Contacts of the helix formed by residues 136 - 154 (chain A) in PDB entry 3SN5
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 HIS 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A GLN 3.5 0.4 + - - -
135A GLY* 1.4 66.7 - - - -
137A ALA* 1.4 66.1 + - - +
138A LEU 3.1 2.5 - - - -
139A ASN* 3.0 26.8 + - - +
140A SER* 4.0 3.1 + - - -
255A GLU* 4.9 0.4 - - - +
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Residues in contact with ALA 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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131A LYS 3.6 10.0 + - - +
132A THR* 3.4 39.7 - - - +
134A GLN 3.4 3.2 + - - +
136A HIS* 1.4 77.6 - - - +
138A LEU* 1.4 61.1 + - - +
140A SER* 3.2 16.6 + - - -
141A LEU* 3.2 12.1 + - - +
255A GLU* 3.4 30.1 - - + +
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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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133A LEU 3.6 26.2 - - - +
134A GLN* 3.6 7.1 + - - +
135A GLY 3.4 15.4 + - - +
136A HIS 3.1 0.2 - - - -
137A ALA* 1.4 77.5 - - - +
139A ASN* 1.3 56.2 + - - +
141A LEU* 4.2 6.1 - - + -
142A THR* 2.6 50.5 + - - +
337A GLN* 3.4 25.8 - - - +
448A LEU* 3.6 34.5 - - + -
449A PHE* 3.8 31.4 - - + -
452A HIS* 4.0 3.4 - - + +
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Residues in contact with ASN 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLY 3.8 8.0 - - - +
136A HIS* 3.0 16.2 + - - +
138A LEU* 1.3 76.8 - - - +
140A SER* 1.3 58.1 + - - +
142A THR* 3.3 4.2 + - - -
143A GLU* 2.9 29.5 + - - +
337A GLN* 2.7 38.4 + - - +
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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 HIS 4.0 2.0 + - - -
137A ALA* 3.2 14.4 + - - -
139A ASN* 1.3 77.4 - - - +
141A LEU* 1.3 52.6 + - - +
143A GLU* 3.3 7.7 + - - +
144A SER* 2.8 36.7 + - - -
255A GLU* 3.4 16.1 + - - -
136B HIS* 3.5 21.1 + - - -
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Residues in contact with LEU 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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132A THR 4.0 12.3 - - - +
133A LEU* 3.7 32.8 - - + -
137A ALA 3.2 16.3 + - - +
138A LEU* 3.7 7.6 - - + +
140A SER* 1.3 78.0 + - - +
142A THR* 1.4 55.5 + - - +
144A SER* 4.5 2.2 - - - -
145A MET* 3.0 25.8 + - - +
186A THR* 3.5 31.7 - - + +
187A ILE* 4.1 11.9 - - + -
254A SER* 4.0 26.2 - - - -
256A LEU* 6.0 1.6 - - + -
449A PHE* 3.7 28.0 - - + -
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Residues in contact with THR 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* 2.6 30.4 + - - +
139A ASN* 3.5 5.2 - - - -
141A LEU* 1.4 76.1 - - - +
143A GLU* 1.3 61.1 + - - +
145A MET* 3.4 3.1 + - - +
146A MET 3.3 9.2 + - - -
335A LEU 5.2 4.3 - - - +
337A GLN* 4.5 7.2 - - + +
340A LEU* 3.7 15.7 - - + -
449A PHE* 4.4 8.6 - - - -
452A HIS* 3.0 38.0 + - + +
456A GLN* 3.0 37.6 + - - +
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Residues in contact with GLU 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 ASN 2.9 18.1 + - - +
140A SER* 3.6 9.0 - - - +
142A THR* 1.3 73.8 - - - +
144A SER* 1.3 62.1 + - - +
146A MET* 3.5 7.6 + - - +
147A GLU* 3.3 37.6 + - - +
334A CYS* 5.5 11.4 - - - -
335A LEU 6.0 1.8 - - - -
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Residues in contact with SER 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 21.6 + - - -
141A LEU* 3.5 6.3 - - - -
143A GLU* 1.3 71.6 - - - +
145A MET* 1.3 59.0 + - - +
147A GLU* 3.2 13.3 + - - +
148A ASN* 2.9 50.0 + - - -
185A LEU 4.8 0.9 + - - -
186A THR* 3.7 16.7 + - - +
190A ARG* 5.0 6.6 + - - -
252A SER* 5.0 8.8 + - - -
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Residues in contact with MET 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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141A LEU 3.0 13.4 + - - +
142A THR 3.4 5.1 + - - +
144A SER* 1.3 74.4 - - - +
146A MET* 1.4 52.7 + - - +
148A ASN 3.4 0.3 + - - -
149A LEU* 2.8 46.8 + - + +
179A MET* 4.0 16.6 - - + +
182A ALA* 3.6 30.3 - - + +
183A GLY* 3.9 9.2 - - - +
186A THR* 3.3 22.6 - - - +
449A PHE* 3.9 13.5 - - + -
453A GLU* 3.4 39.9 - - + +
456A GLN* 3.4 20.2 - - - +
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Residues in contact with MET 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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142A THR 3.3 4.1 + - - +
