Contacts of the strand formed by residues 150 - 158 (chain A) in PDB entry 3O9Z
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 LYS 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A LEU* 4.0 9.2 - - + -
146A GLU* 2.5 44.5 + - - +
147A LYS 3.3 23.2 + - - +
148A GLY 4.0 5.8 - - - +
149A ALA* 1.3 81.5 + - - +
151A ASP* 1.3 63.5 + - - +
152A VAL* 4.3 7.0 - - + -
194A PHE* 4.5 4.9 - - + -
218A GLY 3.0 12.7 + - - +
219A ALA* 3.1 4.7 - - - +
220A ARG* 2.9 26.3 + - - +
249A VAL* 3.8 23.6 - - + -
250A ASP* 3.1 27.4 + - - +
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Residues in contact with ASP 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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149A ALA 5.2 0.3 - - - +
150A LYS* 1.3 71.9 - - - +
152A VAL* 1.3 60.3 + - - +
153A VAL* 5.9 0.4 - - - -
220A ARG* 2.8 52.4 + - - +
248A ALA 3.8 0.9 - - - +
250A ASP* 2.8 40.1 + - - +
251A GLY 4.8 0.3 + - - -
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Residues in contact with VAL 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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150A LYS* 4.1 5.6 - - + +
151A ASP* 1.3 79.4 - - - +
153A VAL* 1.3 73.4 + - - +
154A LEU* 4.4 0.7 - - + +
190A LEU* 4.4 4.3 - - + -
194A PHE* 3.8 28.7 - - + -
219A ALA* 3.9 13.9 - - + -
220A ARG 2.9 10.8 + - - +
221A VAL* 3.3 18.1 - - + -
222A ARG* 3.0 26.7 + - - +
247A ILE* 3.7 28.0 - - + -
248A ALA 3.2 9.6 - - - +
249A VAL* 4.2 8.5 - - + -
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Residues in contact with VAL 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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151A ASP 5.9 0.4 - - - -
152A VAL* 1.3 79.8 - - - +
154A LEU* 1.3 61.0 + - - +
155A THR* 3.9 6.6 + - - +
222A ARG* 3.4 37.7 - - + +
246A SER* 3.8 2.4 + - - +
247A ILE* 3.7 1.2 - - - -
248A ALA* 2.9 44.6 + - + +
306A HIS* 3.5 30.3 - - + +
307A PRO* 4.1 12.6 - - + -
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Residues in contact with LEU 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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152A VAL* 4.1 1.3 - - + -
153A VAL* 1.3 70.8 - - - +
155A THR* 1.3 66.3 + - - +
156A TYR* 3.9 18.8 - - + +
186A PHE* 3.5 49.1 - - + -
189A LEU* 4.5 7.4 - - + -
190A LEU* 4.4 10.3 - - + -
221A VAL* 4.1 11.2 - - + -
222A ARG 2.9 7.0 + - - +
223A TRP* 3.2 15.3 - - + -
224A PHE 3.0 23.4 + - - +
246A SER 3.4 12.3 - - - +
247A ILE* 3.7 28.3 - - + -
256A PHE* 4.9 2.7 - - + -
306A HIS* 3.5 4.0 + - - -
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Residues in contact with THR 155 (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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153A VAL* 3.9 8.0 - - - +
154A LEU* 1.3 72.3 - - - +
156A TYR* 1.3 63.4 + - - +
157A VAL* 4.2 7.0 - - + -
224A PHE* 3.5 5.8 - - + -
244A TYR* 3.4 32.0 - - + +
245A ARG* 3.5 0.2 - - - -
246A SER* 2.8 39.6 + - - +
306A HIS* 2.9 24.0 + - + +
308A PHE* 3.6 34.4 - - + -
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Residues in contact with TYR 156 (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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130A LEU* 4.7 0.7 - - + -
154A LEU* 3.9 4.0 - - + -
155A THR* 1.3 76.4 - - - +
157A VAL* 1.3 61.5 + - - +
158A THR* 4.1 6.1 - - + -
182A ILE* 3.7 19.3 - - + -
185A HIS* 3.7 23.5 - - + +
186A PHE* 3.7 38.1 - + + -
224A PHE 2.8 12.7 + - - +
225A LEU* 3.2 18.3 - - + +
226A SER 2.9 24.6 + - - +
244A TYR 3.6 1.8 - - - -
245A ARG* 3.7 22.9 - - + -
256A PHE* 4.0 21.8 - + - -
260A PHE* 3.4 19.8 - - - -
312A AKG 2.6 30.2 + - - -
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Residues in contact with VAL 157 (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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155A THR* 4.2 16.4 - - + -
156A TYR* 1.3 78.5 - - - +
158A THR* 1.3 65.3 + - - +
224A PHE* 4.4 9.0 - - + -
226A SER* 3.2 8.1 - - - +
228A ASP 3.5 24.9 - - - +
229A PRO* 4.2 4.5 - - + -
231A PHE* 4.0 26.7 - - + +
232A VAL* 3.9 22.0 - - + +
242A ARG 4.7 0.2 - - - +
243A THR* 3.3 3.9 - - - -
244A TYR* 2.8 46.2 + - + +
245A ARG* 4.3 1.9 - - - +
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Residues in contact with THR 158 (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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156A TYR* 4.1 4.3 - - + -
157A VAL* 1.3 76.5 - - - +
159A GLY* 1.3 65.1 + - - +
160A ARG* 2.9 23.0 + - - +
182A ILE* 3.7 28.5 - - + -
226A SER 2.9 13.1 + - - +
227A ILE* 3.3 18.9 - - + +
242A ARG 3.9 2.7 - - - -
243A THR* 3.8 6.8 - - - +
245A ARG* 3.5 12.8 + - - -
312A AKG 2.9 34.1 + - - +
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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