Contacts of the helix formed by residues 280 - 291 (chain A) in PDB entry 4RWN
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 ASN 280 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A PRO* 4.1 21.6 - - + +
167A GLU* 3.7 20.8 + - - -
170A VAL* 3.6 14.3 - - - +
277A ASP* 4.1 2.9 + - - +
278A PHE 3.4 1.3 - - - +
279A THR* 1.3 79.5 - - + +
281A PRO* 1.3 63.6 - - - +
282A VAL* 3.0 32.9 + - - +
283A VAL* 3.2 22.0 + - + +
284A GLY* 2.8 33.1 + - - -
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Residues in contact with PRO 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A PHE 4.8 2.9 - - - +
279A THR 3.4 9.3 - - - +
280A ASN* 1.3 92.1 - - - +
282A VAL* 1.3 64.2 + - + +
284A GLY* 4.0 1.1 - - - +
285A ARG* 3.0 37.9 + - - +
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Residues in contact with VAL 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A VAL* 4.1 27.4 - - + +
173A ILE* 4.2 25.5 - - + +
280A ASN* 3.0 12.9 + - - +
281A PRO* 1.3 81.9 - - + +
283A VAL* 1.3 65.5 + - - +
285A ARG* 3.4 29.4 + - - +
286A CYS* 3.1 21.3 + - - +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A PRO* 4.0 13.5 - - + +
169A TYR* 3.9 25.6 - - + -
170A VAL* 4.4 2.7 - - + -
173A ILE* 3.9 12.3 - - + -
276A TYR* 4.0 24.0 - - + -
277A ASP 3.6 18.2 - - - +
280A ASN* 3.2 24.3 + - + +
282A VAL* 1.3 74.0 - - - +
284A GLY* 1.3 60.7 + - - +
286A CYS* 3.2 3.3 + - - +
287A MET* 2.9 41.0 + - + +
304A PRO* 4.7 9.0 - - + -
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Residues in contact with GLY 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ASP 4.2 0.4 + - - -
278A PHE* 3.7 35.0 - - - -
280A ASN 2.8 20.3 + - - -
281A PRO* 4.0 1.3 - - - -
283A VAL* 1.3 73.5 - - - +
285A ARG* 1.3 58.2 + - - +
287A MET* 3.4 3.8 + - - +
288A LEU* 2.8 31.4 + - - +
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Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ILE* 6.1 0.8 - - - +
281A PRO* 3.0 33.2 + - - +
282A VAL* 3.7 33.3 + - - +
283A VAL 3.2 0.2 - - - -
284A GLY* 1.3 75.6 - - - +
286A CYS* 1.3 58.3 + - - +
288A LEU* 3.4 10.7 + - + +
289A GLN* 2.9 31.6 + - + +
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Residues in contact with CYS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ILE* 3.6 33.0 - - + -
282A VAL 3.1 7.6 + - - +
283A VAL 3.2 7.8 + - - +
285A ARG* 1.3 73.4 - - - +
287A MET* 1.3 65.5 + - - +
289A GLN* 3.2 12.5 + - - +
290A GLN* 3.0 31.7 + - - +
304A PRO* 3.4 25.6 - - + -
305A THR* 3.9 23.1 - - - -
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Residues in contact with MET 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A PHE* 3.9 18.8 - - + -
273A GLU* 4.5 4.0 - - + -
276A TYR* 3.5 42.0 - - + -
277A ASP* 3.7 28.5 - - - +
278A PHE* 3.5 37.5 - - + -
283A VAL* 2.9 22.1 + - + +
284A GLY 3.6 4.5 - - - +
286A CYS* 1.3 75.3 - - - +
288A LEU* 1.3 64.1 + - - +
290A GLN* 3.2 8.9 + - - +
291A LEU* 2.9 29.4 + - + +
299A LEU* 4.6 8.7 - - + +
304A PRO* 4.3 6.1 - - + -
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A PHE* 4.4 10.3 - - + -
284A GLY 2.8 18.8 + - - +
285A ARG* 3.6 11.0 - - + +
286A CYS 3.3 0.2 - - - -
287A MET* 1.3 76.2 - - - +
289A GLN* 1.3 62.5 + - - +
291A LEU* 3.2 16.2 + - + +
292A LYS* 3.1 48.5 + - + +
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Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A LYS* 6.0 2.1 - - - +
285A ARG* 2.9 20.8 + - + +
286A CYS* 3.5 9.9 - - - +
287A MET 3.2 0.2 - - - -
288A LEU* 1.3 73.9 - - - +
290A GLN* 1.3 71.2 + - + +
292A LYS* 3.1 20.9 + - - +
293A LYS* 3.7 12.1 + - + +
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Residues in contact with GLN 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLU* 3.1 25.3 + - - +
286A CYS* 3.0 19.3 + - - +
287A MET 3.5 7.0 - - - +
289A GLN* 1.3 80.7 - - - +
291A LEU* 1.3 58.4 + - - +
292A LYS 3.1 4.3 + - - -
293A LYS* 2.9 51.7 + - - +
297A VAL* 3.6 14.4 - - + +
299A LEU* 3.9 16.4 - - + -
304A PRO 3.3 21.8 - - - +
305A THR* 3.6 20.2 + - - +
307A ASN* 3.6 15.2 + - - +
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Residues in contact with LEU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A CYS* 3.6 22.5 - - - -
270A ILE 4.8 1.1 - - - +
271A PHE* 3.6 51.8 - - + -
278A PHE* 4.1 21.1 - - + -
287A MET* 2.9 23.5 + - + +
288A LEU* 3.6 16.2 - - + +
289A GLN 3.2 0.6 - - - -
290A GLN* 1.3 76.0 - - + +
292A LYS* 1.3 56.6 + - - +
293A LYS 3.4 1.6 - - - -
295A ARG* 2.7 31.6 + - - -
297A VAL* 4.4 11.7 - - + -
299A LEU* 4.9 5.2 - - + -
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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