Contacts of the strand formed by residues 180 - 187 (chain E) in PDB entry 4DOH
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 180 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178E ASN 3.4 14.1 - - - +
179E LEU* 1.3 75.7 - - - +
181E TYR* 1.3 66.1 + - - +
197E CYS* 4.2 24.8 - - + +
198E VAL 3.8 9.6 - - - +
199E THR* 3.9 19.1 - - + -
220E SER* 3.7 1.2 - - - -
221E PHE* 2.7 72.2 + - + +
223E PRO* 5.1 7.0 - - + -
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Residues in contact with TYR 181 (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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140E PRO* 3.8 29.4 - - + -
155E LEU* 4.1 22.0 - - + -
157E ALA* 3.3 20.0 - - + +
158E PRO* 3.6 6.4 - - + +
173E GLN* 2.7 37.5 + - - -
179E LEU* 3.6 12.6 - - + +
180E LYS* 1.3 76.1 - - - +
182E ASN* 1.3 61.0 + - - +
183E VAL* 3.7 1.2 + - + -
196E GLN 3.7 0.9 - - - +
197E CYS* 3.4 9.3 - - - -
198E VAL* 3.0 51.1 + - + +
199E THR* 4.4 3.6 - - - -
201E HIS* 4.2 9.1 + + - -
218E VAL* 4.0 14.6 - - + -
219E GLU 3.5 1.6 - - - -
220E SER* 3.1 29.6 - - - -
221E PHE* 5.2 0.2 - - - -
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Residues in contact with ASN 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E LYS 4.2 0.6 + - - -
181E TYR* 1.3 71.1 - - - +
183E VAL* 1.3 66.2 + - - +
184E SER* 3.7 1.7 + - - -
195E SER* 3.4 22.6 - - - -
196E GLN 3.7 6.4 + - - +
197E CYS* 4.7 7.2 - - - -
217E HIS* 3.7 1.0 + - - +
218E VAL* 3.2 7.3 - - - -
219E GLU* 2.8 43.1 + - + +
221E PHE* 5.1 4.1 - - + -
301E NAG 2.1 72.5 + - + +
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Residues in contact with VAL 183 (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 VAL* 5.0 5.6 - - + -
155E LEU* 4.4 7.9 - - + -
181E TYR* 4.5 0.9 - - + +
182E ASN* 1.3 77.6 + - - +
184E SER* 1.3 60.6 + - - +
185E VAL* 4.0 11.7 + - + +
194E TRP 3.8 0.7 - - - +
195E SER* 3.2 2.3 - - - -
196E GLN* 3.0 38.8 + - + +
198E VAL* 4.0 27.1 - - + -
203E LEU* 4.0 26.5 - - + -
216E VAL* 4.2 22.7 - - + -
217E HIS 3.9 2.7 - - - -
218E VAL* 3.9 19.1 - - + -
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Residues in contact with SER 184 (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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301D NAG 5.1 0.7 - - - +
182E ASN* 3.7 2.1 + - - -
183E VAL* 1.3 72.7 - - - +
185E VAL* 1.3 61.4 + - - +
193E THR* 4.2 9.1 + - - -
194E TRP 3.4 4.8 + - - -
195E SER* 3.6 8.4 + - - +
215E CYS 3.5 1.9 - - - +
216E VAL* 3.4 6.4 - - - +
217E HIS* 3.0 51.2 + - - -
301E NAG 2.8 37.7 + - - -
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Residues in contact with VAL 185 (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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183E VAL* 4.4 13.7 - - + +
184E SER* 1.3 77.3 - - - +
186E LEU* 1.3 62.0 + - - +
187E ASN 4.2 0.7 - - - +
192E ARG 4.1 0.3 - - - +
193E THR* 3.0 7.9 + - - -
194E TRP* 2.7 84.5 + - + +
196E GLN* 5.1 0.2 - - - +
205E LEU* 4.0 20.6 - - + -
214E TYR* 3.9 26.2 - - + -
215E CYS 3.4 6.5 - - - +
216E VAL* 4.2 13.2 - - + -
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Residues in contact with LEU 186 (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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185E VAL* 1.3 74.3 - - - +
187E ASN* 1.3 72.8 + - - +
188E THR* 3.6 16.1 + - + +
191E ASN* 3.9 20.6 - - - +
192E ARG 3.2 24.9 - - - +
193E THR* 3.9 11.4 - - + +
214E TYR* 3.3 9.7 - - - -
215E CYS* 2.7 53.1 + - + +
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Residues in contact with ASN 187 (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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148D ASP* 3.4 23.0 + - - +
185E VAL* 4.2 1.2 - - - +
186E LEU* 1.3 71.3 - - - +
188E THR* 1.3 58.4 + - - +
189E LYS* 2.8 22.5 + - - +
190E SER* 3.1 24.2 + - - +
191E ASN* 2.9 29.8 + - - -
192E ARG 2.9 12.7 + - - +
194E TRP* 5.9 1.5 - - - +
209E GLU* 4.6 9.1 - - - +
212E THR* 3.6 15.4 - - - +
213E LEU 4.0 0.7 - - - -
214E TYR* 3.6 29.4 + - + -
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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