Contacts of the strand formed by residues 316 - 322 (chain B) in PDB entry 4N36
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 LEU 316 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B SER* 3.5 11.4 - - - +
211B LEU* 3.6 34.1 - - - +
212B ILE 3.7 11.0 - - - -
213B PRO* 3.8 7.9 - - + +
249B LEU* 4.0 23.1 - - + -
250B ILE 3.7 7.6 + - - +
251B TYR* 3.2 42.0 - - + +
252B TRP* 2.7 27.5 + - - +
315B PHE* 1.3 79.9 - - - +
317B PHE* 1.3 54.7 + - - +
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Residues in contact with PHE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B TYR* 3.5 1.9 - + - +
210B SER* 2.8 60.4 + - - -
212B ILE* 3.5 13.0 - - + -
214B LYS* 3.6 24.9 - - + -
219B ALA* 3.5 31.9 - - + -
222B PHE* 3.6 42.4 - + + -
223B CYS* 4.1 0.2 - - - -
230B LEU* 3.8 6.7 - - + -
251B TYR* 3.7 3.3 - - - -
252B TRP* 3.5 18.2 - - + +
315B PHE 4.0 5.6 - - - +
316B LEU* 1.3 81.9 - - - +
318B ILE* 1.3 64.3 + - - +
319B CYS* 3.8 19.7 - - - -
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Residues in contact with ILE 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B TYR* 4.2 5.2 - - + -
208B TYR 3.1 6.7 - - - +
209B PHE* 3.4 42.8 - - + -
230B LEU* 3.4 9.1 - - - +
231B THR* 2.9 41.6 + - + +
242B LEU* 4.1 15.9 - - + +
246B ALA* 5.2 0.2 - - + -
251B TYR* 3.6 24.5 - - + -
252B TRP 3.1 8.4 + - - +
253B ILE* 4.3 13.2 - - + -
298B ILE* 4.3 13.9 - - + -
317B PHE* 1.3 77.7 - - - +
319B CYS* 1.3 72.3 + - - +
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Residues in contact with CYS 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B TRP* 3.9 12.6 - - + -
207B TYR* 3.1 5.4 - - - -
208B TYR* 2.9 39.9 + - + -
222B PHE* 4.3 5.6 - - - -
223B CYS* 2.0 51.4 - - - -
226B ARG* 5.8 0.4 - - - -
228B SER* 3.3 14.1 - - - +
229B HIS 3.3 5.6 - - - -
317B PHE* 3.8 17.3 - - - -
318B ILE* 1.3 79.2 - - - +
320B LYS* 1.3 62.3 + - - +
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Residues in contact with LYS 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B TRP* 4.5 0.2 - - - -
205B ASN* 3.6 33.7 - - + +
206B PHE 3.3 4.9 - - - -
207B TYR* 3.7 14.1 - - + -
228B SER* 3.2 14.6 - - - -
229B HIS* 2.8 20.9 + - - +
231B THR* 3.2 31.2 - - - +
232B SER* 2.9 33.5 + - - +
234B THR* 4.9 4.9 + - - +
238B GLU* 2.6 31.8 + - - +
268B ASP* 4.5 6.7 - - - +
319B CYS* 1.3 75.4 - - - +
321B ARG* 1.3 65.3 + - - +
322B PRO* 4.8 1.2 - - + +
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Residues in contact with ARG 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B TRP* 3.5 63.0 - - + +
205B ASN* 3.7 4.0 - - - -
206B PHE* 2.8 50.2 + - + +
226B ARG* 3.2 20.8 + - - +
227B ASN* 3.5 35.2 - - - +
228B SER* 3.6 2.9 - - - -
320B LYS* 1.3 76.0 - - - +
322B PRO* 1.3 77.4 - - + +
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Residues in contact with PRO 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B GLY 3.6 3.1 - - - +
205B ASN* 3.1 19.7 - - - +
206B PHE* 5.0 1.0 - - - -
227B ASN 5.6 0.7 - - - +
320B LYS* 4.8 1.1 - - + +
321B ARG* 1.3 94.9 - - + +
323B TYR* 1.3 67.9 + - - +
324B VAL* 3.3 17.2 + - + +
271C PRO* 4.3 20.4 - - + -
272C PHE 3.8 23.8 - - - +
273C ASN* 5.0 3.8 - - + -
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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