Contacts of the strand formed by residues 182 - 189 (chain E) in PDB entry 6CP3
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 SER 182 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E LEU* 4.9 0.9 - - - +
171E ILE* 3.3 39.2 + - - +
174E ILE* 5.3 2.3 - - - +
180E GLY 5.0 1.4 + - - -
181E PHE* 1.3 78.6 + - - +
183E VAL* 1.3 65.9 + - - +
214E LYS 3.1 12.5 + - - -
215E VAL* 2.9 37.6 - - - -
216E ALA 2.9 4.2 + - - -
252E LEU* 3.5 10.7 - - - +
254E PHE* 4.1 11.7 - - - -
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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
----------------------------------------------------------
182E SER* 1.3 78.8 - - - +
184E PHE* 1.3 65.6 + - - +
185E THR* 4.1 4.5 - - - +
216E ALA* 3.4 15.3 - - + +
218E VAL* 5.1 2.7 - - + -
236E GLY* 3.7 22.7 - - - +
239E ILE* 3.8 31.4 - - + +
240E ALA* 4.3 9.2 - - + +
243E PHE* 4.5 7.9 - - + -
251E VAL* 4.4 14.6 - - + -
252E LEU 2.9 10.3 + - - +
253E LEU* 3.4 17.2 - - + +
254E PHE* 2.9 25.3 + - - -
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Residues in contact with PHE 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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167E ILE* 4.3 19.5 - - + -
171E ILE* 6.0 1.1 - - + -
182E SER 4.0 1.6 - - - -
183E VAL* 1.3 71.6 - - - +
185E THR* 1.3 69.1 + - - +
186E GLY* 3.8 20.9 - - - -
189E GLU* 4.8 5.6 - - - -
197E LEU* 3.6 29.6 - - + -
201E MET* 5.1 4.7 - - + -
215E VAL* 4.1 8.8 - - + +
216E ALA 2.9 9.9 + - - +
217E LEU* 3.7 30.1 - - + -
218E VAL* 2.9 23.6 + - - +
219E PHE* 3.8 15.7 - + - -
254E PHE* 3.6 31.4 - + + -
255E ILE 5.5 0.2 - - - -
256E ASP* 4.5 21.3 - - + -
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Residues in contact with THR 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* 4.1 4.0 - - - +
184E PHE* 1.3 82.8 + - - +
186E GLY* 1.3 59.9 + - - +
187E VAL* 3.5 11.9 + - + -
218E VAL* 3.2 14.0 - - + +
232E VAL* 3.7 33.9 - - + +
233E ALA* 4.1 6.1 - - - -
236E GLY* 3.4 22.6 - - - -
253E LEU* 4.3 1.9 - - - +
254E PHE 2.8 15.1 + - - -
255E ILE* 3.4 11.2 - - + +
256E ASP 3.0 26.0 + - - +
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Residues in contact with GLY 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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184E PHE* 3.8 15.4 - - - -
185E THR* 1.3 71.2 - - - +
187E VAL* 1.3 60.6 + - - -
188E GLY 3.5 0.2 + - - -
189E GLU* 3.7 21.4 + - - +
218E VAL 2.9 10.8 + - - -
219E PHE* 3.7 3.4 - - - +
220E GLY 2.9 33.5 + - - +
256E ASP 3.1 8.7 - - - -
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Residues in contact with VAL 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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185E THR* 3.5 5.7 + - + -
186E GLY* 1.3 69.7 - - - +
188E GLY* 1.3 67.5 + - - +
189E GLU* 4.2 0.2 - - - -
220E GLY 4.2 1.1 - - - -
229E ARG* 3.6 26.2 - - + +
232E VAL* 3.8 13.0 - - + -
233E ALA* 3.5 41.7 - - + +
255E ILE* 4.8 7.4 - - + -
256E ASP 2.8 18.7 + - - +
257E ASN 3.4 12.4 + - - +
260E ARG* 3.5 9.8 + - - +
261E PHE* 3.9 29.8 - - + +
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Residues in contact with GLY 188 (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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301A PHE* 6.3 0.2 - - - -
187E VAL* 1.3 78.0 - - - +
189E GLU* 1.3 63.8 + - - +
190E ARG 3.5 1.0 + - - -
220E GLY 3.0 13.7 + - - -
222E MET* 3.3 17.5 - - - +
229E ARG* 4.2 21.1 - - - +
260E ARG* 2.7 34.9 + - - -
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Residues in contact with GLU 189 (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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184E PHE* 4.8 6.6 - - - -
186E GLY* 3.8 20.9 - - - +
187E VAL 3.2 1.9 - - - -
188E GLY* 1.3 77.4 - - - +
190E ARG* 1.3 85.2 + - - +
191E THR* 3.3 3.0 + - - -
193E GLU* 4.0 22.7 - - - +
194E GLY* 4.2 0.9 - - - -
197E LEU* 5.6 2.4 - - - +
219E PHE* 3.7 32.5 - - + -
220E GLY 3.4 5.1 + - - +
221E GLN* 4.0 5.5 - - - +
222E MET* 3.3 18.6 + - - +
256E ASP* 2.9 31.2 - - - +
260E ARG* 4.3 2.8 + - - +
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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