Contacts of the strand formed by residues 189 - 195 (chain E) in PDB entry 2HU4
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 TRP 189 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123E SER* 3.3 34.1 - - - -
124E CYS* 3.8 6.3 - - - -
125E SER* 4.1 19.1 - - - -
128E GLU* 4.8 5.1 + - + -
130E ARG* 4.0 24.5 - - + +
132E PHE* 3.5 29.8 - + - -
172E ARG* 3.9 26.6 - - - +
174E GLU* 5.9 0.9 - - - +
183E CYS* 3.4 29.4 - - - -
184E HIS* 3.5 35.8 + + + -
188E SER* 1.3 75.7 - - - +
190E LEU* 1.3 60.6 + - - +
191E THR* 4.1 10.8 + - + +
206E LYS 3.5 1.6 - - - +
207E TYR* 3.5 4.8 - - - -
208E ASN* 2.9 30.5 + - - +
209E GLY 4.8 0.5 + - - -
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Residues in contact with LEU 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E ALA* 3.1 7.3 - - - +
183E CYS* 2.8 41.7 + - - +
185E ASP* 6.5 0.2 - - + -
188E SER 3.9 0.8 + - - +
189E TRP* 1.3 73.1 - - - +
191E THR* 1.3 67.4 + - - +
192E ILE* 4.4 9.2 - - + -
205E LEU* 4.6 7.4 - - + -
206E LYS 3.3 11.2 - - - +
207E TYR* 4.7 9.4 - - + -
230E CYS* 3.8 23.3 - - - -
237E CYS* 3.8 25.6 - - + -
257E MET* 3.9 22.7 - - + +
260E GLY* 3.5 33.4 - - - +
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Residues in contact with THR 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E PHE* 4.4 5.6 - - + -
158E LEU* 4.3 12.8 - - + -
174E GLU* 3.5 34.2 + - + +
175E SER* 4.9 2.3 - - - -
181E SER 3.8 2.5 - - - -
182E ALA* 4.2 10.3 - - + -
189E TRP* 4.8 10.3 - - + +
190E LEU* 1.3 81.6 - - - +
192E ILE* 1.3 66.2 + - - +
193E GLY 4.2 0.4 - - - -
204E VAL 3.7 1.4 - - - +
205E LEU* 3.3 4.5 - - - +
206E LYS* 2.9 59.7 + - - +
209E GLY* 5.7 2.5 + - - +
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Residues in contact with ILE 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E LEU* 4.5 3.6 - - - +
180E ALA* 3.0 27.5 - - - +
181E SER* 2.7 30.3 + - - +
190E LEU* 4.4 13.5 - - + -
191E THR* 1.3 78.4 - - - +
193E GLY* 1.3 61.5 + - - +
194E ILE* 5.0 0.4 - - + -
203E ALA* 4.3 5.2 - - + -
204E VAL 3.6 2.5 - - - -
205E LEU* 3.3 30.1 - - + -
225E THR* 4.8 5.4 - - + -
230E CYS* 4.7 2.2 - - - -
239E THR* 4.3 16.4 - - + +
241E MET* 3.7 24.2 - - + -
257E MET* 3.5 32.3 - - + -
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Residues in contact with GLY 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E LEU* 5.5 0.4 - - - -
175E SER* 4.4 12.0 + - - -
176E VAL 4.0 5.5 - - - +
177E ALA* 3.3 21.1 - - - -
180E ALA* 4.5 0.4 - - - -
191E THR 4.2 0.4 - - - -
192E ILE* 1.3 74.7 - - - +
194E ILE* 1.3 61.5 + - - -
195E SER* 3.9 0.7 + - - -
202E VAL 3.6 1.9 - - - +
203E ALA* 3.4 0.6 - - - -
204E VAL* 2.8 44.0 + - - +
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Residues in contact with ILE 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177E ALA* 3.3 1.0 - - - +
178E TRP* 2.8 49.0 + - + -
179E SER* 3.1 17.6 + - - +
192E ILE* 5.0 1.1 - - + -
193E GLY* 1.3 71.4 - - - -
195E SER* 1.3 63.2 - - - +
201E ALA* 3.8 10.8 - - + -
202E VAL 3.3 7.9 - - - +
203E ALA* 3.8 20.4 - - + -
223E LEU* 3.3 36.3 - - + +
224E ARG* 3.6 24.7 - - - -
225E THR* 3.8 15.9 - - + -
241E MET* 4.1 10.8 - - + -
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Residues in contact with SER 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E SER 4.9 1.7 + - - -
154E PRO* 5.0 0.2 - - - +
156E ARG 5.4 0.2 + - - -
176E VAL* 3.6 29.3 - - - +
177E ALA* 4.0 3.8 + - - -
178E TRP* 3.5 12.5 - - - +
193E GLY 3.9 1.4 + - - -
194E ILE* 1.3 75.6 - - - +
196E GLY* 1.3 67.9 + - - +
201E ALA* 3.6 2.4 - - - -
202E VAL* 3.1 36.4 + - - +
204E VAL* 6.3 0.2 - - - +
99H VAL* 4.7 9.6 - - - -
456H TRP* 3.8 6.4 - - - -
458H TRP* 3.3 22.3 + - - -
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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