Contacts of the helix formed by residues 282 - 294 (chain A) in PDB entry 3FCL
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 ARG 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A GLU* 2.8 17.3 + - - +
179A THR 5.0 3.0 + - - -
180A ASP* 2.8 54.7 + - + +
280A GLY* 3.5 15.7 - - - +
281A CYS* 1.3 77.2 - - - +
283A HIS* 1.3 65.0 + - - +
284A PHE 3.2 3.5 + - - -
285A SER* 3.2 16.9 + - - +
286A LYS* 3.1 32.1 + - + +
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Residues in contact with HIS 283 (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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180A ASP* 3.9 0.2 + - - -
243A LEU* 4.0 15.5 - - + -
245A TRP* 2.9 34.0 + + + +
264A LEU* 3.5 47.3 + - + +
265A GLN 3.6 17.0 + - - -
266A THR* 3.6 11.5 - - + +
281A CYS* 3.2 35.4 + - + -
282A ARG* 1.3 78.0 - - - +
284A PHE* 1.3 62.5 + - + +
286A LYS* 3.8 8.5 - - + +
287A THR* 2.7 38.1 + - - -
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Residues in contact with PHE 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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141A ILE* 5.2 0.4 - - + -
173A ILE* 3.8 19.1 - - + -
176A GLU* 3.8 31.9 - - + -
177A LEU* 3.4 42.6 - - + -
180A ASP* 3.1 12.9 + - - +
181A ILE* 3.9 4.3 - - + -
195A TRP* 4.5 3.1 - + - -
243A LEU* 5.0 2.0 - - + -
245A TRP* 3.8 37.0 - + - -
278A PHE* 4.3 5.6 - + - -
283A HIS* 1.3 81.6 - - + +
285A SER* 1.3 65.3 + - - +
287A THR* 3.6 1.4 - - - -
288A ASN* 3.3 15.1 + - - -
301A TRP* 3.1 55.3 + + - +
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Residues in contact with SER 285 (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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180A ASP* 2.5 36.7 + - - -
181A ILE* 3.8 15.8 - - - +
282A ARG* 3.2 22.4 + - - +
284A PHE* 1.3 69.6 - - - +
286A LYS* 1.3 69.3 + - - +
288A ASN* 3.1 7.7 + - - +
289A GLU* 3.1 22.3 + - - +
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Residues in contact with LYS 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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264A LEU* 3.8 25.8 - - + -
280A GLY 5.1 1.6 + - - -
281A CYS* 3.0 24.7 + - - +
282A ARG* 3.1 26.7 + - + +
283A HIS* 3.8 5.3 + - - +
285A SER* 1.3 83.3 + - - +
287A THR* 1.3 63.6 + - - +
289A GLU* 3.3 7.3 + - - +
290A LEU* 3.0 31.3 + - + +
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Residues in contact with THR 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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139A VAL* 3.6 32.5 - - + -
241A VAL* 3.6 18.7 - - + +
243A LEU* 3.4 25.8 - - - +
264A LEU* 4.1 0.4 - - - +
283A HIS 2.7 24.1 + - - -
284A PHE 3.6 5.8 - - - -
286A LYS* 1.3 76.7 - - - +
288A ASN* 1.3 58.2 + - - +
290A LEU* 3.2 5.3 + - - +
291A LEU* 2.9 35.5 + - + +
301A TRP* 3.9 15.9 - - + -
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Residues in contact with ASN 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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181A ILE* 4.8 5.3 - - - +
284A PHE 3.3 3.1 + - - +
285A SER* 3.1 10.9 + - - +
287A THR* 1.3 79.6 - - - +
289A GLU* 1.3 57.2 + - - +
291A LEU* 3.4 7.1 + - - +
292A GLN* 3.0 36.3 + - - +
298A PRO* 3.4 18.7 - - + +
299A ILE* 2.8 51.0 + - - +
301A TRP* 3.3 22.7 + - - +
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Residues in contact with GLU 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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285A SER 3.1 12.1 + - - +
286A LYS* 3.8 9.4 - - - +
287A THR 3.3 0.2 - - - -
288A ASN* 1.3 73.6 - - - +
290A LEU* 1.3 62.0 + - + +
292A GLN* 3.3 21.9 + - - +
293A LYS* 3.0 45.1 + - + +
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Residues in contact with LEU 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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239A GLY 5.4 0.3 - - - +
241A VAL* 3.9 15.9 - - + -
262A HIS* 3.4 50.4 + - + +
264A LEU* 3.9 31.0 - - + -
286A LYS* 3.0 21.9 + - + +
287A THR 3.2 5.4 + - - +
289A GLU* 1.3 75.0 - - + +
291A LEU* 1.3 64.7 + - - +
293A LYS* 3.3 33.4 + - + +
294A SER* 3.3 12.3 + - - -
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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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138A LYS* 3.9 31.4 - - + +
139A VAL* 4.0 9.2 - - + -
239A GLY 4.5 5.4 - - - +
241A VAL* 4.2 9.6 - - + -
287A THR* 2.9 19.3 + - + +
288A ASN* 3.6 17.5 - - - +
289A GLU 3.3 0.2 - - - -
290A LEU* 1.3 77.4 - - - +
292A GLN* 1.3 60.3 + - - +
294A SER* 3.1 10.8 + - - -
296A LYS* 2.9 50.5 + - + +
297A LYS 4.1 15.0 - - - +
298A PRO* 4.5 1.6 - - + -
299A ILE* 3.9 30.5 - - + +
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Residues in contact with GLN 292 (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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288A ASN* 3.0 22.8 + - - +
289A GLU* 3.3 28.0 + - - +
291A LEU* 1.3 76.1 - - - +
293A LYS* 1.3 61.2 + - - +
295A GLY* 3.1 13.3 + - - -
296A LYS 3.5 15.7 - - - +
298A PRO* 3.6 26.7 - - + +
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Residues in contact with LYS 293 (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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262A HIS* 5.3 7.2 - - + -
289A GLU* 3.0 32.5 + - + +
290A LEU* 3.3 30.3 - - + +
291A LEU 3.2 0.2 - - - -
292A GLN* 1.3 77.4 - - - +
294A SER* 1.3 59.1 + - - +
295A GLY 3.3 1.0 + - - -
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Residues in contact with SER 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ASN* 5.3 5.9 + - - +
239A GLY* 4.1 13.7 + - - -
262A HIS* 3.8 15.1 + - - -
290A LEU 3.3 9.2 + - - -
291A LEU* 3.1 10.0 + - - -
293A LYS* 1.3 76.9 - - - +
295A GLY* 1.3 61.7 + - - +
296A LYS* 3.3 27.5 + - - +
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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