Contacts of the strand formed by residues 183 - 192 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181C GLU* 3.3 15.1 - - - +
182C PRO* 1.3 98.1 - - + +
184C ARG* 1.3 70.6 + - - +
216C LEU* 4.0 11.9 - - + -
219C ARG* 3.7 43.5 - - - +
240C TRP* 3.7 25.7 - - + -
241C SER 3.4 13.9 - - - +
242C ASN* 4.0 12.3 - - - +
160D GLY* 4.3 1.7 - - - -
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Residues in contact with ARG 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C PHE* 3.4 45.6 - - - +
181C GLU 4.4 2.9 - - - +
182C PRO 4.5 0.2 + - - -
183C VAL* 1.3 79.5 - - - +
185C ARG* 1.3 60.2 + - - +
240C TRP* 3.3 11.8 - - - -
241C SER 2.9 32.0 + - - +
243C SER* 3.7 19.9 - - - +
246C LEU* 3.4 39.1 - - + +
159D ASP* 3.0 38.2 + - - +
160D GLY 3.8 16.0 + - - +
161D LYS* 3.5 19.1 - - - +
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Residues in contact with ARG 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C ARG* 1.3 79.4 + - - +
186C ASN* 1.3 75.7 + - - +
187C GLU* 3.9 12.7 + - - +
220C GLU* 3.7 18.6 + - - -
238C ARG* 3.8 39.2 - - + +
239C VAL 3.9 7.2 - - - +
240C TRP* 3.5 36.5 - - + +
246C LEU* 3.7 7.1 - - - +
158D ALA* 3.1 39.5 + - - +
159D ASP* 3.3 37.6 + - - +
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Residues in contact with ASN 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ARG* 1.3 76.8 - - - +
187C GLU* 1.3 59.0 + - - +
188C PHE* 4.0 19.1 - - + -
237C VAL 3.7 1.0 - - - +
238C ARG* 3.3 4.9 - - - -
239C VAL* 3.1 35.2 + - + +
241C SER* 3.7 13.7 + - - -
246C LEU* 3.1 54.6 + - - +
249C VAL* 4.4 4.5 - - - +
250C TYR* 3.2 30.0 - - + +
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Residues in contact with GLU 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C ARG* 3.9 13.3 + - - +
186C ASN* 1.3 73.2 - - - +
188C PHE* 1.3 67.7 + - - +
189C ILE* 3.5 20.3 + - + +
236C VAL* 3.8 19.7 - - + -
237C VAL 3.3 4.0 - - - -
238C ARG* 2.7 41.9 + - + +
250C TYR* 3.9 14.2 - - - -
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Residues in contact with PHE 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C ASN* 4.0 10.1 - - + -
187C GLU* 1.3 75.0 - - - +
189C ILE* 1.3 62.7 - - - +
190C ILE* 3.4 19.5 - - + -
235C PHE 3.6 0.5 - - - +
236C VAL* 3.4 5.5 - - - +
237C VAL* 2.8 56.3 + - + +
239C VAL* 3.8 24.7 - - + -
249C VAL* 4.3 1.1 - - + -
250C TYR* 3.3 61.0 - + - -
253C VAL* 3.5 35.0 - - + -
254C LEU* 4.2 9.2 - - + -
257C ILE* 4.5 8.3 - - + -
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Residues in contact with ILE 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C GLU* 3.5 25.1 - - + +
188C PHE* 1.3 78.3 - - - +
190C ILE* 1.3 63.8 + - - +
191C GLY 4.2 0.7 + - - +
226C ASN* 5.1 10.3 - - - +
227C GLU* 5.7 1.3 - - - +
234C ASN* 4.2 27.1 - - + +
235C PHE 3.3 4.7 - - - +
236C VAL* 4.3 13.5 - - + -
250C TYR* 5.9 0.2 + - - -
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Residues in contact with ILE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B LEU* 5.1 8.7 - - + -
188C PHE* 3.4 33.9 - - + +
189C ILE* 1.3 75.5 - - - +
191C GLY* 1.3 60.7 + - - +
192C VAL* 3.9 9.8 + - + -
205C LEU* 4.8 2.9 - - + -
233C ILE 3.6 1.2 - - - +
234C ASN* 3.3 2.7 - - - -
235C PHE* 2.7 48.9 + - + +
237C VAL* 4.7 9.0 - - + -
254C LEU* 5.1 4.7 - - + -
257C ILE* 3.7 32.3 - - + -
261C PHE* 3.7 29.8 - - + -
268C PHE* 3.9 13.2 - - + -
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Residues in contact with GLY 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C ILE* 4.2 2.0 + - - +
190C ILE* 1.3 72.4 - - - +
192C VAL* 1.3 61.5 + - - -
232C SER* 3.8 6.7 - - - -
233C ILE 3.2 8.5 - - - -
234C ASN* 3.4 13.2 - - - -
268C PHE* 3.5 23.1 - - - +
269C PRO* 3.5 12.4 - - - +
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Residues in contact with VAL 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C ILE* 3.9 6.5 - - + -
191C GLY* 1.3 79.5 - - - +
193C ALA* 1.3 63.4 + - - +
196C SER* 3.4 26.0 - - - +
201C VAL* 4.3 5.2 - - + -
232C SER* 3.4 2.6 - - - -
233C ILE* 2.8 36.6 + - + +
235C PHE* 3.7 28.5 - - + -
261C PHE* 3.5 33.4 - - + -
266C ILE* 3.7 10.1 - - + -
267C SER 3.4 9.0 - - - +
268C PHE* 4.7 1.1 - - + -
269C PRO* 3.6 4.9 - - - -
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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