Contacts of the helix formed by residues 155 - 166 (chain B) in PDB entry 3HS3
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 ASN 155 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B VAL* 3.6 1.0 + - - -
154B SER* 1.3 70.2 + - - +
156B ASN* 1.3 54.9 + - - +
157B THR* 3.6 9.7 + - - -
158B LYS* 2.9 44.4 + - + +
159B GLY 2.9 22.7 + - - -
307B ILE* 4.3 20.3 - - + +
308B ILE 2.9 20.6 + - - +
309B ASP* 4.5 7.5 + - - +
310B VAL* 3.6 14.5 - - + +
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Residues in contact with ASN 156 (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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142B SER 4.1 4.3 - - - +
154B SER* 2.7 35.8 + - - +
155B ASN* 1.3 68.7 - - - +
157B THR* 1.3 60.5 + - - +
159B GLY* 3.3 1.6 + - - +
160B GLY 2.9 23.7 + - - -
185B THR* 3.6 44.1 + - - +
188B GLU* 2.9 29.7 + - + +
189B ARG* 3.5 22.7 - - + +
262B TYR* 4.3 14.3 + - - -
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Residues in contact with THR 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ASN* 3.2 8.9 + - - -
156B ASN* 1.3 78.3 - - - +
158B LYS* 1.3 63.7 + - - +
160B GLY 3.3 0.3 + - - -
161B LYS* 3.0 23.4 + - + +
188B GLU* 4.1 19.7 + - - +
192B ALA* 3.1 27.6 - - + +
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Residues in contact with LYS 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B ASN* 2.9 33.0 + - - +
157B THR* 1.3 77.6 - - - +
159B GLY* 1.3 57.3 + - - +
161B LYS* 3.7 8.5 - - + +
162B GLU* 2.8 52.5 + - + +
309B ASP* 2.8 37.9 + - - +
310B VAL* 3.6 20.7 + - + -
312B PRO* 5.2 4.3 - - - -
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Residues in contact with GLY 159 (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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155B ASN 2.9 12.0 + - - -
156B ASN 3.3 0.9 + - - -
157B THR 3.2 0.4 - - - -
158B LYS* 1.3 77.1 - - - +
160B GLY* 1.3 53.6 + - - +
163B SER* 2.7 34.7 + - - -
262B TYR* 3.4 28.9 - - - -
278B ILE* 3.8 9.6 - - - +
310B VAL* 3.8 11.3 - - - +
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Residues in contact with GLY 160 (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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156B ASN 2.9 11.3 + - - -
157B THR 3.8 1.8 - - - -
158B LYS 3.3 0.2 - - - -
159B GLY* 1.3 73.0 - - - +
161B LYS* 1.3 66.4 + - - +
163B SER* 3.2 9.9 + - - -
164B ILE* 3.4 6.2 + - - +
189B ARG* 3.4 32.1 - - - +
193B MET* 3.3 28.4 - - - +
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Residues in contact with LYS 161 (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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157B THR* 3.0 18.7 + - + +
158B LYS* 3.7 8.5 - - + +
160B GLY* 1.3 76.4 - - - +
162B GLU* 1.3 70.6 + - - +
164B ILE 3.3 3.3 + - - -
165B LYS* 3.2 37.2 + - + +
192B ALA* 3.8 8.1 - - + +
196B GLU* 3.6 45.4 - - + +
199B LYS* 6.1 1.7 - - - +
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Residues in contact with GLU 162 (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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158B LYS* 2.8 45.5 + - + +
161B LYS* 1.3 79.2 - - + +
163B SER* 1.3 63.5 - - - +
165B LYS* 3.0 45.7 + - - +
166B LEU* 3.1 27.0 + - - +
278B ILE* 4.1 8.7 - - + -
310B VAL* 5.4 0.7 - - + -
312B PRO* 3.9 36.7 - - + +
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Residues in contact with SER 163 (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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159B GLY 2.7 23.1 + - - -
160B GLY 3.2 7.1 + - - -
162B GLU* 1.3 76.7 - - - +
164B ILE* 1.3 62.5 + - - +
166B LEU* 3.3 25.6 + - - +
167B LEU* 4.0 8.1 + - - +
193B MET* 4.1 18.8 - - - +
232B ILE* 4.0 11.6 - - - +
260B VAL* 4.1 15.5 - - - +
261B GLY 4.8 0.2 + - - -
262B TYR* 4.1 7.6 - - - -
278B ILE* 3.4 15.0 - - - +
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Residues in contact with ILE 164 (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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160B GLY 3.4 3.1 + - - +
161B LYS 3.3 8.4 + - - +
162B GLU 3.2 0.4 - - - -
163B SER* 1.3 76.5 - - - +
165B LYS* 1.3 62.6 + - - +
167B LEU* 3.2 30.6 + - + +
174B VAL* 4.5 5.2 - - + -
176B ILE* 4.5 8.3 - - + -
193B MET* 3.5 42.0 - - + +
196B GLU* 3.8 17.5 - - + -
197B ALA* 4.0 21.1 - - + +
200B LEU* 4.0 15.7 - - + +
202B ILE* 4.1 11.4 - - + +
232B ILE* 3.7 22.4 - - + -
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Residues in contact with LYS 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LYS* 3.2 27.4 + - + +
162B GLU* 3.0 46.0 + - - +
164B ILE* 1.3 77.7 - - - +
166B LEU* 1.3 59.9 + - - +
167B LEU 3.2 8.1 + - - +
169B LYS* 4.7 9.5 + - - -
196B GLU* 3.6 24.7 - - + +
200B LEU* 4.7 7.6 - - + -
314B LYS* 5.1 2.8 + - - -
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Residues in contact with LEU 166 (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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162B GLU 3.1 18.3 + - - +
163B SER* 3.5 7.2 - - - +
164B ILE 3.1 0.8 - - - -
165B LYS* 1.3 76.7 - - - +
167B LEU* 1.3 63.9 + - - +
168B SER 3.7 0.2 + - - -
260B VAL* 3.9 29.8 - - + -
276B SER* 4.5 2.5 - - - -
277B THR 3.7 27.4 - - - +
278B ILE* 4.1 9.4 - - + -
312B PRO* 4.4 11.7 - - + -
313B ILE 4.1 1.6 - - - +
314B LYS* 2.7 69.2 + - + +
318B THR* 3.3 13.3 - - + -
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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