Contacts of the strand formed by residues 183 - 192 (chain E) in PDB entry 5AJI
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 VAL 183 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181E GLU* 3.3 15.2 - - - +
182E PRO* 1.3 98.0 - - + +
184E ARG* 1.3 69.4 + - - +
216E LEU* 4.0 15.3 - - + -
219E ARG* 3.8 41.5 - - - +
240E TRP* 3.7 25.2 - - + -
241E SER 3.4 14.1 - - - +
242E ASN* 4.0 12.1 - - - +
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Residues in contact with ARG 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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178E PHE* 3.4 57.0 - - - +
181E GLU* 4.4 8.1 - - + +
183E VAL* 1.3 80.1 - - - +
185E ARG* 1.3 65.4 + - - +
240E TRP* 3.3 14.2 - - - -
241E SER 2.9 31.6 + - - +
243E SER* 3.7 21.3 - - - +
246E LEU* 3.4 37.7 - - + +
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Residues in contact with ARG 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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184E ARG* 1.3 84.6 + - - +
186E ASN* 1.3 75.2 + - - +
187E GLU* 3.9 12.3 + - - +
220E GLU* 3.8 19.2 + - - -
238E ARG* 3.8 39.2 - - - +
239E VAL 3.8 7.6 - - - +
240E TRP* 3.5 45.6 - - + +
246E LEU* 4.0 7.5 - - - +
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Residues in contact with ASN 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 ARG* 1.3 76.3 - - - +
187E GLU* 1.3 59.4 + - - +
188E PHE* 4.0 18.8 - - + -
237E VAL 3.7 0.7 - - - +
238E ARG* 3.3 5.0 - - - -
239E VAL* 3.1 34.3 + - + +
241E SER* 4.0 13.5 + - - -
246E LEU* 3.2 51.3 + - - +
249E VAL* 4.0 6.9 - - - +
250E TYR* 3.7 28.4 - - + +
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Residues in contact with GLU 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 ARG* 3.9 13.2 + - - +
186E ASN* 1.3 74.0 - - - +
188E PHE* 1.3 67.5 + - - +
189E ILE* 3.5 20.0 - - + +
236E VAL* 3.8 19.3 - - + -
237E VAL 3.3 3.6 - - - -
238E ARG* 2.7 42.2 + - + -
250E TYR* 3.8 14.9 - - - -
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Residues in contact with PHE 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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186E ASN* 4.0 10.8 - - + -
187E GLU* 1.3 75.1 - - - +
189E ILE* 1.3 64.4 + - - +
190E ILE* 3.5 19.3 - - + -
235E PHE 3.6 0.3 - - - +
236E VAL* 3.4 4.9 - - - +
237E VAL* 2.8 56.3 + - + +
239E VAL* 3.8 24.2 - - + -
249E VAL* 4.3 0.9 - - + -
250E TYR* 3.3 61.0 - + - -
253E VAL* 3.5 35.4 - - + -
254E LEU* 4.2 8.3 - - + -
257E ILE* 4.5 9.4 - - + -
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Residues in contact with ILE 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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187E GLU* 3.5 25.5 + - + +
188E PHE* 1.3 78.3 - - - +
190E ILE* 1.3 65.7 + - - +
191E GLY 4.2 0.5 + - - -
226E ASN* 5.1 10.1 - - - +
227E GLU* 5.7 1.3 - - - +
234E ASN* 4.2 24.7 - - + +
235E PHE 3.3 7.0 - - - +
236E VAL* 4.3 12.8 - - + -
250E TYR* 5.8 0.4 + - - -
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Residues in contact with ILE 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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228D LEU* 5.1 9.6 - - + -
188E PHE* 3.5 32.5 - - + +
189E ILE* 1.3 76.2 - - - +
191E GLY* 1.3 61.6 + - - +
192E VAL* 3.9 10.4 + - + -
205E LEU* 4.8 3.6 - - + -
233E ILE 3.6 0.9 - - - +
234E ASN* 3.3 3.3 - - - -
235E PHE* 2.7 48.8 + - + +
237E VAL* 4.7 8.7 - - + -
254E LEU* 5.1 4.7 - - + -
257E ILE* 3.7 31.6 - - + -
261E PHE* 3.7 30.1 - - + -
268E PHE* 4.0 13.5 - - + -
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Residues in contact with GLY 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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189E ILE* 4.2 1.4 + - - +
190E ILE* 1.3 73.7 - - - +
192E VAL* 1.3 62.0 + - - -
232E SER* 3.8 6.5 - - - -
233E ILE 3.2 8.5 - - - -
234E ASN* 3.4 12.8 - - - -
268E PHE* 3.5 23.1 - - - +
269E PRO* 3.5 12.2 - - - +
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Residues in contact with VAL 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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190E ILE* 3.9 6.7 - - + -
191E GLY* 1.3 79.3 - - - +
193E ALA* 1.3 62.0 - - - +
196E SER* 3.4 26.7 - - - +
201E VAL* 4.3 4.9 - - + -
232E SER* 3.4 2.6 - - - -
233E ILE* 2.8 36.7 + - + -
235E PHE* 3.7 28.3 - - + -
261E PHE* 3.5 33.4 - - + -
266E ILE* 3.7 9.6 - - + -
267E SER 3.4 9.6 - - - +
268E PHE* 4.7 0.7 - - + -
269E PRO* 3.6 5.4 - - - -
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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