Contacts of the helix formed by residues 131 - 143 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B THR* 5.6 0.4 - - - -
128B HIS 5.2 4.9 - - - -
129B ALA 4.2 0.8 + - - -
130B TYR* 1.3 80.0 - - - +
132B ARG* 1.3 64.0 + - - +
133B VAL* 3.8 0.7 - - - -
134B VAL* 2.9 39.4 + - - +
135B LEU* 3.1 18.9 + - - +
164B MSE 4.0 9.4 - - - +
196B GLY* 3.7 15.6 - - - -
502B SO4 2.6 24.9 + - - -
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B MSE 4.8 5.7 - - - +
18B PRO 3.6 10.9 + - - -
19B ASP* 3.6 28.4 + - + +
20B MSE 3.1 29.1 + - - -
21B ALA* 3.6 8.5 - - - +
22B SER 4.3 2.8 - - - +
108B ARG* 3.3 31.8 - - - +
130B TYR* 3.9 24.2 - - + +
131B SER* 1.3 72.5 - - - +
133B VAL* 1.3 60.3 + - - +
135B LEU* 3.1 10.5 + - - +
136B ARG* 3.1 26.1 + - - +
502B SO4 2.8 43.9 + - - +
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ARG* 3.8 18.8 - - + +
111B ILE* 3.9 29.8 - - + -
131B SER 3.2 0.6 - - - -
132B ARG* 1.3 78.3 - - - +
134B VAL* 1.3 62.5 + - - +
136B ARG* 3.3 4.8 + - + +
137B VAL* 3.0 26.9 + - + +
229B VAL* 3.1 31.2 - - + +
231B GLU* 3.6 35.0 - - - +
234B LYS* 4.3 1.1 - - - +
502B SO4 3.2 19.3 + - - +
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ILE* 6.1 0.2 - - + -
127B THR* 4.0 17.9 - - - +
131B SER* 2.9 34.0 + - - +
133B VAL* 1.3 75.4 - - - +
135B LEU* 1.3 62.1 - - - +
137B VAL* 3.3 5.8 + - - +
138B LEU* 3.0 36.4 + - + +
164B MSE 3.7 17.7 - - + -
194B ILE* 4.2 15.9 - - + -
195B VAL* 3.9 12.1 - - - -
196B GLY 3.7 18.2 - - - +
229B VAL* 4.0 10.1 - - + -
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B TYR* 4.7 8.3 - - - +
131B SER 3.1 12.6 + - - +
132B ARG* 3.2 13.5 - - - +
134B VAL* 1.3 76.7 - - - +
136B ARG* 1.3 58.3 + - + +
138B LEU* 3.1 5.2 + - - +
139B GLU* 2.9 69.3 + - - +
164B MSE 3.8 14.8 - - + +
167B ALA* 4.0 26.7 - - + -
168B LEU* 3.8 28.3 - - + +
171B LEU* 4.6 7.0 - - + -
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASP* 6.0 2.0 - - - +
105B SER 5.3 5.9 + - - -
108B ARG* 3.5 52.8 - - + +
109B ASN* 3.5 25.2 + - - +
112B ALA* 3.9 13.5 - - + +
132B ARG* 3.1 17.3 + - - +
133B VAL* 3.3 7.6 + - + +
135B LEU* 1.3 75.7 - - + +
137B VAL* 1.3 65.7 + - - +
139B GLU* 2.9 28.2 + - - +
140B ALA* 2.9 24.6 + - - +
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ILE* 4.2 3.6 - - + -
112B ALA* 3.9 20.9 - - - +
115B CYS* 3.7 30.1 - - + -
116B HIS* 3.9 13.4 - - - +
119B ILE* 4.6 9.6 - - + -
133B VAL* 3.0 19.2 + - + +
134B VAL* 3.5 9.2 - - - +
136B ARG* 1.3 76.8 - - + +
138B LEU* 1.3 62.7 + - + +
140B ALA* 3.3 5.2 + - - +
141B ALA* 3.2 17.8 + - - +
194B ILE* 4.7 8.3 - - + -
229B VAL* 3.6 27.1 - - + -
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ILE* 3.9 12.3 - - + -
125B ILE* 3.6 33.4 - - + -
127B THR* 5.9 1.1 - - + -
134B VAL* 3.0 35.5 + - + +
135B LEU 3.6 4.0 - - - +
137B VAL* 1.3 76.2 - - + +
139B GLU* 1.3 65.6 + - + +
141B ALA* 3.0 13.6 + - - +
142B VAL* 3.2 11.8 + - - +
148B PHE* 3.7 20.8 - - + -
150B VAL* 4.0 18.6 - - + -
164B MSE 4.3 3.4 - - + -
168B LEU* 3.8 33.4 - - + -
173B VAL* 6.1 1.1 - - + -
194B ILE* 4.7 7.6 - - + -
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Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B LEU* 2.9 43.0 + - + +
136B ARG* 2.9 33.6 + - - +
138B LEU* 1.3 75.2 - - - +
140B ALA* 1.3 62.2 + - - +
142B VAL* 3.1 10.4 + - - +
143B ALA* 3.1 25.2 + - - +
168B LEU* 6.5 0.2 - - + -
171B LEU* 3.5 33.3 - - + +
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA* 3.9 20.0 - - + +
113B ASP* 5.5 2.9 - - - +
116B HIS* 4.0 23.1 - - + -
136B ARG 2.9 11.1 + - - +
137B VAL 3.5 9.9 - - - +
139B GLU* 1.3 77.6 - - - +
141B ALA* 1.3 59.8 + - - +
143B ALA* 4.1 8.6 - - - +
144B ALA* 3.6 21.1 + - - +
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Residues in contact with ALA 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B HIS* 4.2 8.1 - - + +
119B ILE* 3.8 28.7 - - + -
137B VAL 3.2 7.4 + - - +
138B LEU* 3.0 12.4 + - - +
140B ALA* 1.3 76.1 - - - +
142B VAL* 1.3 64.1 + - - +
144B ALA* 3.6 3.2 + - - +
146B LYS* 3.0 41.4 + - + +
148B PHE* 3.7 16.8 - - + -
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LEU 3.2 12.0 + - - +
139B GLU* 3.1 10.8 + - - +
141B ALA* 1.3 72.7 - - - +
143B ALA* 1.3 56.9 + - - +
144B ALA 2.6 4.6 + - - -
145B LYS* 2.5 33.1 + - - -
146B LYS 3.7 8.2 + - - +
148B PHE* 3.8 18.8 - - + -
171B LEU* 5.2 11.9 - - + +
172B ASN 6.1 0.4 - - - +
173B VAL* 4.4 15.9 - - + -
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B GLU 3.1 11.5 + - - +
140B ALA* 4.2 8.5 - - - +
142B VAL* 1.3 82.8 - - - +
144B ALA* 1.3 55.1 + - - +
145B LYS* 3.2 16.1 + - - +
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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