Contacts of the helix formed by residues 317 - 329 (chain A) in PDB entry 2FWN
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 ASP 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A ALA* 4.9 10.8 - - - +
181A SER* 3.4 22.0 + - - +
182A SER* 4.1 15.6 + - - -
183A VAL* 3.0 22.8 + - - +
214A ALA* 5.4 1.8 - - - +
300A CYS* 5.0 3.6 - - - -
316A ALA* 1.3 75.7 - - - +
318A ILE* 1.3 59.0 + - - +
319A GLY* 2.9 10.3 + - - -
320A ALA* 2.8 27.5 + - + +
321A MET* 3.0 28.9 + - - +
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Residues in contact with ILE 318 (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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210A ASP* 3.7 40.4 - - + +
211A VAL* 3.8 17.7 - - + -
214A ALA* 4.2 4.2 - - + +
216A ALA* 4.3 4.5 - - + -
273A ILE* 3.9 16.6 - - + -
274A GLY* 3.8 7.4 - - - +
298A VAL* 3.8 31.2 - - + +
299A THR 3.9 3.1 - - - -
300A CYS* 3.8 30.4 - - + +
316A ALA 4.0 1.1 - - - +
317A ASP* 1.3 72.2 + - - +
319A GLY* 1.3 61.3 + - - +
321A MET* 4.0 2.4 - - - +
322A ALA* 2.9 30.1 + - - +
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Residues in contact with GLY 319 (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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214A ALA* 3.6 23.4 - - - +
216A ALA* 4.3 8.1 - - - -
219A ASP* 4.6 1.9 - - - +
317A ASP* 2.9 7.9 + - - -
318A ILE* 1.3 78.4 - - - +
320A ALA* 1.3 61.8 + - - +
322A ALA* 4.1 1.0 - - - +
323A SER* 3.1 26.3 + - - -
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Residues in contact with ALA 320 (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 SER* 4.4 8.1 - - - +
183A VAL 3.6 28.5 - - - +
184A ARG* 4.0 14.9 - - + +
317A ASP* 2.8 16.6 + - + +
319A GLY* 1.3 73.0 - - - +
321A MET* 1.3 58.1 + - - +
323A SER* 3.9 4.1 - - - -
324A ALA* 3.0 29.6 + - - +
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Residues in contact with MET 321 (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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184A ARG* 3.6 7.6 - - + -
185A LEU* 3.5 35.0 - - + -
190A LEU* 4.3 12.3 - - + -
193A LEU* 4.3 17.7 - - + -
273A ILE* 6.0 0.9 - - + -
298A VAL* 3.9 37.5 - - + -
314A ILE* 4.2 14.8 - - + -
316A ALA* 3.5 19.5 - - + -
317A ASP 3.0 21.4 + - - +
318A ILE 4.0 2.0 - - - +
320A ALA* 1.3 74.5 - - - +
322A ALA* 1.3 59.9 + - - +
324A ALA* 3.3 2.0 + - - +
325A LEU* 2.9 43.5 + - + +
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Residues in contact with ALA 322 (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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216A ALA* 3.7 22.9 - - + -
219A ASP* 3.7 11.8 - - + +
220A CYS* 4.2 15.9 - - - +
223A LEU* 5.4 2.2 - - + +
273A ILE* 5.1 9.1 - - + +
318A ILE* 2.9 25.2 + - + +
319A GLY 4.1 0.7 - - - +
321A MET* 1.3 73.1 - - - +
323A SER* 1.3 58.3 + - - +
325A LEU* 3.5 6.3 + - - +
326A ALA* 2.9 32.7 + - - +
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Residues in contact with SER 323 (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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219A ASP* 3.5 24.2 + - - -
319A GLY 3.1 19.1 + - - -
320A ALA* 3.9 4.7 - - - -
322A ALA* 1.3 78.3 - - - +
324A ALA* 1.3 63.2 + - - +
326A ALA* 3.8 0.2 - - - +
327A ASN* 2.8 38.2 + - - +
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Residues in contact with ALA 324 (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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184A ARG* 4.7 13.0 - - + +
190A LEU* 4.1 25.6 - - + -
320A ALA 3.0 18.8 + - - +
321A MET* 3.8 5.2 - - - +
323A SER* 1.3 77.8 - - - +
325A LEU* 1.3 61.5 + - - +
327A ASN* 3.2 4.6 + - - +
328A LEU* 3.1 34.6 + - + +
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Residues in contact with LEU 325 (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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190A LEU* 3.9 26.7 - - + -
193A LEU* 4.0 20.9 - - + -
194A VAL* 3.9 16.2 - - + -
197A LEU* 4.1 12.3 - - + -
223A LEU* 4.0 17.7 - - + -
271A LEU* 4.2 23.3 - - + -
273A ILE* 4.8 6.1 - - + -
298A VAL* 4.8 7.4 - - + -
321A MET* 2.9 31.3 + - + +
322A ALA* 4.0 3.1 - - - +
324A ALA* 1.3 75.7 - - - +
326A ALA* 1.3 64.1 + - - +
327A ASN 3.2 0.2 + - - -
328A LEU* 4.8 1.8 - - - -
329A VAL* 3.1 30.2 + - + +
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Residues in contact with ALA 326 (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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219A ASP* 3.3 32.3 - - + +
222A MET* 3.8 26.9 - - + +
223A LEU* 4.1 13.0 - - + +
226A ARG* 4.3 8.8 + - - +
322A ALA 2.9 19.9 + - - +
323A SER 3.8 3.8 - - - +
325A LEU* 1.3 78.8 - - - +
327A ASN* 1.3 65.8 + - - +
328A LEU 3.8 0.2 + - - -
329A VAL* 4.3 8.7 - - - +
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Residues in contact with ASN 327 (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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219A ASP* 4.5 6.1 + - - -
222A MET* 4.1 13.7 - - - +
226A ARG* 6.2 0.2 - - - -
323A SER* 2.8 37.8 + - - +
324A ALA* 4.0 3.6 - - - +
325A LEU 3.1 0.6 - - - -
326A ALA* 1.3 83.4 - - - +
328A LEU* 1.3 66.7 + - + +
329A VAL 4.8 2.0 - - - +
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Residues in contact with LEU 328 (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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184A ARG* 6.2 0.4 - - - +
190A LEU* 3.7 35.0 - - + -
191A ASP* 5.2 9.0 - - - +
194A VAL* 3.9 28.3 - - + +
198A ASN* 5.0 0.7 + - - -
324A ALA* 3.1 24.9 + - + +
325A LEU 4.2 0.4 - - - +
327A ASN* 1.3 82.6 - - + +
329A VAL* 1.3 66.8 + - - +
330A GLU* 3.7 1.9 + - - +
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Residues in contact with VAL 329 (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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194A VAL* 4.1 15.0 - - + -
197A LEU* 4.1 25.4 - - + -
198A ASN* 3.6 12.1 - - - +
223A LEU* 3.8 22.9 - - + -
226A ARG* 3.6 40.1 + - + -
227A LEU* 4.2 8.3 - - + -
325A LEU 3.1 18.3 + - - +
326A ALA 4.3 4.2 - - - +
327A ASN 4.8 2.1 - - - +
328A LEU* 1.3 79.8 + - - +
330A GLU* 1.3 64.2 + - - +
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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