Contacts of the helix formed by residues 134 - 146 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A CYS* 3.2 8.8 - - - +
133A ASN* 1.3 86.7 - - + +
135A PRO* 1.4 64.8 - - - +
136A LEU* 3.0 30.7 + - + +
137A ASP* 3.1 48.7 + - - +
138A MET 4.1 0.9 + - - -
165A ARG* 2.6 41.5 + - - -
165B ARG* 5.3 8.1 + - - +
215X PHE* 4.8 1.1 - - - +
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Residues in contact with PRO 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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129A GLY 3.5 29.8 - - - +
130A ARG* 4.8 6.5 - - - +
132A CYS* 3.5 11.9 - - + +
133A ASN 3.6 4.9 - - - +
134A GLU* 1.4 93.4 - - - +
136A LEU* 1.3 61.6 + - - +
138A MET* 3.0 15.5 + - + +
139A TYR* 3.2 27.3 + - + -
161A GLU* 3.7 31.0 - - - +
165A ARG* 4.6 2.0 - - - +
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Residues in contact with LEU 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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134A GLU* 3.0 18.7 + - + +
135A PRO* 1.3 76.4 - - - +
137A ASP* 1.3 63.9 + - - +
139A TYR* 3.3 3.7 + - + +
140A SER* 3.0 31.1 + - - +
158A TRP* 3.9 17.2 + - + +
161A GLU* 3.6 22.7 - - + -
162A TYR* 3.7 44.0 - - + +
165A ARG* 3.7 30.5 - - - +
165B ARG 5.5 1.1 - - - +
166B GLU* 6.4 1.1 - - + -
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Residues in contact with ASP 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLU* 3.1 36.9 + - - +
136A LEU* 1.3 75.9 - - - +
138A MET* 1.3 58.0 + - - +
140A SER* 3.7 4.6 + - - -
141A TYR* 3.1 27.9 + - - +
215X PHE* 3.5 26.8 + - + +
216X ASN* 3.9 26.6 + - - +
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Residues in contact with MET 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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125A TRP* 3.6 29.6 - - + +
126A LEU* 4.1 7.4 - - + +
128A LEU* 5.2 0.2 - - + -
129A GLY* 3.8 27.6 - - - +
132A CYS* 5.2 0.7 - - - -
134A GLU 4.1 0.8 + - - -
135A PRO* 3.0 8.3 + - + +
137A ASP* 1.3 77.3 - - - +
139A TYR* 1.3 107.0 + - + +
141A TYR* 3.1 2.9 + - - +
142A LEU* 3.0 46.3 + - - +
215X PHE* 3.7 36.2 - - + -
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Residues in contact with TYR 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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126A LEU* 3.5 28.5 + - + +
135A PRO* 3.2 32.2 + - + -
136A LEU* 3.3 7.8 + - + +
138A MET* 1.3 94.8 - - + +
140A SER* 1.3 58.4 + - - +
142A LEU 3.4 0.5 + - - -
143A HIS* 3.0 27.6 + - - +
154A PHE* 3.4 22.2 - + - -
157A SER* 3.3 26.2 + - - -
158A TRP* 3.3 59.2 - + + +
161A GLU* 3.9 21.3 - - + +
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Residues in contact with SER 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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136A LEU* 3.0 18.3 + - - +
137A ASP* 4.1 5.4 - - - -
139A TYR* 1.3 73.8 - - - +
141A TYR* 1.3 61.3 + - - +
143A HIS* 3.4 7.2 + - - +
144A ASN* 2.8 44.4 + - - +
158A TRP* 4.2 14.7 + - - -
162A TYR* 5.6 0.9 + - - -
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Residues in contact with TYR 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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125A TRP* 3.6 32.2 - + - -
137A ASP 3.1 19.7 + - - +
138A MET 3.1 4.9 + - - +
140A SER* 1.3 72.6 - - - +
142A LEU* 1.3 72.3 + - + +
144A ASN* 3.1 12.6 + - + +
145A GLN* 2.9 64.9 + - + +
147A ILE* 4.7 2.9 - - + -
215X PHE* 3.5 25.6 - + + -
219X ILE* 3.7 32.2 - - + +
222X LEU* 5.5 1.4 - - - +
223X LYS* 5.7 3.1 - - - -
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Residues in contact with LEU 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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122A LEU* 3.6 30.7 - - + -
125A TRP* 3.5 43.1 - - + -
126A LEU* 4.6 1.1 - - + -
138A MET* 3.0 36.4 + - - +
139A TYR 3.7 6.1 - - - +
141A TYR* 1.3 77.0 - - + +
143A HIS* 1.3 57.1 + - - +
145A GLN 3.3 0.7 + - - +
146A GLY* 2.8 11.1 + - - -
147A ILE* 2.8 61.6 + - + +
149A VAL* 4.1 0.2 - - - +
154A PHE* 3.7 15.0 - - + -
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Residues in contact with HIS 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 TYR 3.0 17.4 + - - +
140A SER* 3.4 6.5 - - - +
141A TYR 3.2 0.2 - - - -
142A LEU* 1.3 79.3 - - - +
144A ASN* 1.3 68.4 + - - +
146A GLY* 3.3 8.5 + - - -
149A VAL* 4.1 20.5 - - + +
154A PHE* 3.9 4.7 - + + -
155A TYR* 5.2 2.5 - - - -
158A TRP* 3.7 32.1 - + + -
177A GLU* 2.6 35.7 + - - -
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Residues in contact with ASN 144 (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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140A SER* 2.8 37.2 + - - +
141A TYR* 3.1 12.0 + - + +
143A HIS* 1.3 80.9 + - - +
145A GLN* 1.3 63.9 + - + +
146A GLY 3.5 0.3 + - - -
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Residues in contact with GLN 145 (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 TYR* 3.3 31.5 + - + -
141A TYR* 2.9 64.0 + - + +
142A LEU 3.9 0.7 - - - +
144A ASN* 1.3 79.1 - - + +
146A GLY* 1.3 60.9 + - - +
147A ILE* 3.9 19.5 - - + -
223X LYS* 6.3 0.4 - - - +
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Residues in contact with GLY 146 (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 TYR* 3.7 15.2 - - - +
142A LEU 2.8 7.6 + - - -
143A HIS 3.3 4.0 + - - -
144A ASN 3.3 4.4 + - - -
145A GLN* 1.3 78.6 - - - +
147A ILE* 1.3 60.5 + - - -
148A GLY 3.6 2.8 + - - -
149A VAL* 3.8 28.2 - - - +
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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