Contacts of the helix formed by residues 131 - 144 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127D THR* 5.4 0.9 - - - -
128D HIS 5.1 5.6 - - - -
129D ALA 4.0 1.0 + - - -
130D TYR* 1.3 79.9 - - - +
132D ARG* 1.3 62.0 + - - +
133D VAL* 3.5 5.7 - - - +
134D VAL* 2.9 48.8 + - - +
135D LEU* 3.0 8.5 + - - +
164D MSE 3.8 7.8 - - - +
196D GLY* 3.7 18.1 - - - -
504D SO4 2.8 22.3 + - - -
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Residues in contact with ARG 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D PRO 3.5 15.4 + - - +
19D ASP* 3.0 42.6 - - + +
20D MSE 3.8 11.3 + - - -
21D ALA* 4.0 3.4 - - - +
22D SER* 4.0 22.0 - - - +
108D ARG* 4.2 10.8 - - - +
130D TYR* 3.8 25.5 - - + +
131D SER* 1.3 72.3 - - - +
133D VAL* 1.3 56.3 + - - +
135D LEU* 3.1 10.1 + - + +
136D ARG* 2.9 29.6 + - - +
504D SO4 2.7 39.5 + - - +
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Residues in contact with VAL 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ARG* 4.0 25.5 - - + +
111D ILE* 5.2 7.0 - - + -
131D SER* 3.5 10.3 - - - +
132D ARG* 1.3 77.2 - - - +
134D VAL* 1.3 62.3 + - - +
136D ARG* 3.2 2.6 + - - +
137D VAL* 2.9 33.5 + - + +
229D VAL* 3.2 40.2 - - + +
231D GLU* 3.3 38.1 - - + +
234D LYS* 5.5 0.2 - - - +
504D SO4 3.5 13.5 - - - +
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D THR* 4.1 11.9 - - + +
131D SER* 2.9 38.9 + - - +
133D VAL* 1.3 81.2 - - - +
135D LEU* 1.3 62.9 + - - +
137D VAL* 3.1 7.3 + - + +
138D LEU* 2.9 41.2 + - + +
164D MSE 3.2 20.6 - - + -
194D ILE* 3.3 42.8 - - + +
196D GLY 5.1 1.8 - - - +
229D VAL* 4.2 6.1 - - + -
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D ASP* 5.6 4.0 - - - +
130D TYR* 3.3 25.6 - - + +
131D SER 3.0 8.5 + - - +
132D ARG* 3.2 13.5 - - + +
134D VAL* 1.3 85.3 - - - +
136D ARG* 1.3 62.5 + - + +
138D LEU* 3.2 2.5 + - - -
139D GLU* 3.1 36.9 + - - +
164D MSE 4.1 17.0 - - + -
167D ALA* 4.0 16.8 - - + -
168D LEU* 4.2 14.6 - - + -
171D LEU* 3.6 28.3 - - + -
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Residues in contact with ARG 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D SER 5.5 4.6 + - - -
108D ARG* 3.1 55.3 - - + +
109D ASN* 2.5 49.1 + - - +
112D ALA* 3.8 10.6 - - + +
132D ARG 2.9 12.5 + - - +
133D VAL 3.8 6.5 - - - +
135D LEU* 1.3 77.2 - - + +
137D VAL* 1.3 62.2 + - - +
139D GLU* 3.2 19.9 + - - +
140D ALA* 3.1 22.7 + - - +
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Residues in contact with VAL 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ARG 5.8 0.4 - - - +
111D ILE* 4.1 8.7 - - + -
112D ALA* 4.0 21.8 - - - +
115D CYS* 3.8 28.3 - - + -
116D HIS* 3.9 14.2 - - - +
119D ILE* 4.6 9.0 - - + -
133D VAL 2.9 28.4 + - - +
134D VAL* 3.1 10.3 + - + +
136D ARG* 1.3 76.9 - - - +
138D LEU* 1.3 66.2 + - + +
140D ALA* 3.3 7.1 + - - +
141D ALA* 3.2 18.0 + - - +
194D ILE* 5.2 5.4 - - + -
229D VAL* 4.0 21.5 - - + -
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ILE* 3.9 13.2 - - + -
125D ILE* 3.7 30.5 - - + -
127D THR* 5.0 5.4 - - - +
134D VAL* 2.9 28.2 + - + +
135D LEU* 3.7 4.5 - - + +
137D VAL* 1.3 77.3 - - + +
139D GLU* 1.3 63.1 + - - +
141D ALA* 3.2 15.1 - - - +
142D VAL* 3.3 15.8 + - - +
148D PHE* 3.5 17.8 - - + -
150D VAL* 4.0 16.8 - - + -
164D MSE 4.4 12.1 - - + -
168D LEU* 3.9 29.2 - - + -
171D LEU* 5.4 2.5 - - + -
173D VAL* 6.0 0.6 - - + +
194D ILE* 5.0 4.9 - - + -
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Residues in contact with GLU 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D LEU* 3.1 25.4 + - - +
136D ARG* 3.2 34.4 - - - +
137D VAL 3.2 0.2 - - - -
138D LEU* 1.3 72.7 - - - +
140D ALA* 1.3 63.7 + - - +
141D ALA 2.8 4.7 - - - -
142D VAL* 2.9 31.7 - - + +
143D ALA* 3.0 8.3 + - - +
171D LEU* 3.4 36.4 - - + +
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Residues in contact with ALA 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ALA* 3.8 30.3 - - + +
113D ASP* 4.8 4.3 - - - +
116D HIS* 3.4 20.1 + - + +
136D ARG 3.1 13.1 + - - +
137D VAL 3.3 11.4 - - - +
139D GLU* 1.3 77.4 - - - +
141D ALA* 1.3 58.8 + - - +
143D ALA* 3.9 8.8 - - - +
144D ALA* 3.4 14.0 + - - +
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Residues in contact with ALA 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D HIS* 4.1 10.1 - - + -
119D ILE* 4.1 17.9 - - + -
137D VAL 3.2 8.4 + - - +
138D LEU* 3.2 17.3 - - - +
139D GLU 2.8 0.4 - - - -
140D ALA* 1.3 78.1 - - - +
142D VAL* 1.3 66.6 + - - +
143D ALA 3.1 1.1 - - - -
144D ALA* 3.2 5.7 + - - +
146D LYS* 3.1 30.8 + - + +
148D PHE* 3.4 20.2 - - + -
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Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LEU 3.4 13.0 - - - +
139D GLU* 2.9 22.7 - - + +
141D ALA* 1.3 75.5 - - - +
143D ALA* 1.3 72.9 + - + +
145D LYS* 2.8 29.1 + - - +
146D LYS 4.3 9.4 - - - +
148D PHE* 4.0 15.3 - - + -
171D LEU* 4.9 20.6 - - + +
173D VAL* 5.1 10.5 - - + -
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Residues in contact with ALA 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D GLU 3.0 12.9 + - - +
140D ALA* 3.9 9.2 - - - +
142D VAL* 1.3 81.1 - - + +
144D ALA* 1.3 57.4 + - - +
145D LYS* 2.9 23.6 + - - +
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Residues in contact with ALA 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ASP* 4.4 8.3 - - - +
116D HIS* 3.4 37.2 - - + +
140D ALA 3.4 4.1 + - - +
141D ALA 3.2 7.4 + - - +
143D ALA* 1.3 76.0 - - - +
145D LYS* 1.3 72.0 + - - +
146D LYS* 3.1 14.8 + - + +
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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