Contacts of the strand formed by residues 275 - 282 (chain S) in PDB entry 6NZO
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 275 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112S CYS* 4.9 14.4 - - - -
114S TYR* 5.2 4.9 - - + -
117S ARG* 3.5 56.0 - - - +
121S SER* 3.2 26.3 - - - -
122S SER* 3.0 4.5 + - - +
271S VAL* 3.5 1.0 - - - -
272S VAL* 2.9 36.5 + - - +
273S GLY* 3.4 14.1 - - - +
274S ASP* 1.3 94.7 - - - +
276S LEU* 1.3 65.0 + - - +
277S ARG* 3.5 16.7 + - + +
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Residues in contact with LEU 276 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E TYR* 4.1 9.4 - - + +
114S TYR* 4.8 6.4 + - - -
121S SER* 4.0 14.8 - - - +
122S SER* 2.6 16.9 + - - +
239S LEU* 3.3 49.7 - - + +
240S THR* 4.0 22.7 - - + +
269S LYS* 3.7 27.1 - - + -
270S TRP 3.3 18.6 - - - +
271S VAL* 4.4 4.9 - - + -
275S LYS* 1.3 72.2 - - - +
277S ARG* 1.3 65.0 + - - +
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Residues in contact with ARG 277 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111S ASP* 5.1 2.4 - - - +
112S CYS* 4.0 30.1 - - - +
114S TYR* 3.4 30.7 + - + +
174S PHE* 4.0 32.4 + - + +
175S GLN* 5.6 1.0 - - - +
208S GLU* 3.4 25.5 + - - +
209S TYR 5.9 0.7 - - - +
210S VAL* 5.5 1.7 - - - +
239S LEU* 3.8 4.9 - - - -
269S LYS* 3.4 5.5 - - - -
270S TRP* 2.9 32.2 + - - +
272S VAL* 3.5 42.6 + - + +
275S LYS* 3.5 9.4 + - - +
276S LEU* 1.3 80.6 - - - +
278S MET* 1.3 66.3 + - - +
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Residues in contact with MET 278 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E PRO* 3.7 28.0 - - + -
174S PHE* 3.7 6.5 - - - -
208S GLU* 3.5 24.4 - - - +
209S TYR* 3.5 32.3 + - + +
237S MET* 3.7 24.2 - - + -
238S SER 4.5 6.3 - - - +
239S LEU* 3.7 20.6 - - + +
245S VAL* 5.3 5.2 - - + -
267S VAL* 3.7 27.4 - - + -
268S ASP 3.8 3.6 - - - +
269S LYS* 3.8 25.8 - - + -
270S TRP 5.3 0.2 - - - -
277S ARG* 1.3 80.1 - - - +
279S GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 279 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174S PHE* 3.9 13.6 - - - -
207S TYR 3.6 9.2 - - - -
208S GLU* 4.4 0.7 - - - -
209S TYR* 4.8 0.4 - - - -
267S VAL* 3.3 5.9 - - - +
268S ASP* 2.9 38.3 + - - +
270S TRP* 5.1 2.0 - - - -
278S MET* 1.3 76.8 - - - +
280S ILE* 1.3 61.3 + - - -
281S PHE* 3.8 12.4 + - - -
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Residues in contact with ILE 280 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194S LEU* 4.8 16.4 - - + -
206S ILE* 3.3 9.8 - - + +
207S TYR* 2.9 62.4 + - + +
208S GLU* 4.2 5.1 - - - +
209S TYR* 5.2 8.0 - - + +
254S GLY* 5.1 7.4 - - - +
257S CYS* 5.2 2.2 - - - -
265S CYS* 5.0 6.7 - - + -
266S TYR 3.1 12.1 - - - +
267S VAL* 3.7 18.6 - - + -
279S GLY* 1.3 70.6 - - - -
281S PHE* 1.3 64.7 + - - +
292S LEU* 6.1 1.8 - - + +
294S PHE* 3.6 34.3 - - + -
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Residues in contact with PHE 281 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155S LYS* 6.3 0.7 - - - -
173S ARG* 3.3 24.2 - - - -
174S PHE* 5.2 4.5 - + - -
203S ASN* 5.5 3.6 - - - -
204S ASP 3.5 18.6 - - - +
205S PHE* 3.4 33.4 - + - -
206S ILE* 3.8 4.3 - - - -
265S CYS* 3.2 3.6 - - - -
266S TYR* 2.9 68.7 + + + +
268S ASP* 5.2 3.1 - - + -
270S TRP* 3.3 41.3 - + - -
279S GLY* 4.6 10.5 - - - +
280S ILE* 1.3 83.1 - - - +
282S ALA* 1.3 60.2 + - - +
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Residues in contact with ALA 282 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201S GLN 4.6 1.8 - - - +
202S PRO* 4.6 2.9 - - + -
203S ASN* 3.3 28.1 - - - +
204S ASP 3.6 2.4 + - - -
206S ILE* 3.3 26.5 - - + +
264S ASN 4.8 0.2 - - - +
265S CYS* 3.9 11.7 - - - +
266S TYR* 3.4 10.4 + - - -
281S PHE* 1.3 77.1 - - - +
283S ALA* 1.3 60.7 + - - +
284S ARG 4.2 4.5 - - - +
286S ILE* 3.9 26.2 - - + -
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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