +
144F ALA 3.1 0.2 - - - -
145F LYS* 2.9 21.8 + - - +
146F LYS 4.1 10.8 - - - +
148F PHE* 3.8 7.9 - - + -
171F LEU* 4.3 23.1 - - + +
173F VAL* 3.6 31.0 - - + -
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Residues in contact with ALA 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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139F GLU 3.0 18.0 + - - +
140F ALA* 3.6 9.4 - - - +
142F VAL* 1.3 76.5 - - + +
144F ALA* 1.3 57.7 + - - +
145F LYS* 3.0 13.5 + - - +
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Residues in contact with ALA 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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116F HIS* 3.6 23.1 - - + +
140F ALA 2.9 17.9 + - - +
141F ALA* 3.5 8.3 - - - +
142F VAL 3.1 0.6 - - - -
143F ALA* 1.3 76.4 - - - +
145F LYS* 1.3 71.5 + - - +
146F LYS* 3.3 14.4 + - + +
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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