Contacts of the helix formed by residues 134 - 146 (chain B) in PDB entry 3SI5
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 GLU 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A ASN* 3.6 18.8 + - - +
132B CYS* 4.1 8.1 - - - +
133B ASN* 1.3 82.8 - - + +
135B PRO* 1.3 65.4 - - - +
136B LEU* 3.1 28.9 + - + +
137B ASP* 3.1 47.4 + - - +
138B MET 4.0 1.6 + - - -
165B ARG* 2.6 43.4 + - - -
209X SER* 3.9 10.5 - - - +
214Y ASP* 6.3 0.2 - - - +
215Y PHE* 4.7 3.7 - - - +
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Residues in contact with PRO 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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129B GLY* 3.5 29.6 - - - +
130B ARG* 5.4 2.2 - - - -
132B CYS* 3.9 9.0 - - + +
133B ASN 3.6 8.3 - - - +
134B GLU* 1.3 92.8 - - - +
136B LEU* 1.3 60.4 + - - +
138B MET* 3.0 19.7 + - + +
139B TYR* 3.1 26.6 + - + -
161B GLU* 3.8 23.8 - - - +
165B ARG* 3.7 8.5 - - - +
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Residues in contact with LEU 136 (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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134B GLU* 3.1 16.3 + - + +
135B PRO* 1.3 78.1 - - - +
137B ASP* 1.3 59.0 + - - +
139B TYR* 3.5 5.0 + - + +
140B SER* 2.8 33.1 + - - +
158B TRP* 3.9 19.4 + - + +
161B GLU* 3.5 27.1 - - + -
162B TYR* 3.8 48.5 - - + +
165B ARG* 3.5 32.1 - - + +
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Residues in contact with ASP 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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134B GLU* 3.1 25.3 + - - +
136B LEU* 1.3 75.3 - - - +
138B MET* 1.3 61.9 + - - +
140B SER* 3.3 6.0 + - - -
141B TYR* 2.9 30.7 + - - +
208X SER* 3.8 5.9 - - - +
209X SER* 2.9 46.4 + - - -
215Y PHE* 3.8 14.3 + - + +
216Y ASN* 3.6 29.3 + - - +
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Residues in contact with MET 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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125B TRP* 3.9 28.5 - - + +
126B LEU* 4.3 8.7 - - + +
128B LEU* 5.6 0.2 - - + -
129B GLY* 3.9 28.0 - - - +
132B CYS* 5.0 1.1 - - - -
134B GLU 4.0 1.0 + - - +
135B PRO* 3.0 13.9 + - + +
137B ASP* 1.3 79.9 - - - +
139B TYR* 1.3 104.3 + - + +
141B TYR* 3.2 2.4 + - - +
142B LEU* 3.0 45.4 + - - +
215Y PHE* 3.7 35.9 - - + -
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Residues in contact with TYR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.8 14.0 + - + +
135B PRO* 3.1 34.9 + - + -
136B LEU* 3.9 7.0 - - + +
137B ASP 3.3 0.2 - - - -
138B MET* 1.3 105.2 - - + +
140B SER* 1.3 62.5 + - - +
142B LEU 3.4 0.5 + - - -
143B HIS* 3.1 20.3 + - - +
154B PHE* 3.5 26.4 - + - -
157B SER* 3.3 30.9 + - - -
158B TRP* 3.2 56.5 - + + +
161B GLU* 4.1 19.7 + - + +
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Residues in contact with SER 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LEU* 2.8 23.6 + - - +
137B ASP* 3.7 6.5 - - - -
139B TYR* 1.3 71.8 - - - +
141B TYR* 1.3 60.7 + - - +
143B HIS* 3.2 9.1 + - - +
144B ASN* 2.9 41.0 + - - -
158B TRP* 4.4 12.1 + - - -
162B TYR* 5.2 4.5 + - - -
208X SER* 4.3 24.3 + - - -
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Residues in contact with TYR 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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125B TRP* 3.8 28.7 - + - -
137B ASP 2.9 14.3 + - - +
138B MET 3.3 8.7 - - - +
140B SER* 1.3 75.4 - - - +
142B LEU* 1.3 63.6 + - + +
144B ASN* 3.1 8.3 + - + +
145B GLN* 2.8 69.9 + - + +
147B ILE* 4.7 2.9 - - + -
215Y PHE* 3.6 23.1 - + + -
219Y ILE* 3.7 36.4 - - + +
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Residues in contact with LEU 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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122B LEU* 3.8 19.1 - - + -
125B TRP* 3.5 42.4 - - + -
126B LEU* 5.1 0.9 - - + -
138B MET* 3.0 31.6 + - - +
139B TYR 3.7 0.9 - - - +
141B TYR* 1.3 81.1 - - + +
143B HIS* 1.3 58.5 + - - +
145B GLN* 3.2 2.3 + - - -
146B GLY 2.9 25.8 + - - -
147B ILE* 2.9 42.9 + - + +
154B PHE* 3.5 34.1 - - + -
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Residues in contact with HIS 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 TYR 3.1 11.5 + - - +
140B SER* 3.2 8.0 + - - +
142B LEU* 1.3 76.5 - - - +
144B ASN* 1.3 78.4 + - - +
146B GLY* 3.2 12.8 + - - -
149B VAL* 4.3 17.6 - - + +
154B PHE* 3.9 7.3 - + + -
155B TYR* 5.3 3.1 - + - -
158B TRP* 3.7 33.7 - + + -
177B GLU* 3.1 27.2 + - + +
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Residues in contact with ASN 144 (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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140B SER* 2.9 24.0 + - - +
141B TYR* 3.5 8.0 + - + +
143B HIS* 1.3 94.5 + - - +
145B GLN* 1.3 68.5 + - - +
146B GLY 3.6 0.2 + - - -
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Residues in contact with GLN 145 (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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113B LYS* 5.5 2.6 - - - -
116B TYR* 3.5 25.4 + - + +
141B TYR* 2.8 66.4 + - + +
142B LEU 3.8 3.6 - - - +
144B ASN* 1.3 79.9 + - - +
146B GLY* 1.3 60.3 + - - +
147B ILE* 3.9 19.1 - - + -
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Residues in contact with GLY 146 (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 TYR* 3.8 16.3 - - - +
142B LEU 2.9 5.7 + - - -
143B HIS 3.2 11.3 + - - -
144B ASN 3.3 1.0 + - - -
145B GLN* 1.3 78.0 - - - +
147B ILE* 1.3 62.4 + - - +
148B GLY 3.7 2.4 + - - -
149B VAL* 3.7 26.1 + - - +
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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