Contacts of the strand formed by residues 304 - 308 (chain W) in PDB entry 6NE3
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 TYR 304 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195W TYR* 3.2 33.0 - + - +
215W THR* 6.0 0.2 - - - -
218W LEU* 3.6 34.5 - - + +
219W LEU* 4.3 6.7 - - + -
222W MET* 3.5 32.6 - - + +
228W ILE* 5.5 2.5 - - + -
231W PRO 3.9 0.6 + - - -
232W HIS* 3.4 41.2 + + + +
233W MET* 4.4 3.6 + - - +
302W TRP* 3.8 17.0 - - - +
303W ARG* 1.3 80.7 - - + +
305W LEU* 1.3 64.3 + - - +
306W VAL* 4.9 8.5 - - + -
329W THR* 3.8 0.3 + - - -
331W ASN* 3.2 41.0 - - + +
333W LEU* 3.7 18.8 - - + -
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Residues in contact with LEU 305 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233W MET* 3.7 37.2 - - + -
235W LEU* 4.5 8.1 - - + -
302W TRP* 6.5 0.2 - - + -
304W TYR* 1.3 77.9 - - - +
306W VAL* 1.3 61.2 + - - +
307W ILE* 4.3 14.8 - - + -
324W VAL* 3.8 27.1 - - + +
327W PHE* 4.7 9.2 - - + -
329W THR* 4.5 11.7 - - + +
331W ASN 3.0 14.2 + - - +
332W ARG* 3.5 24.3 - - + +
333W LEU* 2.5 36.0 + - - +
353W PHE* 3.9 7.0 - - + -
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Residues in contact with VAL 306 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215W THR* 3.8 36.8 - - + +
218W LEU* 5.9 0.4 - - + -
232W HIS* 6.5 0.4 - - + -
233W MET 3.4 12.4 + - - +
234W VAL* 3.3 16.6 - - + -
235W LEU* 3.0 22.3 + - - +
244W TRP* 4.9 3.4 - - + -
304W TYR* 4.9 8.7 - - + -
305W LEU* 1.3 78.5 - - - +
307W ILE* 1.3 68.6 + - - +
308W ASP 3.9 2.4 + - - +
333W LEU* 3.3 33.0 - - + +
335W LEU* 4.5 14.6 - - + -
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Residues in contact with ILE 307 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235W LEU* 3.8 28.0 - - + -
287W TYR* 4.4 9.9 - - + +
305W LEU* 4.3 8.5 - - + -
306W VAL* 1.3 75.3 - - - +
308W ASP* 1.3 69.3 + - - +
309W GLU 4.6 0.2 - - - +
310W ALA* 3.8 17.9 - - - +
312W ARG* 6.5 0.4 - - + -
313W ILE* 4.2 13.0 - - + -
320W LEU* 6.1 4.0 - - + -
324W VAL* 3.9 16.2 - - + -
333W LEU 3.3 7.0 + - - +
334W LEU* 3.8 23.1 - - + -
335W LEU* 3.1 28.3 + - - +
353W PHE* 3.9 24.5 - - + -
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Residues in contact with ASP 308 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211W LYS* 5.4 1.0 + - - -
234W VAL* 5.0 0.9 - - + +
235W LEU 2.7 22.2 + - - +
236W VAL* 3.7 10.5 - - + +
237W PRO* 4.1 2.9 - - - +
240W THR* 4.4 5.7 - - - +
244W TRP* 2.7 49.5 + - + -
287W TYR* 2.8 26.9 + - - -
306W VAL* 3.9 3.8 + - - +
307W ILE* 1.3 72.4 - - - +
309W GLU* 1.3 71.7 + - - +
335W LEU* 3.4 13.6 - - - +
565W GLY* 6.0 0.9 - - - -
801W ADP 3.3 24.0 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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