Contacts of the helix formed by residues 131 - 143 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A THR* 5.7 0.7 - - - -
128A HIS 5.5 3.8 - - - -
129A ALA 4.3 0.6 + - - -
130A TYR* 1.3 81.2 - - - +
132A ARG* 1.3 64.5 + - - +
133A VAL* 3.9 0.5 - - - -
134A VAL* 3.1 37.7 + - - +
135A LEU* 3.0 22.7 + - - +
164A MSE 3.8 9.3 - - - +
196A GLY* 3.7 13.6 - - - -
501A SO4 2.8 25.8 + - - -
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Residues in contact with ARG 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A MSE 4.5 13.5 - - - +
18A PRO* 2.7 30.1 + - - +
19A ASP* 2.9 31.2 + - - +
20A MSE 3.3 15.9 + - - -
21A ALA* 4.4 4.6 - - - +
22A SER* 4.8 3.0 - - - +
108A ARG* 3.4 30.1 - - - +
130A TYR* 3.9 27.1 + - + +
131A SER* 1.3 71.7 - - - +
133A VAL* 1.3 56.5 + - - +
135A LEU* 3.5 7.8 - - - +
136A ARG* 3.1 31.4 + - - +
501A SO4 2.5 39.1 + - - +
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ARG* 4.2 15.5 - - + +
111A ILE* 3.5 31.9 - - + -
131A SER* 3.9 0.7 - - - +
132A ARG* 1.3 75.7 - - - +
134A VAL* 1.3 66.1 + - - +
136A ARG* 3.1 8.5 + - + +
137A VAL* 2.9 21.2 + - + +
229A VAL* 3.5 29.8 - - + +
231A GLU* 3.6 35.7 - - - +
234A LYS* 4.5 2.0 - - - +
501A SO4 2.8 20.5 + - - +
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ILE* 6.5 0.4 - - + -
127A THR* 3.9 15.0 - - - +
131A SER* 3.1 29.8 + - - +
133A VAL* 1.3 75.0 - - - +
135A LEU* 1.3 58.9 + - - +
137A VAL* 2.8 22.4 + - + +
138A LEU* 2.9 25.5 + - + +
164A MSE 3.7 17.5 - - + -
194A ILE* 4.1 16.6 - - + +
195A VAL* 3.6 9.4 - - - -
196A GLY 3.5 19.7 - - - +
229A VAL* 3.6 15.7 - - + -
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ASP* 5.6 4.0 - - - +
130A TYR* 4.1 18.4 - - + +
131A SER 3.0 12.4 + - - +
132A ARG* 3.5 10.5 - - - +
134A VAL* 1.3 76.1 - - - +
136A ARG* 1.3 63.4 + - + +
138A LEU* 3.1 4.7 + - - +
139A GLU* 2.9 30.8 + - - +
164A MSE 3.8 18.6 - - + +
167A ALA* 4.0 23.6 - - + -
168A LEU* 4.4 13.2 - - + -
171A LEU* 3.3 33.7 - - + -
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Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ASP* 5.7 3.4 - - - +
108A ARG* 3.6 29.6 - - + +
109A ASN* 2.7 42.4 + - - +
112A ALA* 3.7 19.5 - - + +
132A ARG 3.1 14.5 + - - +
133A VAL* 3.1 12.4 + - + +
135A LEU* 1.3 80.0 - - + +
137A VAL* 1.3 63.1 + - - +
139A GLU* 3.4 23.1 + - - +
140A ALA* 3.1 22.2 + - - +
601A CL 3.4 26.3 - - - +
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A ILE* 3.8 14.8 - - + +
112A ALA* 4.0 10.5 - - - +
115A CYS* 3.8 37.9 - - + -
116A HIS* 3.5 15.9 - - - +
119A ILE* 4.1 11.9 - - + -
133A VAL* 2.9 15.7 + - + +
134A VAL* 2.8 12.7 + - - +
136A ARG* 1.3 77.6 - - - +
138A LEU* 1.3 63.2 + - + +
140A ALA* 3.2 7.1 + - - +
141A ALA* 3.1 17.5 + - - +
194A ILE* 4.8 9.0 - - + -
229A VAL* 4.0 15.3 - - + -
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Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ILE* 4.4 9.9 - - + -
125A ILE* 3.9 24.7 - - + -
127A THR* 5.9 1.8 - - + -
134A VAL* 2.9 31.0 + - + +
135A LEU* 3.8 6.5 - - + +
137A VAL* 1.3 75.1 - - + +
139A GLU* 1.3 66.2 + - - +
141A ALA* 3.1 14.5 + - - +
142A VAL* 3.1 19.0 + - + +
148A PHE* 3.6 23.9 - - + -
150A VAL* 4.1 14.4 - - + -
164A MSE 4.6 4.0 - - + -
168A LEU* 3.6 39.7 - - + -
171A LEU* 5.8 0.7 - - + -
173A VAL* 5.8 0.7 - - + -
194A ILE* 4.8 5.8 - - + -
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Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 2.9 30.5 + - - +
136A ARG* 3.6 28.4 + - - +
138A LEU* 1.3 75.2 - - - +
140A ALA* 1.3 64.4 + - - +
142A VAL* 3.0 14.3 - - + +
143A ALA* 3.0 22.9 + - - +
171A LEU* 3.2 46.8 - - + +
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Residues in contact with ALA 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ALA* 3.7 16.6 - - + +
113A ASP* 6.0 0.9 - - - +
116A HIS* 3.5 28.7 + - + +
136A ARG 3.1 13.4 + - - +
137A VAL 3.3 10.5 - - - +
139A GLU* 1.3 76.6 - - - +
141A ALA* 1.3 61.9 + - - +
143A ALA* 3.3 9.7 + - - +
144A ALA* 3.1 21.3 + - - +
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A HIS* 3.7 11.4 - - + +
119A ILE* 4.0 21.1 - - + -
137A VAL 3.1 11.3 + - - +
138A LEU* 3.1 10.9 + - - +
140A ALA* 1.3 74.3 - - - +
142A VAL* 1.3 65.2 + - - +
144A ALA* 3.1 7.6 + - - +
146A LYS* 3.0 36.3 + - + +
148A PHE* 3.6 18.6 - - + -
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LEU 3.1 14.4 + - - +
139A GLU* 3.0 21.3 - - + +
141A ALA* 1.3 74.0 - - - +
143A ALA* 1.3 64.1 + - + +
144A ALA 3.0 0.7 - - - -
145A LYS* 2.8 25.1 + - - +
146A LYS 4.2 9.2 - - - +
148A PHE* 3.7 18.4 - - + -
171A LEU* 4.8 11.9 - - + +
173A VAL* 4.3 17.5 - - + -
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A GLU 3.0 13.2 + - - +
140A ALA* 3.5 10.3 - - - +
141A ALA 3.2 0.2 - - - -
142A VAL* 1.3 84.7 - - + +
144A ALA* 1.3 54.3 + - - +
145A LYS* 3.3 16.4 + - - +
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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