143A GLU* 3.7 10.3 - - - +
144A SER 3.3 0.2 - - - -
145A MET* 1.4 76.8 - - - +
147A GLU* 1.4 62.6 + - + +
149A LEU* 3.6 2.2 + - - +
150A GLN* 3.2 49.3 + - - +
333A ILE* 3.7 31.9 - - + +
334A CYS* 5.1 3.8 - - - -
335A LEU* 3.8 28.7 - - + +
340A LEU* 5.2 0.2 - - + -
456A GLN* 3.4 47.2 + - + +
459A ILE* 4.9 2.5 - - + -
460A LEU* 3.9 22.9 - - + -
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Residues in contact with GLU 147 (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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143A GLU* 3.3 27.7 + - - +
144A SER* 3.2 14.5 + - - +
146A MET* 1.4 77.0 - - + +
148A ASN* 1.4 58.4 + - - +
150A GLN* 3.5 7.5 + - - +
151A ARG* 3.0 57.7 + - - +
190A ARG* 4.4 7.7 + - - +
332A PRO* 5.5 13.5 - - + -
334A CYS* 5.7 6.2 - - - -
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Residues in contact with ASN 148 (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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144A SER* 2.9 31.3 + - - +
145A MET 3.8 3.1 - - - +
147A GLU* 1.4 72.2 - - - +
149A LEU* 1.4 64.9 + - - +
151A ARG* 2.9 29.9 + - - +
152A ILE* 3.1 31.3 + - + +
182A ALA* 4.0 13.5 - - - +
185A LEU* 3.8 19.5 + - + +
186A THR* 2.8 35.4 + - - +
190A ARG* 3.2 15.9 + - - +
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Residues in contact with LEU 149 (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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145A MET* 2.8 39.9 + - + +
146A MET* 4.0 1.1 - - - +
148A ASN* 1.4 71.1 - - - +
150A GLN* 1.3 52.9 + - - +
152A ILE* 3.2 4.6 + - - +
153A MET* 2.8 44.8 + - - +
178A VAL* 3.7 28.9 - - + -
179A MET* 4.1 14.6 - - - -
182A ALA* 3.7 20.4 - - + +
453A GLU 4.2 3.1 - - - +
456A GLN* 3.8 30.3 - - + -
457A PHE* 4.0 12.8 - - + +
460A LEU* 3.6 16.4 - - + -
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Residues in contact with GLN 150 (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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146A MET* 3.2 32.2 + - - +
147A GLU* 3.8 4.6 - - - +
149A LEU* 1.3 72.4 - - - +
151A ARG* 1.4 65.0 + - - +
153A MET 4.5 0.4 - - - +
154A ARG* 3.1 41.7 + - - +
332A PRO* 3.4 19.7 - - + +
333A ILE* 3.0 57.3 + - - +
460A LEU* 3.7 16.8 - - + -
464A TYR* 3.2 27.8 + - - +
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Residues in contact with ARG 151 (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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147A GLU* 3.0 31.5 + - - +
148A ASN* 2.9 51.4 + - - +
150A GLN* 1.4 76.0 - - - +
152A ILE* 1.3 64.6 + - + +
154A ARG* 4.2 9.4 + - - +
185A LEU* 6.2 2.7 - - + -
190A ARG* 3.2 40.3 - - - +
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Residues in contact with ILE 152 (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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148A ASN 3.1 18.4 + - - +
149A LEU* 3.6 6.1 - - - +
151A ARG* 1.3 81.9 - - + +
153A MET* 1.3 60.2 + - - +
154A ARG 3.7 2.9 + - - +
177A ARG* 5.1 7.7 + - - +
178A VAL* 4.3 31.6 - - + +
181A GLU* 3.6 39.0 - - + +
182A ALA* 3.4 38.4 - - + +
185A LEU* 4.3 9.6 - - + -
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Residues in contact with MET 153 (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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149A LEU* 2.8 32.9 + - - +
152A ILE* 1.3 72.7 - - - +
154A ARG* 1.3 63.0 + - - +
174A PHE* 5.4 2.9 - - + -
178A VAL* 3.8 35.4 - - + -
457A PHE* 4.1 8.7 - - + +
460A LEU* 3.7 33.0 - - + -
461A MET* 3.7 41.1 - - + +
464A TYR* 4.0 15.7 - - + -
465A PHE* 3.7 16.2 - - + -
501A PHE* 3.5 17.2 - - - -
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Residues in contact with ARG 154 (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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150A GLN* 3.1 30.2 + - - +
151A ARG* 4.2 7.2 + - - +
152A ILE 3.6 3.9 - - - +
153A MET* 1.3 79.7 - - - +
327A SER 2.8 24.5 + - - -
328A LEU* 3.2 35.0 + - + +
330A GLY 3.5 12.9 + - - -
331A ASN 3.2 25.1 + - - -
332A PRO* 3.6 26.1 - - - +
333A ILE* 6.1 0.6 - - - +
464A TYR* 3.4 29.5 + - + +
501A PHE* 3.6 24.9 - - - -
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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
------------------------------------------------------------
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